Contacts of the strand formed by residues 92 - 101 (chain B) in PDB entry 3IEQ
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 ALA 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY 4.1 0.6 + - - -
91B PHE* 1.3 73.6 - - - +
93B ILE* 1.3 66.6 + - - +
94B ARG* 3.5 3.2 + - - +
156B VAL* 3.4 3.6 - - - -
157B VAL* 2.9 46.8 + - + +
158B ARG 5.3 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.7 35.0 - - + -
83B ALA* 4.5 13.9 - - + +
86B VAL* 4.4 13.5 - - + -
91B PHE 5.2 0.7 - - - +
92B ALA* 1.3 73.7 - - - +
94B ARG* 1.3 65.1 + - - +
95B ASN 4.1 11.2 - - - +
96B VAL* 4.4 3.8 - - + -
122B LEU* 3.9 33.4 - - + +
124B LEU* 3.3 40.2 - - + +
128B ARG* 5.2 0.9 - - - -
155B LEU 4.0 8.5 - - - +
156B VAL* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 3.0 26.9 + - - -
2A ASP* 4.0 11.1 + - - +
3A PHE 4.3 4.9 - - - +
4A ARG* 5.0 0.2 - - - -
1B MET* 3.6 30.9 - - - +
3B PHE* 3.8 16.6 - - + -
92B ALA* 3.5 4.4 + - - +
93B ILE* 1.3 78.6 - - - +
95B ASN* 1.3 60.8 + - - +
124B LEU* 4.8 0.7 - - - -
128B ARG* 2.8 50.3 + - - +
155B LEU* 2.8 32.4 + - + +
156B VAL 4.6 0.7 - - - -
157B VAL* 3.4 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 3.4 26.4 - - - +
5A ILE* 2.8 47.3 + - - +
52A GLY 4.6 2.2 + - - -
53A ALA 4.3 5.3 + - - -
93B ILE* 3.8 4.0 - - - +
94B ARG* 1.3 81.6 - - - +
96B VAL* 1.3 80.7 + - - +
97B ASP* 4.6 1.4 - - - +
124B LEU* 4.9 0.9 - - - -
128B ARG* 3.2 18.3 - - + +
154B ALA* 3.4 1.9 - - - +
155B LEU* 3.1 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.8 40.6 - - + -
49B ALA* 6.5 0.2 - - + -
50B LEU* 4.6 1.8 - - + -
93B ILE* 4.4 8.1 - - + -
95B ASN* 1.3 86.5 + - - +
97B ASP* 1.3 70.0 + - - +
118B ILE* 5.0 1.1 - - + -
122B LEU* 3.8 27.4 - - + -
124B LEU* 4.7 1.3 - - + -
128B ARG 2.9 11.1 + - - +
129B VAL* 4.8 11.9 - - + -
130B ASN* 2.9 28.1 + - - +
152B ALA* 5.2 0.9 - - + -
153B ALA 3.4 6.5 - - - +
154B ALA* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE 3.7 17.9 - - - +
6A GLY* 3.3 2.9 - - - -
7A GLN* 3.0 24.6 + - + +
52A GLY* 3.3 23.2 - - - +
95B ASN* 4.3 0.8 - - - +
96B VAL* 1.3 75.1 - - - +
98B SER* 1.3 71.7 + - - +
130B ASN* 3.0 30.6 + - - +
132B LYS* 2.9 20.9 + - - -
152B ALA* 3.4 2.3 - - - +
153B ALA* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN* 3.2 9.2 - - - -
42B LEU* 3.5 22.1 - - - +
46B ILE* 4.5 6.5 - - - +
97B ASP* 1.3 81.6 + - - +
99B THR* 1.3 60.1 + - - +
130B ASN 3.0 14.7 + - - -
131B VAL* 3.3 18.9 - - - +
132B LYS* 2.9 32.2 + - - +
151B GLN 3.1 14.1 - - - -
152B ALA* 4.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN* 2.6 24.4 + - - -
9A TYR* 4.6 12.5 + - + -
48A ASP* 5.3 0.9 - - - +
98B SER* 1.3 72.6 - - - +
100B ILE* 1.3 72.0 + - - +
101B ILE* 4.0 8.8 + - + +
132B LYS* 3.1 28.0 + - + +
134B LYS* 3.9 28.9 - - + -
149B GLU 4.0 0.2 - - - +
150B ALA* 3.2 5.4 - - - +
151B GLN* 2.8 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.7 21.3 - - + -
41B VAL* 5.2 1.3 - - + -
42B LEU* 4.1 15.9 - - + -
99B THR* 1.3 77.0 - - - +
101B ILE* 1.3 64.3 + - - +
102B ALA* 3.8 0.6 + - + -
107B LEU* 3.6 30.2 - - + +
111B ILE* 4.8 3.1 - - + -
114B MET* 3.7 30.3 - - - -
131B VAL* 3.7 16.2 - - + -
132B LYS 2.8 13.3 + - - +
133B ALA* 3.4 2.5 - - + +
134B LYS* 2.9 26.3 + - - +
148B ILE* 3.8 25.6 - - + -
149B GLU 3.4 4.7 - - - +
150B ALA* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.5 34.8 - - + -
99B THR* 4.4 9.6 - - + +
100B ILE* 1.3 73.5 - - - +
102B ALA* 1.3 63.9 + - - +
134B LYS* 3.3 9.9 - - + +
135B THR 4.1 5.4 - - - +
136B ASN* 3.6 28.7 - - + +
142B LEU* 3.7 20.0 - - + +
148B ILE* 3.4 5.2 - - - +
149B GLU* 2.7 67.2 + - + +
151B GLN* 3.6 11.7 - - - +
----------------------------------------------------------
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