Contacts of the helix formed by residues 141 - 164 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L VAL* 4.8 11.9 - - + +
25L GLU* 3.4 9.8 + - - +
29L THR* 3.8 16.0 + - - +
83L ARG* 2.7 34.5 + - - -
87L LEU* 4.2 7.3 - - + +
139L ALA* 3.6 1.3 - - - +
140L LYS* 1.3 78.1 - - - +
142L ASP* 1.3 67.8 + - - +
143L ASP* 3.8 3.5 + - - +
144L THR* 2.6 32.9 + - - +
145L ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140L LYS 3.3 7.4 + - - +
141L ASP* 1.3 74.3 + - - +
143L ASP* 1.3 69.4 + - - +
145L ALA* 3.0 10.1 + - - +
146L ASP* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L ARG* 3.3 39.5 + - - +
141L ASP* 3.4 2.1 + - - -
142L ASP* 1.3 80.7 - - - +
144L THR* 1.3 63.5 + - - +
146L ASP* 3.1 10.2 + - - +
147L ILE* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L THR* 3.1 22.0 - - + +
32L LEU* 5.1 4.0 - - + -
33L LEU* 3.5 29.4 - - + -
83L ARG* 3.5 11.1 - - - +
139L ALA* 4.4 7.4 - - + -
141L ASP* 2.6 32.9 + - - -
143L ASP* 1.3 78.9 - - - +
145L ALA* 1.3 62.2 + - - +
147L ILE* 3.2 10.7 + - - +
148L LEU* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L ILE* 3.9 24.2 - - + +
139L ALA* 3.9 16.6 - - + +
141L ASP 2.9 13.1 + - - +
142L ASP* 3.0 13.0 + - - +
144L THR* 1.3 76.2 - - - +
146L ASP* 1.3 52.7 + - - +
148L LEU* 3.4 5.0 + - - +
149L THR* 2.6 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J ASP* 4.2 8.7 - - - +
612J TRS 2.7 40.5 + - - -
142L ASP 2.9 11.6 + - - +
143L ASP* 3.2 13.5 - - - +
145L ALA* 1.3 74.2 - - - +
147L ILE* 1.3 68.4 + - + +
149L THR* 3.0 8.9 + - - -
150L ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L LEU* 5.2 1.6 - - + -
76L HIS* 4.7 3.4 + - - +
79L THR* 3.8 31.4 - - + +
80L MET* 3.6 31.2 - - + -
83L ARG* 3.6 40.8 - - + -
143L ASP* 3.0 19.4 + - + +
144L THR* 3.4 8.5 - - + +
146L ASP* 1.3 79.9 - - + +
148L LEU* 1.3 63.6 + - + +
150L ALA* 3.3 8.3 + - - +
151L ALA* 3.1 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L LEU* 4.2 8.3 - - + -
33L LEU* 4.6 7.9 - - + -
36L GLN* 4.0 10.8 - - + -
80L MET* 3.8 27.6 - - - -
132L VAL* 3.9 20.3 - - + +
135L ALA* 3.7 33.2 - - + +
136L ILE* 3.9 12.9 - - + +
139L ALA* 4.1 7.2 - - + -
144L THR* 2.9 35.8 + - + +
145L ALA 3.8 4.3 - - - +
147L ILE* 1.3 73.2 - - + +
149L THR* 1.3 55.7 + - - +
151L ALA* 3.7 3.6 - - - +
152L SER* 2.7 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J ASP* 4.2 5.9 - - - +
143J ASP* 3.4 20.1 - - - +
146J ASP* 3.7 36.3 - - + +
136L ILE* 3.5 23.7 - - + +
145L ALA 2.6 21.8 + - - -
146L ASP* 3.0 11.7 + - - -
148L LEU* 1.3 73.8 - - - +
150L ALA* 1.3 57.4 + - - +
152L SER 3.2 0.2 + - - -
153L ARG* 2.8 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J ASP* 5.2 0.9 - - - -
