Contacts of the strand formed by residues 18 - 26 (chain A) in PDB entry 2PU1
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 PRO 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.7 25.6 - - + +
11A VAL 3.3 8.1 - - - +
12A LEU* 4.0 4.2 - - + -
13A ASP* 5.0 0.7 - - - +
17A ASN* 1.3 88.5 - - + +
19A THR* 1.3 61.8 + - - +
50A ARG* 2.9 26.6 + - - -
57A TYR* 3.3 50.9 - - + -
60A LYS* 3.4 27.8 - - + +
61A GLY* 3.9 0.7 - - - -
62A CYS* 4.1 3.4 - - - +
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Residues in contact with THR 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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10A GLU* 3.3 9.7 - - - +
11A VAL* 2.6 47.1 + - + +
13A ASP* 4.2 15.5 - - + +
18A PRO* 1.3 75.5 - - - +
20A VAL* 1.3 71.0 + - - +
35A VAL* 2.7 35.5 + - - +
36A PRO 4.3 3.6 + - - -
37A SER* 5.0 5.6 - - - -
50A ARG* 5.5 1.0 + - - -
62A CYS* 3.9 9.3 - - - -
107A ASN* 5.5 2.1 + - - +
376A THR* 3.8 21.5 - - + -
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Residues in contact with VAL 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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8A GLY* 5.3 0.2 - - - -
9A ARG 3.8 2.9 - - - +
19A THR* 1.3 87.5 + - - +
21A GLU* 1.3 67.0 + - - +
22A VAL* 3.9 22.2 - - + -
34A ALA* 3.5 2.4 - - - +
35A VAL* 2.9 33.8 + - + +
62A CYS* 3.8 13.4 - - + -
65A ALA* 3.7 24.9 - - + -
66A VAL* 4.1 13.9 - - + -
69A VAL* 4.5 9.6 - - + -
107A ASN* 3.3 35.9 - - - +
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Residues in contact with GLU 21 (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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7A HIS 4.0 0.2 - - - +
8A GLY* 3.1 4.5 - - - -
9A ARG* 2.7 73.1 + - + +
11A VAL* 3.7 28.9 - - + +
19A THR 4.1 0.4 + - - -
20A VAL* 1.3 75.2 - - - +
22A VAL* 1.3 67.4 + - - +
32A ARG* 3.6 38.1 + - + +
33A SER 3.3 9.4 - - - +
34A ALA* 4.1 9.7 - - + +
377A GLU* 4.7 10.2 - - - +
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Residues in contact with VAL 22 (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 VAL* 3.9 24.5 - - + -
7A HIS 3.4 8.7 - - - +
20A VAL* 3.9 14.6 - - + -
21A GLU* 1.3 80.1 - - - +
23A GLU* 1.3 70.4 + - - +
24A VAL* 4.1 4.5 - - + -
31A PHE 3.6 1.7 - - - +
32A ARG* 3.3 2.3 - - - -
33A SER 2.9 32.3 + - - -
69A VAL* 4.0 20.9 - - + -
108A ALA 4.4 0.4 - - - +
111A GLY* 3.7 30.1 - - - +
112A CYS* 3.9 18.4 - - - +
115A ALA* 3.9 2.4 - - - +
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Residues in contact with GLU 23 (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 LYS* 3.9 1.2 - - - +
6A VAL* 3.3 4.9 - - - -
7A HIS* 2.8 43.5 + - + +
9A ARG* 2.9 38.5 + - - +
22A VAL* 1.3 76.5 - - - +
24A VAL* 1.3 63.5 + - - +
25A THR* 4.2 3.0 + - - +
30A VAL* 3.8 29.2 - - + +
31A PHE 3.3 3.4 - - - -
32A ARG* 2.9 47.7 + - + -
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Residues in contact with VAL 24 (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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3A ILE* 4.0 31.4 - - + -
5A LYS 3.5 3.1 - - - -
6A VAL* 4.3 15.9 - - + -
22A VAL* 4.5 6.5 - - + -
23A GLU* 1.3 76.5 - - - +
25A THR* 1.3 66.0 + - - +
26A THR* 4.4 0.4 - - + -
30A VAL* 4.7 0.2 - - - -
31A PHE* 2.9 40.0 + - - -
77A LEU* 5.4 0.9 - - + -
112A CYS* 4.5 3.1 - - - +
115A ALA* 3.5 29.6 - - + +
116A ILE* 4.1 18.2 - - + +
119A ALA* 4.0 21.5 - - + -
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Residues in contact with THR 25 (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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3A ILE* 3.8 1.0 - - - -
4A GLN* 2.8 43.6 + - + +
5A LYS* 2.9 33.1 + - + +
23A GLU* 5.1 3.1 + - - +
24A VAL* 1.3 74.9 - - - +
26A THR* 1.3 71.9 + - - +
29A GLY 3.4 8.5 - - - +
30A VAL* 3.8 25.5 - - + +
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Residues in contact with THR 26 (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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1A MET 4.6 2.7 - - - -
2A THR 3.8 16.4 - - - +
3A ILE* 4.2 5.8 - - - -
4A GLN* 3.1 16.4 - - - +
24A VAL* 4.1 2.9 + - + -
25A THR* 1.3 82.6 - - - +
27A GLU* 1.3 66.1 + - - +
28A LYS* 3.1 17.4 + - - +
29A GLY* 3.0 17.5 + - - +
31A PHE* 3.5 14.7 - - - -
82A GLU* 3.8 26.3 + - - +
119A ALA* 3.9 23.3 + - + +
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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