Contacts of the strand formed by residues 7 - 14 (chain A) in PDB entry 1S3Y
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 LEU 7 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS 4.3 7.6 - - - +
6A SER* 1.3 80.0 - - - +
8A THR* 1.3 66.2 + - - +
56A LEU* 5.1 1.1 - - + -
98A LEU* 4.0 36.1 - - + -
102A LEU* 3.8 31.6 - - + -
120A ILE* 3.9 21.1 - - + +
122A VAL* 4.5 14.8 - - + -
132A ALA* 5.5 0.7 - - + -
135A HIS* 4.3 16.2 - - + -
137A LYS* 3.3 16.4 + - + -
138A LEU* 3.3 26.2 - - + +
139A ASP* 3.5 17.3 + - - +
140A ARG 4.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 5.0 2.4 + - - -
7A LEU* 1.3 79.1 + - - +
9A LEU* 1.3 65.9 - - - +
119A ARG* 5.9 0.9 - - - +
120A ILE 3.0 14.9 + - - -
121A PHE* 3.1 23.2 - - + +
122A VAL* 2.6 34.6 + - - +
138A LEU* 3.9 1.8 - - - -
139A ASP* 5.0 0.5 + - - -
140A ARG* 3.6 29.9 + - + +
142A MET* 3.7 22.0 - - + -
180A TRP* 3.6 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 1.3 75.9 - - - +
10A ILE* 1.3 54.4 + - - +
11A VAL* 3.4 33.7 - - + -
122A VAL* 3.4 7.4 - - + +
129A TYR* 3.5 28.3 - - + -
132A ALA* 4.2 16.6 - - + -
133A MET* 3.8 19.3 - - + -
138A LEU* 3.5 9.1 - - + +
140A ARG 3.0 13.5 + - - +
141A ILE* 3.2 11.8 - - + -
142A MET 2.6 32.9 + - - +
156A PHE* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 1.3 73.4 - - - +
11A VAL* 1.3 65.5 + - - +
35A TYR* 5.0 4.0 - - + -
36A PHE* 3.8 24.5 - - + -
39A VAL* 4.2 26.0 - - + -
40A THR* 4.0 15.9 - - + -
121A PHE* 4.6 8.5 - - + -
122A VAL 2.9 12.1 + - - +
123A ILE* 3.4 33.0 - - + -
129A TYR* 2.9 16.6 + - - -
142A MET* 3.2 21.1 - - + +
208A TQT 2.9 28.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
9A LEU* 3.4 23.3 - - + -
10A ILE* 1.3 74.4 - - - +
12A ALA* 1.3 78.9 + - - +
13A LEU* 3.9 15.7 - - + -
19A ILE* 4.1 14.1 - - + -
129A TYR* 3.4 28.7 - - + +
141A ILE* 4.3 8.1 - - + -
142A MET 2.8 12.0 + - - +
143A ALA* 3.3 4.0 - - - -
144A THR 2.9 22.0 + - - -
156A PHE* 4.1 10.3 - - + -
160A PHE* 5.2 0.9 - - + -
208A TQT 3.3 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 1.3 81.7 - - - +
13A LEU* 1.3 63.3 + - - +
19A ILE* 3.8 12.6 - - - +
27A TRP* 4.3 16.4 - - + +
32A GLU* 4.2 7.9 - - + +
144A THR* 3.4 17.3 - - + +
146A ILE* 4.7 10.8 - - + -
207A NAP 5.0 8.5 + - - +
208A TQT 3.8 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.9 20.6 - - + +
12A ALA* 1.3 78.0 - - - +
14A THR* 1.3 68.4 + - - +
17A TYR* 3.4 41.5 - - + -
18A GLY 3.3 13.7 - - - +
19A ILE* 3.5 9.0 - - + -
27A TRP* 4.9 2.5 - - - -
143A ALA* 4.2 15.3 - - + -
144A THR 2.8 19.6 + - - +
145A ILE* 3.5 11.8 - - + +
146A ILE* 2.8 26.2 + - - +
156A PHE* 3.9 17.3 - - + -
160A PHE* 4.2 11.2 - - + -
161A ARG* 5.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 1.3 80.6 - - - +
15A THR* 1.3 57.3 + - - +
16A SER* 2.9 11.5 + - - -
17A TYR* 2.6 27.0 + - - -
18A GLY* 3.0 26.4 + - - +
27A TRP* 3.7 16.6 - - + -
145A ILE* 4.9 1.8 - - - -
146A ILE* 3.3 16.8 - - + +
148A LYS 3.5 15.9 - - - +
149A ASP* 5.3 1.8 - - - -
150A ILE* 3.5 32.7 - - + +
----------------------------------------------------------
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