Contacts of the strand formed by residues 135 - 147 (chain D) in PDB entry 1ZQ1
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 PHE 135 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 3.8 21.5 - - + -
211B PRO* 4.3 9.4 - - + -
123D ARG* 3.4 54.1 - - + -
124D LYS 3.1 22.7 - - - +
125D ILE* 4.0 3.8 - - + -
126D VAL 4.0 2.5 - - - +
131D ASN* 3.5 19.9 - - - +
133D SER* 3.4 44.2 - - - -
134D GLY* 1.3 81.3 - - - +
136D GLN* 1.3 58.0 + - - +
137D ARG* 3.7 22.2 + - + -
163D GLU* 4.4 3.8 - - - +
433D TYR* 4.2 5.2 - + - -
435D GLU* 3.6 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ARG* 3.5 1.4 - - - -
124D LYS* 2.9 65.6 + - + +
126D VAL* 4.0 4.9 - - + +
131D ASN* 3.9 22.0 - - - +
135D PHE* 1.3 75.0 - - - +
137D ARG* 1.3 69.7 + - - +
138D THR* 3.5 15.2 + - - +
162D GLU* 3.3 22.2 + - - +
163D GLU* 2.5 32.4 + - + +
164D ASP* 4.8 0.4 - - - +
165D ALA 5.3 1.6 - - - +
187D LEU* 4.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 5.4 0.8 - - - +
31D PHE* 3.5 31.2 - - + -
86D VAL* 4.3 15.0 + - - +
87D TYR* 5.1 4.4 - - - -
93D PRO* 3.0 39.4 - - - +
121D TYR* 3.7 8.5 - - + -
122D MET 3.3 7.6 - - - +
133D SER* 3.5 22.2 + - - -
135D PHE* 3.7 20.0 - - + -
136D GLN* 1.3 73.4 - - - +
138D THR* 1.3 59.2 + - - +
162D GLU* 3.2 3.5 - - - +
163D GLU* 2.9 59.9 + - - +
435D GLU* 2.9 41.5 + - + +
437D ASP* 4.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.0 32.3 - - + +
121D TYR* 2.8 20.4 - - - -
122D MET* 2.8 27.2 + - - -
124D LYS* 3.8 8.8 - - - +
136D GLN* 3.5 18.3 + - - +
137D ARG* 1.3 75.3 - - - +
139D ALA* 1.3 70.3 + - - +
160D CYS* 4.0 10.5 - - + -
162D GLU* 3.0 38.3 + - + +
432D MET* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.7 10.0 - - - -
119D VAL* 3.9 9.4 - - + -
120D TYR 3.6 13.9 - - - +
121D TYR* 3.3 35.0 - - + +
122D MET 4.8 0.4 - - - +
138D THR* 1.3 84.5 - - - +
140D ILE* 1.3 62.6 + - - +
141D ILE* 3.6 3.1 + - + +
160D CYS* 3.2 23.4 - - - -
161D LEU 3.2 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.5 30.5 - - + -
53B ASN* 4.6 5.2 - - - -
55B TYR* 3.5 37.4 - - + -
56B ASN 4.8 5.9 + - - +
57B ILE* 3.8 24.9 - - + +
116D VAL* 3.8 15.6 - - + +
119D VAL* 3.8 17.2 - - - +
120D TYR 4.6 3.3 + - - +
139D ALA* 1.3 72.2 - - - +
141D ILE* 1.3 65.7 + - - +
142D ALA 4.0 7.4 - - - +
143D THR* 4.1 10.3 - - + -
158D THR* 3.3 28.3 - - + -
159D ILE 3.9 3.1 - - - -
160D CYS* 4.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PRO* 6.3 0.7 - - + -
101D LEU* 4.8 10.1 - - + -
104D ALA* 3.8 20.2 - - + +
105D LEU* 4.3 24.9 - - + +
108D ALA* 5.3 0.4 - - + -
115D PRO* 3.3 4.3 - - - +
116D VAL* 2.9 29.5 + - - +
119D VAL* 4.3 16.4 - - + -
121D TYR* 5.4 1.3 - - + +
139D ALA* 4.0 6.3 - - + +
140D ILE* 1.3 79.1 - - - +
142D ALA* 1.3 64.6 + - + +
159D ILE* 2.9 16.0 + - + +
160D CYS 5.2 0.2 - - - -
161D LEU* 3.2 47.6 - - + +
443D ILE* 5.0 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA* 3.7 30.1 - - + -
113D ALA* 3.9 9.0 - - + -
114D LYS 3.2 18.8 - - - +
115D PRO* 3.8 1.6 - - + -
116D VAL* 4.4 2.0 - - - -
140D ILE* 4.0 2.0 - - - +
141D ILE* 1.3 83.2 - - + +
143D THR* 1.3 67.7 + - - +
158D THR* 3.7 2.4 - - - -
159D ILE* 3.1 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 4.0 4.5 - - - +
31B TYR* 3.4 38.4 + - + -
51B LEU* 4.7 3.8 - - + -
57B ILE* 4.2 5.2 - - + -
113D ALA* 3.6 1.8 - - - -
114D LYS* 2.9 26.5 + - - +
116D VAL* 5.0 1.3 - - + +
140D ILE* 4.1 23.6 - - + -
142D ALA* 1.3 79.1 - - - +
144D ASP* 1.3 86.2 + - - +
145D GLY 3.3 2.3 + - - -
156D ILE 3.9 0.9 - - - -
157D PRO 3.1 12.8 - - - +
159D ILE* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 4.0 14.0 - - + +
30B THR* 4.1 15.8 - - - +
31B TYR* 5.4 0.7 - - - -
114D LYS* 3.3 32.7 + - + +
143D THR* 1.3 88.0 + - - +
145D GLY* 1.3 61.6 + - - +
156D ILE 3.2 7.0 - - - -
157D PRO* 3.2 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU 3.2 13.5 - - - -
112D ASN 3.6 1.8 - - - -
113D ALA* 3.3 17.9 - - - +
143D THR 3.3 1.4 + - - -
144D ASP* 1.3 78.2 - - - +
146D LYS* 1.3 62.1 + - - +
155D GLY* 3.5 2.9 - - - -
156D ILE* 2.6 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU* 2.7 16.8 + - - +
112D ASN* 2.7 44.4 + - + +
145D GLY* 1.3 75.8 - - - +
147D VAL* 1.3 67.9 + - - +
148D GLU* 3.1 39.9 + - - +
153D ALA* 4.6 10.0 - - + +
154D VAL 3.5 11.0 - - - +
155D GLY* 4.5 2.9 - - - -
156D ILE* 3.6 1.8 - - - +
208D PHE* 4.6 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU* 4.6 3.8 - - + -
112D ASN* 4.8 0.2 - - - +
146D LYS* 1.3 80.8 - - - +
148D GLU* 1.3 71.9 + - - +
149D THR* 3.5 2.3 + - - -
152D GLY 4.2 0.5 - - - +
153D ALA* 4.5 1.1 - - - -
154D VAL* 2.9 33.9 + - - +
156D ILE* 3.5 17.9 - - + -
204D VAL* 5.1 1.6 - - + -
205D VAL* 3.8 40.4 - - + +
208D PHE* 3.4 39.9 - - + -
209D ILE* 4.4 8.5 - - + -
----------------------------------------------------------
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