Contacts of the helix formed by residues 141 - 164 (chain I) in PDB entry 1F33
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 141 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I VAL* 4.8 8.8 - - + +
25I GLU* 3.4 10.0 + - - +
29I THR* 3.8 16.9 + - - +
83I ARG* 2.7 34.3 + - - -
87I LEU* 4.2 6.5 - - + +
139I ALA* 3.5 1.4 - - - +
140I LYS* 1.3 77.0 - - - +
142I ASP* 1.3 68.4 + - - +
143I ASP* 3.8 2.8 + - - -
144I THR* 2.5 32.9 + - - +
145I ALA* 2.9 21.4 + - - +
133K ARG* 4.3 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I LYS 3.3 8.6 + - - +
141I ASP* 1.3 71.8 + - - +
143I ASP* 1.3 65.6 + - - +
145I ALA* 3.0 10.6 + - - +
146I ASP* 2.9 22.2 + - - +
133K ARG* 4.4 7.9 - - + +
136K ILE* 3.8 41.8 - - + +
137K GLY* 4.4 9.0 + - - -
149K THR* 4.3 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I ARG* 3.3 34.9 + - - +
141I ASP* 3.3 2.9 + - - -
142I ASP* 1.3 77.0 - - - +
144I THR* 1.3 62.9 + - - +
146I ASP* 3.1 4.7 + - - +
147I ILE* 3.0 27.4 + - - +
133K ARG* 4.0 3.8 - - - -
136K ILE* 3.5 8.7 - - - +
149K THR* 3.4 27.2 - - - +
152K SER* 2.6 30.3 + - - -
153K ARG* 3.7 19.9 + - - +
156K ASP* 3.4 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I THR* 3.1 22.5 - - + +
32I LEU* 5.0 4.5 - - + -
33I LEU* 3.6 28.3 - - + -
83I ARG* 3.7 9.6 + - - +
139I ALA* 4.4 8.1 - - + -
141I ASP* 2.5 33.0 + - - -
143I ASP* 1.3 77.6 - - - +
145I ALA* 1.3 63.8 + - - +
147I ILE* 3.2 10.0 + - - +
148I LEU* 2.9 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ILE* 4.0 23.6 - - + +
139I ALA* 3.9 16.4 - - + +
141I ASP 2.9 12.4 + - - +
142I ASP* 3.0 12.8 + - - +
144I THR* 1.3 76.3 - - - +
146I ASP* 1.3 53.7 + - - +
148I LEU* 3.4 4.8 + - - +
149I THR* 2.6 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ASP* 4.3 5.2 - - - +
607G TRS 2.7 45.0 + - - -
142I ASP 2.9 12.9 + - - +
143I ASP 3.1 9.4 + - - +
145I ALA* 1.3 74.3 - - - +
147I ILE* 1.3 67.1 + - - +
149I THR* 3.0 7.7 + - - -
150I ALA* 2.9 22.7 + - - +
146K ASP* 4.3 6.1 - - - +
149K THR* 3.7 20.9 - - + +
150K ALA 5.3 0.5 + - - -
153K ARG* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 5.2 2.2 - - + -
76I HIS* 4.7 3.8 + - - +
79I THR* 3.8 24.9 - - + +
80I MET* 3.6 31.0 - - + -
83I ARG* 3.6 41.1 - - + -
143I ASP 3.0 19.2 + - - +
144I THR* 3.4 8.7 - - - +
146I ASP* 1.3 77.0 - - - +
148I LEU* 1.3 58.1 + - + +
150I ALA* 3.3 4.7 + - - +
151I ALA* 3.0 25.3 + - + +
153K ARG* 3.5 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LEU* 4.3 7.9 - - + -
33I LEU* 4.6 7.6 - - + -
36I GLN* 4.0 11.2 - - + -
80I MET* 3.8 28.3 - - + -
132I VAL* 3.9 19.0 - - + +
135I ALA* 3.7 34.3 - - + +
136I ILE* 3.9 13.2 - - + -
139I ALA* 4.1 7.0 - - + -
144I THR* 2.9 36.2 + - + +
145I ALA 3.7 3.6 - - - +
147I ILE* 1.3 72.0 - - + +
149I THR* 1.3 56.8 + - - +
