Contacts of the strand formed by residues 4 - 13 (chain B) in PDB entry 3QN3
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 ILE 4 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 1.3 73.9 - - - +
5B GLU* 1.3 58.7 + - - +
6B ASP 4.2 6.1 - - - +
7B VAL* 4.8 0.7 - - + -
25B VAL* 4.1 16.6 - - + -
26B THR 4.0 2.5 - - - -
27B LEU* 4.0 14.1 - - + -
78B ILE* 3.6 46.0 - - + +
79B LEU* 3.5 21.8 - - + +
80B GLY* 2.8 26.7 + - - -
81B LEU* 3.0 18.0 + - + +
82B ASP 5.2 1.6 - - - +
83B ALA* 4.4 5.4 - - - -
89B LEU* 4.3 11.2 - - + -
117B THR* 3.9 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 3.3 3.0 + - + -
4B ILE* 1.3 72.8 - - - +
6B ASP* 1.3 60.7 + - + +
26B THR* 2.8 21.7 + - + +
27B LEU 3.8 17.7 - - - +
28B SER* 3.5 27.0 - - - +
79B LEU* 3.3 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.2 1.4 - - - +
5B GLU* 1.3 84.6 - - + +
7B VAL* 1.3 71.6 + - - +
8B ARG* 4.1 21.9 - - - +
24B GLU* 5.0 1.0 - - - +
25B VAL* 3.3 5.2 - - - +
26B THR* 2.8 51.3 + - + +
79B LEU* 3.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.8 1.1 - - + -
6B ASP* 1.3 85.3 + - - +
8B ARG* 1.3 67.8 + - - +
23B ALA* 5.5 0.2 - - + -
24B GLU 3.4 10.1 - - - +
25B VAL* 4.0 17.7 - - + -
70B VAL* 3.5 23.3 - - + -
71B ASN* 4.0 7.1 - - - +
74B ILE* 5.1 0.4 - - + -
75B ALA* 3.4 42.2 - - + +
78B ILE* 4.1 15.9 - - + -
79B LEU* 4.0 9.9 - - + +
113B VAL* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A PHE* 3.5 46.1 - - - +
6B ASP* 4.1 13.9 - - - +
7B VAL* 1.3 78.1 - - - +
9B ALA* 1.3 62.2 + - - +
10B TYR* 4.0 19.7 + - + -
23B ALA* 3.2 5.2 - - - +
24B GLU* 2.8 82.1 + - + +
70B VAL* 4.1 4.7 - - - +
71B ASN* 3.1 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A PHE* 5.5 0.7 - - - -
8B ARG* 1.3 78.1 + - - +
10B TYR* 1.3 69.6 + - - +
21B VAL* 3.9 12.6 - - + -
22B LYS 3.1 14.4 - - - +
23B ALA* 4.2 1.1 - - - -
67B VAL* 3.5 13.2 - - - +
70B VAL* 3.6 31.4 - - + +
71B ASN* 2.8 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS* 6.0 0.4 - - - +
400A LEU* 5.4 2.0 - - + -
401A GLU* 2.4 50.4 + - + +
404A PHE* 3.6 33.7 - + + -
8B ARG* 4.0 32.5 - - - -
9B ALA* 1.3 82.2 - - - +
11B GLU* 1.3 64.7 + - - +
12B VAL* 3.6 24.5 - - + -
20B THR 3.9 0.3 - - - +
22B LYS* 3.0 49.8 + - + +
24B GLU* 4.6 20.1 + - + +
67B VAL* 3.5 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS* 3.0 24.0 + - - +
400A LEU* 3.6 17.5 - - + +
404A PHE* 5.9 0.2 - - - -
10B TYR* 1.3 79.3 - - - +
12B VAL* 1.3 64.2 + - - +
19B PRO* 4.1 8.9 - - + +
20B THR 3.6 4.0 - - - -
57B ARG* 2.7 43.3 + - - -
58B PHE* 4.1 6.3 - - - -
62B GLY* 3.5 3.8 - - - -
63B VAL* 3.0 40.5 + - + +
64B LEU* 3.5 19.6 - - + +
67B VAL* 3.8 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASN* 3.5 32.3 - - + +
400A LEU* 4.0 7.2 - - + -
401A GLU* 5.4 0.2 - - + -
10B TYR* 3.6 29.4 + - + -
11B GLU* 1.3 79.9 - - - +
13B LEU* 1.3 65.2 + - - +
19B PRO* 3.2 8.0 - - - +
20B THR* 2.9 38.4 + - + +
22B LYS* 3.8 20.4 - - + +
36B ILE* 3.9 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.2 26.0 - - + -
182A CYS* 3.6 33.9 - - - -
387A LEU* 4.7 5.8 - - + -
393A THR* 4.2 18.7 + - + -
396A TYR* 4.4 11.2 - - + -
397A ASN* 2.9 34.9 + - - +
400A LEU* 5.0 1.8 - - + -
12B VAL* 1.3 82.1 - - - +
14B ASP* 1.3 67.7 + - - +
17B GLY* 3.9 17.7 - - - +
18B ASN 3.5 6.5 - - - +
19B PRO* 4.4 1.3 - - + -
20B THR* 4.4 3.9 - - - +
58B PHE* 4.1 17.0 - - + -
365B SER* 5.0 2.4 - - - -
366B GLU* 4.5 3.5 - - - +
----------------------------------------------------------
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