Contacts of the strand formed by residues 13 - 20 (chain A) in PDB entry 2P18
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 PHE 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 3.7 2.8 - - - +
9A PHE* 2.8 74.6 + + + +
11A SER 3.8 1.0 - - - -
12A ALA* 1.3 89.4 - - + +
14A SER* 1.3 72.6 + - - +
15A VAL* 4.1 9.9 - - + -
29A ILE* 4.4 2.2 - - + -
30A ASN 3.1 15.9 - - - +
31A ASP* 4.0 0.2 - - - -
32A HIS* 3.7 8.5 - - - -
129A LEU* 3.7 36.6 - - + -
148A VAL* 3.7 27.4 - - + -
149A GLN* 4.0 16.4 - - - -
150A HIS* 4.1 4.3 - - + -
153A HIS 6.2 0.2 - - - -
156A ASP* 5.7 1.1 - - + -
157A GLY 4.1 5.8 - - - -
159A ALA* 4.1 8.3 - - + -
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Residues in contact with SER 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 3.8 14.0 - - - +
7A LYS 3.3 13.2 - - - -
8A THR* 3.7 15.9 - - - -
9A PHE* 4.3 0.7 - - - -
13A PHE* 1.3 80.3 - - - +
15A VAL* 1.3 67.4 + - - +
16A THR* 4.2 2.9 + - - -
28A LEU 3.8 0.3 - - - +
29A ILE* 3.6 0.9 - - - -
30A ASN* 2.9 41.4 + - - +
32A HIS* 3.2 19.0 + - - -
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A CYS 4.0 0.2 - - - +
6A THR* 3.5 1.9 - - - -
7A LYS* 2.8 36.4 + - - +
9A PHE* 3.9 8.1 - - + -
13A PHE* 4.1 7.9 - - + -
14A SER* 1.3 79.8 - - - +
16A THR* 1.3 62.6 + - - +
17A VAL* 3.8 1.2 + - - +
27A TYR* 3.9 14.1 - - + -
28A LEU 3.5 4.7 - - - +
29A ILE* 4.5 6.5 - - + -
159A ALA* 3.8 27.1 - - + -
161A PHE* 3.7 27.8 - - + -
207A PHE* 3.7 30.7 - - + -
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 4.5 5.4 - - + -
5A CYS 3.4 10.3 - - - +
6A THR* 3.0 22.6 + - - +
14A SER* 4.9 2.4 + - - -
15A VAL* 1.3 71.0 - - - +
17A VAL* 1.3 65.7 - - - +
18A VAL* 3.5 17.1 + - + +
27A TYR* 3.3 10.7 - - - -
28A LEU* 2.8 44.4 + - - +
30A ASN* 6.0 1.4 - - - +
52A TYR* 3.3 44.1 + - + -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.3 27.5 - - - +
5A CYS* 2.6 35.8 + - - +
7A LYS 5.7 0.9 - - - +
15A VAL 4.7 1.8 - - - +
16A THR* 1.3 72.2 - - - +
18A VAL* 1.3 57.9 + - - +
19A PRO* 3.5 1.4 - - - +
25A PHE* 3.4 36.1 - - + -
27A TYR* 3.6 23.1 - - + -
207A PHE* 4.0 19.5 - - + -
251A PRO* 3.8 8.5 - - + -
253A VAL* 3.7 19.7 - - + +
254A PRO* 4.7 0.9 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 5.1 2.9 - - + -
16A THR* 3.8 25.4 - - + +
17A VAL* 1.3 75.5 - - - +
19A PRO* 1.3 68.8 - - + +
20A THR* 3.3 5.4 + - + +
25A PHE* 3.7 2.6 - - - -
26A SER* 2.9 44.3 + - - +
28A LEU* 4.5 11.7 - - + +
48A PRO* 3.7 41.5 - - + +
49A ILE* 3.9 23.1 - - + +
52A TYR* 5.0 6.1 - - + -
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Residues in contact with PRO 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.3 55.2 - - + +
3A ASN 3.4 30.5 - - - +
4A TYR* 4.0 3.8 - - + +
17A VAL* 3.5 7.6 - - + +
18A VAL* 1.3 87.4 - - + +
20A THR* 1.3 62.4 + - - +
24A ASN 3.7 7.4 - - - +
25A PHE* 4.3 6.3 - - + -
45A ASP* 4.6 0.3 - - - +
48A PRO* 4.3 10.3 - - + +
251A PRO* 5.4 0.2 - - + -
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Residues in contact with THR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 2.9 10.1 + - - +
18A VAL* 3.3 17.2 + - + +
19A PRO* 1.3 78.4 - - - +
21A LEU* 1.3 70.9 + - - +
24A ASN* 3.0 27.2 + - - +
26A SER* 3.2 27.5 + - - +
43A ASN* 2.9 25.5 + - - -
45A ASP* 3.2 31.6 - - - +
48A PRO* 4.6 4.0 - - + -
49A ILE* 5.1 2.7 - - + -
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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