Contacts of the strand formed by residues 5 - 14 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS 3.7 2.4 + - - +
4D LYS* 1.3 71.7 - - - +
6D SER* 1.3 75.5 + - - +
34D TYR* 2.7 18.0 + - + +
35D VAL* 3.1 26.4 - - + -
36D GLU 3.3 4.9 + - - -
351D GLU* 3.4 32.8 - - + +
352D LEU* 3.9 28.9 - - + +
354D PHE* 6.0 2.2 - - + -
355D PHE* 3.7 22.7 - - + -
409D LEU* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LYS 3.4 5.7 + - - -
5D ILE* 1.3 82.4 - - - +
7D GLY* 1.3 60.9 + - - +
8D GLY* 4.2 5.9 + - - -
36D GLU 3.9 5.6 + - - +
349D ASN* 3.1 25.6 + - - -
351D GLU* 5.8 0.6 - - - +
352D LEU* 4.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE 3.6 0.6 + - - -
6D SER* 1.3 75.2 + - - +
8D GLY* 1.3 58.5 + - - +
35D VAL* 4.0 5.4 - - - -
36D GLU 2.9 13.3 + - - -
37D LEU* 3.4 25.6 - - - -
343D ARG* 3.4 12.8 - - - +
347D ASP* 4.7 1.6 - - - +
349D ASN* 4.1 5.6 + - - -
352D LEU* 3.4 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D SER* 3.9 5.3 + - - -
7D GLY* 1.3 77.7 - - - +
9D SER* 1.3 59.7 + - - -
10D VAL* 4.4 1.8 - - - -
36D GLU 4.3 0.2 + - - -
37D LEU* 3.3 11.3 - - - +
38D ASP* 2.4 35.8 + - - +
343D ARG* 4.8 4.7 - - - -
347D ASP* 4.9 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLY* 1.3 71.4 - - - -
10D VAL* 1.3 60.1 + - - +
38D ASP* 2.9 31.9 + - - +
40D HIS* 4.3 1.1 - - - -
67D HIS* 4.0 24.5 - - - +
69D VAL* 4.4 1.4 - - - +
343D ARG* 3.1 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLY 3.7 2.0 + - - +
9D SER* 1.3 79.4 - - - +
11D VAL* 1.3 72.5 + - - +
37D LEU* 4.0 33.4 - - + -
38D ASP 3.1 7.1 + - - +
39D LEU* 3.4 11.5 - - + +
40D HIS* 3.0 24.2 + - - -
69D VAL* 3.8 24.5 - - + +
71D VAL* 4.3 16.4 - - + -
336D TRP* 5.1 1.6 - - + -
340D LEU* 4.2 19.5 - - + -
343D ARG* 4.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 1.3 75.4 - - - +
12D GLU* 1.3 61.7 + - - +
13D MET* 4.7 6.3 - - + -
40D HIS* 3.4 16.2 - - + +
42D TYR* 4.0 21.8 - - + -
60D ALA 4.3 2.2 - - - +
63D ALA* 3.8 27.8 - - + +
64D ILE* 4.2 16.4 - - + +
67D HIS* 3.8 22.0 - - + -
69D VAL 2.9 18.3 + - - +
70D GLY* 3.2 4.8 - - - -
71D VAL* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL 3.9 1.0 + - - -
11D VAL* 1.3 75.0 - - - +
13D MET* 1.3 65.2 + - - +
14D GLN* 3.0 22.0 + - - +
23D TRP* 2.8 28.1 + - - -
27D LYS* 2.5 39.2 + - - +
39D LEU* 4.0 18.7 - - + +
40D HIS 2.9 8.8 + - - +
41D SER* 3.8 23.7 + - - +
42D TYR* 3.0 27.7 + - - +
71D VAL* 3.3 14.1 - - + +
336D TRP* 3.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 4.7 5.8 - - + +
12D GLU* 1.3 77.9 - - - +
14D GLN* 1.3 62.7 + - - +
23D TRP* 4.2 5.0 - - - -
42D TYR* 3.2 4.0 - - + +
44D LEU* 3.4 26.2 - - + -
60D ALA* 3.7 24.7 - - + -
64D ILE* 3.7 30.1 - - + -
70D GLY* 4.6 0.9 - - - -
71D VAL 3.0 31.0 + - - +
72D LYS* 3.7 25.8 - - + -
73D CYS* 2.9 30.8 + - - +
99D ILE* 4.4 18.2 - - - -
304D GLU* 4.1 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLU* 3.0 28.2 + - - +
13D MET* 1.3 74.1 - - - +
15D GLY* 1.3 60.6 + - - +
20D ARG* 5.7 5.6 - - + -
23D TRP* 4.5 5.8 - - + +
24D GLU* 4.1 16.2 + - - +
27D LYS* 4.0 4.8 - - - +
41D SER* 4.4 13.9 - - - -
42D TYR 2.9 10.5 + - - +
43D ASP* 3.6 34.2 - - - +
44D LEU* 3.1 28.7 + - - +
45D GLY 4.2 0.7 - - - -
73D CYS* 4.2 3.5 - - - +
75D THR* 4.1 2.1 - - - +
----------------------------------------------------------
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