612J TRS 4.4 21.5 + - - +
76L HIS* 3.4 18.5 - - + +
146L ASP* 3.0 11.0 + - - +
147L ILE* 3.5 11.0 - - - +
149L THR* 1.3 78.5 - - - +
151L ALA* 1.3 62.1 + - - +
153L ARG* 3.3 8.9 + - - +
154L ASP* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L PHE* 3.9 21.8 - - + -
76L HIS* 3.4 32.0 - - + +
80L MET* 5.0 6.1 - - - -
132L VAL* 4.7 2.7 - - + -
147L ILE* 3.1 15.4 + - + +
148L LEU* 3.7 7.4 - - - +
150L ALA* 1.3 75.2 - - - +
152L SER* 1.3 65.7 + - - +
154L ASP* 3.1 4.0 + - - +
155L LEU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J ASP* 2.6 32.4 + - - -
132L VAL* 4.0 21.8 - - - +
133L ARG* 3.7 19.0 - - - +
136L ILE* 3.7 9.4 - - - -
148L LEU 2.7 20.9 + - - -
149L THR 3.2 0.4 + - - -
151L ALA* 1.3 73.5 - - - +
153L ARG* 1.3 65.6 + - - +
154L ASP 3.1 0.5 + - - -
155L LEU* 3.1 1.1 + - - +
156L ASP* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J THR* 3.5 18.6 - - - +
83J ARG* 5.3 2.9 - - - +
86J GLN* 4.3 3.9 - - - +
143J ASP* 3.7 27.5 + - + +
146J ASP* 2.9 28.1 + - - -
147J ILE* 3.3 46.0 - - + +
150J ALA* 4.8 8.3 - - - +
612J TRS 4.1 10.5 + - - -
149L THR 2.8 18.6 + - - +
150L ALA* 3.4 10.2 - - - +
152L SER* 1.3 75.2 - - - +
154L ASP* 1.3 63.2 + - - +
156L ASP* 3.7 4.0 + - - +
157L LYS* 3.4 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L ALA* 4.1 9.4 - - - +
76L HIS* 2.6 36.9 + - + +
150L ALA 3.3 4.3 + - - -
151L ALA 3.1 4.1 + - - +
153L ARG* 1.3 79.4 - - - +
155L LEU* 1.3 61.6 + - + +
157L LYS* 2.9 11.8 + - - +
158L PHE* 2.8 58.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L PHE* 3.2 38.1 - - + -
43L LEU* 3.8 17.3 - - + -
73L LEU* 4.2 15.5 - - + -
76L HIS* 5.4 1.1 - - + -
125L TYR* 4.3 10.0 - - + +
128L VAL* 3.5 33.9 - - + -
129L ALA* 3.9 20.6 - - + +
132L VAL* 4.8 2.2 - - + -
151L ALA* 3.0 24.1 + - + +
152L SER* 3.8 5.6 - - - +
154L ASP* 1.3 78.6 - - + +
156L ASP* 1.3 58.0 + - - +
158L PHE* 3.2 8.0 + - + +
159L LEU* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J ASN* 3.3 17.2 + - - +
83J ARG* 2.7 41.6 + - - +
86J GLN* 3.7 9.7 - - + +
143J ASP* 3.4 4.5 - - - +
129L ALA* 3.7 11.3 - - - +
133L ARG* 2.6 33.8 + - - -
152L SER* 2.9 19.0 + - - +
153L ARG 4.0 1.8 - - - +
155L LEU* 1.3 76.7 - - - +
157L LYS* 1.3 62.0 + - - +
159L LEU* 3.6 7.4 + - - +
160L TRP* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J GLU* 4.0 20.4 + - - +
86J GLN* 3.8 24.0 + - - +
153L ARG 3.4 12.2 + - - +
154L ASP* 2.9 17.8 + - - +
156L ASP* 1.3 76.5 - - - +
158L PHE* 1.3 75.2 + - + +
160L TRP* 3.3 10.8 + - + +
161L PHE* 2.8 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L GLY 5.6 0.2 - - - -