151I ALA* 3.3 4.0 + - - +
152I SER* 2.7 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G ASP* 4.3 4.2 - - + +
143G ASP* 3.5 19.9 - - - +
146G ASP* 3.6 38.4 - - + +
136I ILE* 3.4 25.0 - - + +
145I ALA* 2.6 23.7 + - - +
146I ASP* 3.0 8.2 + - - -
148I LEU* 1.3 75.8 - - - +
150I ALA* 1.3 58.9 + - - +
152I SER* 3.2 1.7 + - - -
153I ARG* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ASP* 5.2 0.4 - - - -
607G TRS 4.6 17.4 + - - +
76I HIS* 3.4 19.9 - - + +
146I ASP 2.9 11.2 + - - +
147I ILE* 3.5 11.4 - - - +
149I THR* 1.3 79.1 - - - +
151I ALA* 1.3 61.7 + - - +
153I ARG* 3.4 8.3 + - - +
154I ASP* 3.3 16.3 + - - +
153K ARG* 4.9 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I PHE* 3.9 22.2 - - + -
76I HIS* 3.3 32.0 - - + +
80I MET* 5.0 5.6 - - - -
132I VAL* 4.7 2.5 - - + -
147I ILE* 3.0 15.2 + - + +
148I LEU* 3.7 8.1 - - - +
150I ALA* 1.3 77.4 - - - +
152I SER* 1.3 62.8 + - - +
154I ASP* 3.0 4.7 + - - +
155I LEU* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G ASP* 2.6 33.6 + - - -
132I VAL* 3.9 21.1 - - - +
133I ARG* 3.6 19.7 + - - +
136I ILE* 3.7 9.2 - - - -
148I LEU 2.7 21.6 + - - -
149I THR 3.5 0.2 - - - -
151I ALA* 1.3 72.5 - - - +
153I ARG* 1.3 64.4 + - - +
155I LEU* 3.1 2.1 + - - +
156I ASP* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G THR* 3.5 19.6 - - - +
83G ARG* 5.2 3.1 - - - +
86G GLN* 4.3 4.6 + - - +
143G ASP* 3.7 26.6 + - + +
146G ASP* 3.0 26.4 + - - -
147G ILE* 3.4 45.0 - - + +
150G ALA* 4.8 11.1 - - - +
607G TRS 4.2 7.7 + - - -
149I THR 2.8 15.2 + - - +
150I ALA* 3.4 9.3 - - - +
152I SER* 1.3 77.3 - - - +
154I ASP* 1.3 63.5 + - - +
156I ASP* 4.0 3.9 - - - +
157I LYS* 3.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ALA* 4.3 8.0 - - - +
76I HIS* 2.7 32.3 + - + +
150I ALA 3.3 3.5 + - - -
151I ALA 3.0 8.6 + - - +
153I ARG* 1.3 81.5 - - - +
155I LEU* 1.3 61.2 + - + +
157I LYS* 3.1 11.7 + - - +
158I PHE* 2.8 56.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I PHE* 3.3 37.9 - - + -
43I LEU* 3.8 19.3 - - + -
73I LEU* 4.2 14.4 - - + -
76I HIS* 5.5 1.1 - - + -
125I TYR* 4.2 10.6 - - + +
128I VAL* 3.5 31.9 - - + -
129I ALA* 3.8 22.4 - - + +
132I VAL* 4.8 2.2 - - + -
151I ALA* 2.9 25.2 + - + +
152I SER* 3.1 5.1 + - - +
154I ASP* 1.3 78.2 - - + +
156I ASP* 1.3 58.9 + - - +
158I PHE* 3.2 7.2 + - + +
159I LEU* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASN* 3.4 16.2 + - - +
83G ARG* 2.7 41.7 + - - +
86G GLN* 3.7 9.7 - - + +
143G ASP* 3.4 4.5 - - - +
129I ALA* 3.7 11.1 - - - +
133I ARG* 2.6 33.6 + - - -
152I SER* 2.9 19.6 + - - +
153I ARG 4.0 1.6 - - - +
155I LEU* 1.3 75.7 - - - +
157I LYS* 1.3 62.9 + - - +
159I LEU* 3.7 6.6 - - - +
160I TRP* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G GLU* 4.0 20.6 + - - +
86G GLN* 3.8 23.3 + - - +
