Contacts of the strand formed by residues 8 - 18 (chain E) in PDB entry 1S9V
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 VAL 8 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.5 28.9 - - + -
13D TYR 3.6 3.6 - - - +
14D GLN* 3.8 6.7 - - + +
70D LEU* 3.8 8.1 - - - +
82D ALA* 4.4 2.0 - - + -
113D PHE* 4.1 17.9 - - + -
114D PRO* 4.0 14.8 - - + -
115D PRO* 4.2 2.5 - - + -
6E ASP* 3.3 27.8 - - - +
7E PHE* 1.3 74.6 - - - +
9E TYR* 1.3 65.6 + - - +
10E GLN* 4.2 9.0 - - + -
32E TYR* 3.6 4.2 - - - -
33E ASN* 2.6 47.6 + - - +
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Residues in contact with TYR 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.6 4.7 - - - +
13D TYR* 2.7 39.1 + - + +
66D LEU* 3.4 47.1 - - + +
69D ASN* 3.0 30.5 + - + -
70D LEU* 3.9 29.6 - - + +
73D LEU* 3.8 29.2 - - + -
8E VAL* 1.3 75.3 - - - +
10E GLN* 1.3 77.5 + - - +
30E SER* 3.6 14.8 + - - -
31E ILE 3.4 11.2 - - - -
37E ILE* 5.3 2.0 - - + +
61E TRP* 5.6 0.9 - - - -
8F GLU* 2.7 23.3 + - - -
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Residues in contact with GLN 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 5.8 0.9 - - + +
11D ASN 3.2 7.9 - - - +
12D LEU* 4.2 3.1 - - + -
113D PHE* 3.6 11.1 - - - -
143D HIS* 2.9 27.7 + - - +
145D PHE* 3.2 27.3 - - + -
8E VAL* 4.2 9.9 - - + -
9E TYR* 1.3 84.4 - - - +
11E PHE* 1.3 59.5 + - - +
12E LYS* 3.5 24.0 + - + -
29E ARG 3.5 0.2 - - - +
30E SER* 3.5 1.9 - - - -
31E ILE* 2.6 57.0 + - + +
33E ASN 2.8 27.3 + - - +
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Residues in contact with PHE 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLY* 5.9 0.2 - - - -
10D VAL* 3.8 0.2 - - - -
11D ASN* 2.7 58.9 + - + -
66D LEU* 3.8 22.1 - - + +
10E GLN* 1.3 75.4 - - - +
12E LYS* 1.3 62.4 + - - +
13E GLY 4.1 10.3 - - - -
28E SER* 3.8 32.1 - - - -
29E ARG 3.2 13.7 - - - -
30E SER* 3.8 5.2 - - - -
71E LYS* 4.5 2.0 - - - -
6F GLN* 3.5 30.1 - - + -
7F PRO 3.5 19.1 - - - -
8F GLU* 3.2 40.2 - - + +
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Residues in contact with LYS 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D SER* 4.8 3.8 - - - +
9D GLY 3.1 6.7 - - - +
10D VAL* 4.8 12.1 - - + -
11D ASN 5.6 0.2 - - - +
139D SER* 3.9 24.1 + - - +
140D LYS 3.0 28.3 + - - -
141D SER* 4.9 1.0 - - - +
143D HIS* 3.1 32.4 + - + +
10E GLN* 3.5 25.5 + - + -
11E PHE* 1.3 83.8 - - - +
13E GLY* 1.3 59.7 + - - +
14E MET* 3.3 32.1 + - + +
27E VAL 3.5 0.9 - - - +
28E SER* 3.3 4.9 - - - -
29E ARG* 2.9 38.7 + - + +
31E ILE* 5.0 2.0 - - + -
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Residues in contact with GLY 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D SER* 4.4 0.4 - - - -
9D GLY* 2.9 43.7 + - - +
11E PHE* 4.1 5.5 - - - -
12E LYS* 1.3 69.2 - - - +
14E MET* 1.3 58.4 + - - -
15E CYS* 4.0 0.5 + - - -
27E VAL 4.3 0.2 - - - -
6F GLN* 2.9 47.8 + - - -
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Residues in contact with MET 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 4.0 20.9 - - + -
7D ALA 3.2 4.9 - - - +
8D SER* 3.6 20.6 - - - +
139D SER* 5.5 4.0 - - - +
141D SER* 6.3 3.1 - - - -
12E LYS* 3.7 30.3 - - + +
13E GLY* 1.3 73.2 - - - -
15E CYS* 1.3 61.2 + - - +
16E TYR* 3.8 25.1 - - + +
26E LEU* 3.4 3.8 - - - -
27E VAL* 2.8 42.5 + - + +
29E ARG* 3.4 29.8 - - - -
6F GLN* 3.5 6.6 + - - -
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Residues in contact with CYS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D HIS 3.9 0.7 - - - +
6D VAL* 3.5 3.6 - - - +
7D ALA* 2.8 35.9 + - + +
9D TYR* 3.6 22.2 - - + -
14E MET* 1.3 77.8 - - - +
16E TYR* 1.3 63.9 + - - +
17E PHE* 3.7 20.8 - - + -
25E ARG 3.5 4.5 - - - -
78E VAL* 4.2 0.2 - - - -
79E CYS* 2.0 52.5 - - + -
6F GLN* 4.0 9.4 - - - -
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Residues in contact with TYR 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D VAL 5.2 10.3 - - - +
3D ALA* 4.0 15.7 - - + -
5D HIS 3.6 2.5 - - - -
6D VAL* 3.7 31.9 - - + -
14E MET* 3.8 34.0 - - + +
15E CYS* 1.3 75.9 - - - +
17E PHE* 1.3 61.6 + - - +
23E ARG 3.7 0.2 - - - +
24E VAL* 3.3 7.8 - - - +
25E ARG* 2.7 57.1 + - + +
27E VAL* 3.8 25.1 - - + -
29E ARG* 2.8 25.0 + - - -
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Residues in contact with PHE 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ALA* 3.2 1.2 - - - +
4D ASP* 2.8 25.0 + - - -
5D HIS* 2.9 34.2 + - + +
6D VAL 5.1 0.4 - - - -
7D ALA* 4.5 12.1 - - + -
9D TYR* 4.5 8.1 - + - -
26D PHE* 4.8 3.1 - + - -
15E CYS* 3.7 29.8 - - + -
16E TYR* 1.3 75.5 - - - +
18E THR* 1.3 63.6 + - - +
20E GLY 3.7 10.8 - - - +
21E THR* 4.5 1.1 - - + -
23E ARG 3.5 2.9 - - - -
24E VAL* 3.7 24.0 - - + -
79E CYS* 3.2 41.7 - - + -
80E ARG* 4.6 0.9 - - - -
83E TYR* 3.4 41.7 - + + -
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Residues in contact with THR 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D VAL 4.0 4.0 + - - +
3D ALA* 3.4 20.6 - - - +
4D ASP* 3.5 19.3 - - - +
17E PHE* 1.3 78.9 + - - +
19E ASN* 1.3 90.2 + - - +
20E GLY 3.3 3.1 + - - +
23E ARG* 3.1 40.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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