69L PHE* 3.4 59.0 - + + -
72L ALA* 3.5 33.4 - - + -
73L LEU* 4.1 13.5 - - + -
76L HIS* 5.8 0.2 - + - -
125L TYR* 3.8 19.1 - + + -
154L ASP* 2.8 44.1 + - + +
155L LEU* 3.7 5.8 - - - +
157L LYS* 1.3 89.3 - - + +
159L LEU* 1.3 55.4 + - - +
161L PHE* 2.9 3.2 + + - +
162L ILE* 2.7 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J THR* 4.4 1.8 - - - +
18J ARG 4.1 1.1 - - - -
19J ASN* 3.7 41.1 - - + +
122L ALA* 3.4 30.1 - - - +
125L TYR* 4.1 12.0 - - + -
126L ALA* 3.9 22.9 - - + +
129L ALA* 4.4 10.3 - - + -
155L LEU 2.8 17.3 + - - +
156L ASP* 3.8 5.8 - - - +
158L PHE* 1.3 75.2 - - - +
160L TRP* 1.3 58.8 + - - +
162L ILE* 3.2 5.3 + - - +
163L GLU* 2.8 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 160 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I TRP* 3.8 22.0 + - - -
54I MET 5.1 1.8 + - - -
55I ARG* 4.0 18.4 - - - +
59I PHE* 4.3 12.9 - + - -
63I HIS* 4.0 12.8 - + - -
17J THR* 5.7 1.3 - - - -
82J GLU* 3.9 31.9 - - + -
85J VAL* 3.2 25.4 - - + +
86J GLN* 3.5 42.2 - - + +
156L ASP 3.1 11.8 + - - +
157L LYS* 3.4 10.8 - - + +
159L LEU* 1.3 81.1 - - - +
161L PHE* 1.3 87.0 + + - +
163L GLU* 3.9 8.0 - - - +
164L SER* 2.6 64.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I PHE* 3.7 19.0 - + - -
60I ILE* 3.5 21.3 - - + -
63I HIS* 3.9 24.5 - + - -
64I GLU* 5.1 3.6 - - - -
82J GLU* 5.7 0.4 - - - -
65L MET* 4.0 5.6 - - + -
69L PHE* 3.7 30.5 - + + -
157L LYS* 2.8 37.6 + - + +
158L PHE 2.9 6.9 + - - +
160L TRP* 1.3 113.6 - + - +
162L ILE* 1.3 62.0 + - - +
164L SER* 3.5 2.3 + - - -
165L ASN* 2.7 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L MET* 4.4 10.1 - - + -
66L LEU* 4.8 5.2 - - + -
69L PHE* 3.7 15.0 - - + -
118L LEU* 3.3 41.4 - - + +
121L LEU* 4.1 9.6 - - + -
122L ALA* 3.9 10.8 - - + +
125L TYR* 3.5 54.3 - - + -
158L PHE 2.7 18.7 + - - +
159L LEU* 3.6 5.8 - - - +
161L PHE* 1.3 71.5 - - - +
163L GLU* 1.3 65.9 + - - +
165L ASN* 3.0 19.5 + - - +
166L ILE* 3.6 7.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ARG* 4.6 12.8 + - - +
16J TYR* 4.2 4.2 - - - +
17J THR* 2.8 31.7 + - - -
18J ARG* 2.8 61.6 + - - +
122L ALA* 4.3 3.8 - - + -
159L LEU* 2.8 34.7 + - + +
160L TRP* 3.9 6.8 - - - +
162L ILE* 1.3 72.4 - - - +
164L SER* 1.3 56.6 + - - +
166L ILE* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ARG* 3.6 23.2 + - - +
56I GLY 2.7 32.8 + - - +
59I PHE* 3.2 37.2 - - - +
160L TRP* 2.6 46.2 + - - -
161L PHE 3.9 0.7 - - - -
162L ILE 3.2 0.4 - - - -
163L GLU* 1.3 75.5 - - - +
165L ASN* 1.3 55.1 + - - +
166L ILE 3.4 0.4 - - - -
----------------------------------------------------------
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