Contacts of the strand formed by residues 170 - 178 (chain B) in PDB entry 3Q2T
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 GLU 170 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 4.3 9.0 - - - +
76B MET* 3.2 12.3 - - - +
77B ARG* 3.2 39.5 + - + +
79B THR* 2.8 33.1 + - - +
149B TRP* 3.5 1.0 - - - -
150B ARG* 2.9 69.3 + - + +
157B GLN* 4.8 1.6 - - - +
169B LYS* 1.3 79.3 - - - +
171B HIS* 1.3 65.1 + - - +
172B LYS* 4.1 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 3.3 27.4 - - + -
77B ARG 2.7 12.4 + - - +
78B ARG* 3.8 12.1 - - + +
79B THR 3.1 23.0 + - - +
117B GLU* 5.2 3.8 - - - -
147B ASN* 3.0 24.7 + - - -
148B TRP 3.7 3.8 - - - -
149B TRP* 3.1 35.8 + + - -
170B GLU* 1.3 72.6 - - - +
172B LYS* 1.3 69.2 + - - +
173B LYS* 4.4 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 3.2 31.2 - - + +
81B GLU* 3.1 39.2 + - + +
147B ASN* 3.5 1.7 - - - -
148B TRP* 2.8 44.8 + - + +
150B ARG* 4.9 4.4 - - - +
157B GLN* 3.5 23.9 + - - +
170B GLU* 4.1 14.8 + - + +
171B HIS* 1.3 83.6 - - - +
173B LYS* 1.3 59.8 + - - +
174B LEU* 4.6 9.2 - - + -
211B ILE* 3.7 23.9 - - + +
2F U 5.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 4.8 6.5 + - - -
34A GLU* 4.3 16.4 + - - +
79B THR 2.8 12.6 + - - +
80B VAL* 3.2 28.7 - - + +
81B GLU 3.2 3.1 + - - -
117B GLU* 3.0 43.7 + - + +
144B CYS* 3.7 22.9 - - - -
146B GLY 3.9 5.4 - - - +
147B ASN* 3.4 20.6 - - - +
171B HIS* 4.4 13.5 - - + +
172B LYS* 1.3 76.6 - - - +
174B LEU* 1.3 64.1 + - - +
175B PHE* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 3.3 45.8 - - + +
83B VAL* 4.5 1.3 - - + -
106B LEU* 3.7 11.2 - - + -
144B CYS* 3.6 7.4 - - - -
145B ILE* 3.0 38.3 + - + -
146B GLY* 3.3 18.8 + - - +
148B TRP* 4.3 19.3 - - + +
172B LYS* 4.6 7.2 - - + -
173B LYS* 1.3 72.8 - - - +
175B PHE* 1.3 65.7 - - - +
211B ILE* 3.6 26.5 - - + -
215B LEU* 4.5 15.5 - - + -
218B LEU* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.7 26.9 - - + -
80B VAL* 4.5 10.8 - - + -
81B GLU 3.1 5.2 + - - -
82B GLY* 3.7 0.3 - - - -
83B VAL* 2.8 33.6 + - - +
117B GLU* 3.8 29.4 - - + -
118B VAL* 4.4 8.3 - - + -
121B LEU* 4.1 22.2 - - + -
141B ILE* 3.7 22.4 - - + -
143B ASP 3.1 20.4 - - - +
144B CYS* 3.9 12.6 - - + -
145B ILE* 4.3 2.5 - - - +
173B LYS* 3.5 45.5 - - + -
174B LEU* 1.3 77.1 - - - +
176B LEU* 1.3 61.0 + - - +
177B VAL* 3.5 0.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.9 31.4 - - + -
83B VAL* 3.2 24.5 - - + +
85B ILE* 3.5 25.8 - - + -
141B ILE* 3.8 18.7 - - - +
142B ASP 4.2 3.8 + - - -
143B ASP* 2.9 24.3 + - + +
145B ILE* 3.8 10.8 - - + +
175B PHE* 1.3 72.0 - - - +
177B VAL* 1.3 67.0 + - - +
178B GLN* 3.7 7.7 + - - +
219B LEU* 4.7 2.7 - - + -
222B PHE* 3.6 35.7 - - + -
224B PHE* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY* 4.1 17.5 - - - -
83B VAL 3.6 5.5 + - - +
84B LEU* 3.9 32.9 - - + -
85B ILE 4.4 3.1 + - - -
121B LEU* 4.3 2.9 - - + -
125B MET* 3.4 35.7 - - + -
139B TRP* 4.0 12.1 - - + -
140B VAL 3.6 7.6 - - - +
141B ILE* 3.6 22.4 - - + -
175B PHE 3.5 3.3 + - - +
176B LEU* 1.3 79.4 - - - +
178B GLN* 1.3 72.6 + - - +
179B LEU* 3.5 4.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 3.6 24.9 + - - +
37B ILE* 3.4 31.6 - - + +
38B ASN 5.2 3.2 + - - +
138B ASP 5.5 0.9 - - - +
139B TRP* 5.2 0.9 - - - -
140B VAL* 2.8 47.9 + - + +
141B ILE 4.4 0.4 - - - +
142B ASP* 3.8 16.8 + - - +
143B ASP* 3.8 10.3 + - - +
176B LEU* 3.8 9.1 + - - +
177B VAL* 1.3 84.7 - - - +
179B LEU* 1.3 64.3 + - - +
----------------------------------------------------------
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