Contacts of the strand formed by residues 3 - 9 (chain D) in PDB entry 6C6S
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 SER 3 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D GLN* 1.3 78.1 - - - +
4D TRP* 1.3 77.9 + - - +
5D TYR* 4.2 9.4 + - - -
58D GLU* 3.2 5.6 - - - +
59D PHE 2.9 34.4 + - - +
61D PRO* 6.2 1.6 - - - -
87D ILE* 3.4 34.6 - - - +
88D VAL 5.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 4 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D SER* 1.3 92.2 + - - +
5D TYR* 1.3 64.7 + - - +
27D ASN* 4.2 9.6 - - + -
28D CYS 5.3 1.6 - - - -
29D LEU* 4.2 26.7 - - + -
56D PHE* 4.3 2.7 - - + -
57D VAL 3.1 30.5 - - - -
58D GLU* 3.2 43.4 + - + -
87D ILE* 3.9 5.4 - - - +
88D VAL* 3.6 42.7 + - + +
90D SER* 5.1 11.2 + - - -
93D ILE* 3.7 47.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 5 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D SER* 4.3 11.6 - - - -
4D TRP* 1.3 77.3 - - - +
6D LEU* 1.3 61.6 + - - +
56D PHE* 3.5 6.6 - - - +
57D VAL* 2.8 37.0 + - + +
59D PHE* 3.5 49.8 - + - -
61D PRO* 3.6 24.1 - - + +
66D THR* 5.1 4.7 - - + -
78D PHE* 3.6 20.4 - + + -
84D SER* 5.7 0.7 - - - -
85D PRO* 4.1 27.6 - - + -
86D ALA 3.2 22.0 - - - -
87D ILE* 3.5 25.0 - - + +
88D VAL* 4.9 4.9 - - - +
375I PRO* 5.1 5.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D TYR* 1.3 76.1 - - - +
7D LEU* 1.3 66.8 + - - +
54D TYR* 3.6 35.4 - - + -
55D LEU 3.5 8.1 - - - +
56D PHE* 3.5 27.6 - - + -
78D PHE* 3.6 10.1 - - - -
79D VAL* 3.2 41.9 + - + +
86D ALA* 4.5 8.3 + - + +
88D VAL* 4.3 9.6 - - + +
290J ILE* 3.7 31.4 - - + +
291J ILE* 3.9 16.2 - - + +
294J ASN* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D TYR 4.2 0.2 - - - -
6D LEU* 1.3 76.6 - - - +
8D TYR* 1.3 62.8 + - - +
9D CYS* 3.8 5.8 + - - -
21D LEU* 4.2 11.4 - - + -
54D TYR* 3.5 1.7 - - - -
55D LEU* 2.9 42.0 + - + +
57D VAL* 3.7 29.2 - - + -
69D ILE* 3.7 17.5 - - + -
70D ASN* 5.6 0.2 - - - -
75D VAL* 3.8 32.1 - - + -
77D HIS 3.7 0.4 - - - -
78D PHE* 3.6 50.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A G 5.1 8.3 + - - -
6D LEU* 4.2 2.6 - - - +
7D LEU* 1.3 73.3 - - - +
9D CYS* 1.3 76.4 + - - +
11D ARG* 5.2 0.7 + - - -
53D ASN* 3.2 29.0 + - + -
54D TYR* 3.4 33.2 - + + -
75D VAL* 4.1 2.4 - - - +
76D SER* 3.1 8.5 + - - -
77D HIS* 2.9 70.8 + + + +
79D VAL* 4.4 2.1 - - + +
275J ARG* 3.9 16.2 + - - -
278J ARG* 2.8 44.1 + - - -
294J ASN* 4.6 5.2 - - - +
298J MET* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LEU* 4.3 9.9 - - - -
8D TYR* 1.3 93.9 - - - +
10D LYS* 1.3 70.9 + - - +
11D ARG 3.9 0.2 + - - -
14D LEU* 4.9 9.9 - - - +
17D ALA* 4.3 4.3 - - - -
53D ASN* 3.1 33.1 + - + +
55D LEU* 4.1 25.1 - - - -
74D GLY 3.3 17.0 - - - +
75D VAL* 4.2 15.5 - - - -
76D SER* 3.5 10.2 - - - +
----------------------------------------------------------
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