153I ARG 3.4 13.5 + - - +
154I ASP* 3.1 17.6 + - - +
156I ASP* 1.3 80.7 - - - +
158I PHE* 1.3 71.4 + - + +
160I TRP* 3.3 10.3 + - + +
161I PHE* 2.9 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I GLY 5.3 0.4 - - - -
69I PHE* 3.4 62.6 - + + -
72I ALA* 3.5 32.1 - - + -
73I LEU* 4.1 13.0 - - + -
76I HIS* 5.8 0.2 - + - -
125I TYR* 3.7 18.4 - + + -
154I ASP* 2.8 44.7 + - + +
155I LEU* 3.7 5.8 - - - +
157I LYS* 1.3 92.0 - - + +
159I LEU* 1.3 54.9 + - - +
161I PHE* 3.0 1.9 + - - +
162I ILE* 2.8 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G THR* 4.5 1.6 - - - +
18G ARG 4.3 0.2 - - - -
19G ASN* 3.8 39.5 - - + +
122I ALA* 3.5 28.9 - - - +
125I TYR* 4.1 11.8 - - + -
126I ALA* 3.9 24.0 - - + +
129I ALA* 4.4 11.2 - - + -
155I LEU 2.8 17.3 + - - +
156I ASP* 3.7 5.8 - - - +
158I PHE* 1.3 74.9 - - - +
160I TRP* 1.3 59.0 + - - +
162I ILE* 3.1 4.9 + - - +
163I GLU* 2.8 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 160 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G THR* 5.8 1.1 - - - -
82G GLU* 3.8 32.1 - - + -
85G VAL* 3.3 29.8 - - + +
86G GLN* 3.5 42.6 - - + +
52H TRP* 3.9 21.7 + - - -
54H MET 5.3 2.0 + - - -
55H ARG* 4.2 13.9 - - - +
59H PHE* 4.3 13.1 - + - -
63H HIS* 4.1 13.5 - + - -
156I ASP 3.1 11.5 + - - +
157I LYS* 3.4 9.9 - - + +
159I LEU* 1.3 81.1 - - - +
161I PHE* 1.3 88.1 + + - +
163I GLU* 3.9 8.2 - - - +
164I SER* 2.6 64.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G GLU* 5.5 1.1 - - - -
59H PHE* 3.9 12.7 - + - -
60H ILE* 3.6 24.0 - - + -
63H HIS* 3.9 26.0 - + - -
64H GLU* 5.0 4.0 - - - -
65I MET* 4.0 5.8 - - + -
69I PHE* 3.7 30.1 - + + -
157I LYS* 2.9 38.7 + - - +
158I PHE 3.0 7.4 + - - +
160I TRP* 1.3 113.2 - + - +
162I ILE* 1.3 61.3 + - - +
164I SER* 3.5 2.3 + - - -
165I ASN* 2.7 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I MET* 4.5 10.8 - - + -
66I LEU* 4.8 4.5 - - + -
69I PHE* 3.8 15.3 - - + -
118I LEU* 3.3 39.9 - - + +
121I LEU* 4.1 9.6 - - + -
122I ALA* 3.8 11.4 - - + +
125I TYR* 3.5 53.4 - - + -
158I PHE 2.8 19.2 + - - +
159I LEU* 3.5 6.3 - - - +
161I PHE* 1.3 71.8 - - - +
163I GLU* 1.3 65.3 + - - +
165I ASN* 2.9 19.3 + - - +
166I ILE* 3.6 6.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G TYR* 4.3 3.8 - - - +
17G THR* 2.8 29.9 + - - -
18G ARG* 2.8 60.7 + - - +
55H ARG* 4.7 13.7 + - - +
122I ALA* 4.3 4.5 - - + -
159I LEU* 2.8 35.6 + - + +
160I TRP* 3.9 7.4 - - - +
162I ILE* 1.3 72.7 - - - +
164I SER* 1.3 58.0 + - - +
166I ILE* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ARG* 3.7 23.3 + - - +
56H GLY 2.9 26.2 + - - -
59H PHE* 3.1 41.9 - - - +
160I TRP* 2.6 47.0 + - - -
161I PHE 3.8 0.7 - - - -
162I ILE 3.2 0.4 - - - -
163I GLU* 1.3 74.8 - - - +
165I ASN* 1.3 56.6 + - - +
166I ILE 3.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il