Contacts of the strand formed by residues 5 - 10 (chain A) in PDB entry 6ISB
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 TRP 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.6 5.1 - - - +
4A LEU* 1.3 80.1 - - - +
6A HIS* 1.3 61.3 + - - +
7A THR* 3.7 15.1 - - + +
18A GLU* 4.4 14.1 - - - -
20A VAL* 3.5 27.6 - - + -
22A PRO* 4.9 3.4 - - + -
100A TRP* 3.8 21.3 - + + -
101A GLN 3.8 0.8 + - - -
102A LYS* 3.2 42.8 - - + +
103A VAL 2.8 30.7 + - - -
154A GLN* 6.1 1.1 - - - -
156A ASP* 3.4 21.4 + - + -
157A LEU 5.9 0.2 - - - -
169A PHE* 4.0 3.2 - - - -
171A SER* 4.7 3.1 - - - -
172A LYS 4.4 0.7 - - - +
173A PHE* 3.4 39.9 + + + -
174A PRO* 4.1 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.6 3.8 - - + -
5A TRP* 1.3 77.9 - - - +
7A THR* 1.3 78.2 + - - +
8A SER* 4.4 10.0 + - - -
87A TYR* 4.0 14.7 + + - -
103A VAL* 3.2 31.6 - - + +
105A GLN* 4.8 3.6 - - + -
156A ASP* 3.8 0.3 - - - -
157A LEU* 2.8 66.6 + - + +
160A TYR* 5.9 2.7 - + - -
169A PHE* 3.9 14.0 - + + -
26C ILE* 3.9 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TRP* 3.7 14.6 - - - +
6A HIS* 1.3 83.9 + - - +
8A SER* 1.3 65.1 + - - +
9A VAL* 4.4 4.0 - - - +
102A LYS* 3.8 15.4 + - - +
103A VAL 3.0 7.1 + - - +
104A ILE* 3.4 26.7 - - - +
105A GLN* 2.9 23.6 + - - +
154A GLN* 4.2 17.6 + - - +
155A ILE 3.1 9.2 - - - -
156A ASP* 3.5 26.9 - - - +
157A LEU 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 4.4 6.9 + - - -
7A THR* 1.3 76.5 + - - +
9A VAL* 1.3 64.8 + - - +
105A GLN* 3.2 26.3 + - - +
107A VAL* 4.9 7.2 - - - -
112A PHE* 3.5 11.5 - - - -
154A GLN* 3.3 7.4 - - - +
155A ILE* 2.9 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 4.4 2.9 - - - +
8A SER* 1.3 79.7 - - - +
10A PRO* 1.3 78.6 - - + +
15A MET* 5.2 3.1 - - + -
16A SER 4.9 9.4 - - - +
17A LEU* 3.9 28.5 - - + -
18A GLU* 6.0 2.0 - - + +
104A ILE* 4.3 13.5 - - + -
105A GLN 2.9 12.3 + - - +
106A VAL* 3.4 6.2 - - + -
107A VAL* 3.0 23.4 + - - +
112A PHE* 3.9 4.5 - - - -
153A ARG 3.8 8.1 - - - +
154A GLN* 4.2 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 1.3 95.7 - - + +
11A PHE* 1.3 68.3 + - - +
12A ALA* 3.6 4.2 + - + +
15A MET* 4.3 6.8 - - - +
107A VAL* 3.3 7.2 - - + +
109A SER 3.2 27.1 - - - +
110A ASP 4.6 3.1 - - - +
112A PHE* 3.5 16.8 - - + -
152A PRO 4.9 2.2 - - - +
153A ARG* 3.1 31.6 - - + +
----------------------------------------------------------
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