Contacts of the strand formed by residues 5 - 14 (chain A) in PDB entry 6B0Z
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 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 5.4 2.5 - - - +
4A LYS* 1.3 74.5 - - - +
6A SER* 1.3 71.5 + - - +
7A GLY 4.8 0.2 - - - +
34A TYR* 2.9 19.9 + - + +
35A VAL* 3.4 9.0 - - + -
36A GLU* 2.6 35.7 + - - +
349A ASN* 4.3 1.8 - - - +
351A GLU* 3.7 44.0 - - + +
352A LEU* 4.0 14.4 - - + +
355A PHE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS 3.8 3.1 + - - -
5A ILE* 1.3 73.5 - - - +
7A GLY* 1.3 60.8 + - - +
8A GLY 3.5 2.6 + - - -
36A GLU* 3.7 9.2 - - - +
349A ASN* 2.8 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE 3.5 1.6 + - - -
6A SER* 1.3 74.3 - - - +
8A GLY* 1.3 59.8 + - - +
35A VAL* 3.7 9.6 - - - -
36A GLU 2.7 19.6 + - - -
37A LEU* 3.6 14.7 - - - +
343A ARG* 3.2 26.3 - - - +
347A ASP* 4.4 2.6 - - - +
349A ASN* 4.7 2.2 + - - -
352A LEU* 3.4 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 3.5 3.2 - - - -
7A GLY* 1.3 80.1 - - - +
9A SER* 1.3 65.3 + - - -
10A VAL 3.3 2.6 + - - -
36A GLU 3.9 3.4 + - - -
37A LEU* 3.7 8.1 - - - +
38A ASP* 3.1 35.3 + - - +
343A ARG* 4.3 2.2 - - - -
347A ASP* 4.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY* 1.3 69.8 - - - -
10A VAL* 1.3 57.8 + - - +
38A ASP* 3.6 13.3 + - - +
40A HIS* 2.6 28.3 + - - -
67A HIS* 2.8 26.7 + - - +
69A VAL* 4.3 2.1 - - - +
343A ARG* 2.8 46.1 + - - +
347A ASP* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 3.3 5.4 + - - +
9A SER* 1.3 79.3 + - - +
11A VAL* 1.3 75.9 + - - +
37A LEU* 4.0 22.9 - - + -
38A ASP 3.4 4.4 + - - -
39A LEU* 3.7 16.5 - - + +
40A HIS* 2.9 25.7 + - - +
69A VAL* 4.0 17.9 - - + +
71A VAL* 4.1 17.3 - - + -
336A TRP* 4.7 3.4 - - + -
340A LEU* 4.0 26.5 - - + -
343A ARG* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 1.3 74.2 - - - +
12A GLU* 1.3 57.9 + - - +
13A MET* 4.1 8.7 - - + +
40A HIS* 3.3 16.8 - - + +
42A TYR* 4.2 8.7 - - + -
60A ALA 4.0 9.2 - - - +
63A ALA* 3.5 37.9 - - + +
64A ILE* 3.6 24.9 - - + +
67A HIS* 4.0 13.7 - - + -
69A VAL 2.9 20.6 + - - +
70A GLY* 3.2 1.4 - - - -
71A VAL* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL 3.8 0.6 + - - -
11A VAL* 1.3 73.1 - - - +
13A MET* 1.3 67.0 + - - +
14A GLN* 3.4 12.0 - - - +
23A TRP* 2.8 29.3 + - + +
27A LYS* 2.7 35.7 + - - -
39A LEU* 3.8 24.6 - - + +
40A HIS 2.8 10.3 + - - +
41A SER* 2.7 27.7 + - - -
42A TYR* 2.9 28.1 + - - -
71A VAL* 3.4 8.1 - - + +
336A TRP* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.1 10.8 - - + +
12A GLU* 1.3 79.1 - - - +
14A GLN* 1.3 63.7 - - - +
23A TRP* 4.1 3.3 - - - -
42A TYR* 3.2 4.7 - - + -
44A LEU* 3.8 19.5 - - + -
60A ALA* 3.7 28.3 - - + -
64A ILE* 3.5 26.5 - - + -
70A GLY* 4.1 1.1 - - - -
71A VAL 3.0 38.8 + - - +
72A LYS* 3.8 17.9 - - + -
73A CYS* 2.9 30.5 + - - +
99A ILE* 3.8 28.0 - - - -
304A GLU* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.4 17.7 - - - +
13A MET* 1.3 72.9 - - - +
15A GLY* 1.3 59.2 + - - +
20A ARG* 3.4 25.6 + - + +
23A TRP* 4.6 3.8 - - + +
24A GLU* 3.8 16.2 + - - +
27A LYS* 3.5 21.0 - - - +
41A SER* 3.7 16.2 + - - -
42A TYR 2.8 14.2 + - - +
43A ASP* 3.6 21.2 - - - +
44A LEU* 2.8 32.5 + - - +
73A CYS* 4.3 3.4 - - - -
75A THR* 4.4 0.5 - - - +
48B ASN* 5.6 5.3 - - - +
----------------------------------------------------------
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