Contacts of the strand formed by residues 6 - 12 (chain A) in PDB entry 5PNT
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 LYS 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLN* 3.8 14.7 + - - +
4A ALA* 3.2 33.2 + - + +
5A THR* 1.3 77.4 - - - +
7A SER* 1.3 60.8 + - - +
38A ASN* 2.7 11.3 + - + +
39A TRP* 3.2 40.1 - - + +
40A ARG* 2.8 24.1 + - - +
86A ASP* 3.2 5.2 - - - +
156A ALA 4.7 5.2 - - - -
157A HIS* 3.0 47.9 - - + +
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Residues in contact with SER 7 (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 THR 5.5 0.4 - - - -
6A LYS* 1.3 76.4 - - - +
8A VAL* 1.3 62.0 + - - +
39A TRP* 4.3 2.0 - - - -
40A ARG* 3.1 31.9 - - - -
84A THR 3.4 5.7 + - - -
85A PHE* 3.2 21.4 - - - -
86A ASP* 2.9 28.7 + - - +
87A TYR* 3.2 23.9 + - - +
110A LYS* 5.6 0.2 + - - -
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Residues in contact with VAL 8 (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 SER* 1.3 75.3 - - - +
9A LEU* 1.3 64.0 + - - +
10A PHE* 3.9 19.7 - - + -
26A PHE* 3.6 37.9 - - + -
39A TRP* 4.0 13.5 - - + -
40A ARG 2.8 9.1 + - - +
41A VAL* 3.5 6.7 - - + -
42A ASP 3.1 24.4 + - - +
85A PHE* 3.7 4.1 - - - -
87A TYR* 3.5 15.7 - - + +
89A LEU* 3.8 31.0 - - + -
152A PHE* 4.3 3.4 - - + -
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Residues in contact with LEU 9 (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 VAL* 1.3 73.7 - - - +
10A PHE* 1.3 61.6 + - - +
11A VAL* 3.9 21.9 + - + -
42A ASP* 3.4 7.0 - - + -
43A SER* 3.6 31.0 - - - +
44A ALA* 3.9 2.9 - - + +
75A ARG* 3.5 22.7 - - - +
77A ILE* 4.1 12.1 - - + -
81A ASP* 4.0 29.8 - - + +
85A PHE* 3.7 17.7 - - + -
87A TYR 2.9 10.2 + - - +
88A ILE* 3.3 12.7 - - + +
89A LEU* 2.9 25.1 + - - +
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Residues in contact with PHE 10 (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 VAL* 3.9 15.9 - - + -
9A LEU* 1.3 72.9 - - - +
11A VAL* 1.3 59.8 + - - +
19A SER* 3.6 21.3 - - - +
22A ALA* 3.8 17.0 - - + -
23A GLU* 3.5 18.8 - - + -
26A PHE* 3.6 42.6 - + + -
41A VAL* 3.8 14.4 - - + -
42A ASP 3.0 16.5 + - - +
43A SER* 3.0 7.6 - - - -
44A ALA 2.9 24.6 + - - -
89A LEU* 3.4 35.0 - - + +
91A MET* 4.3 1.3 - - + -
116A LEU* 4.2 15.7 - - + -
149A CYS* 4.3 8.7 - - - -
152A PHE* 5.6 0.7 - + - -
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Residues in contact with VAL 11 (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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9A LEU* 4.0 18.4 - - + -
10A PHE* 1.3 79.9 - - - +
12A CYS* 1.3 71.5 + - - +
19A SER* 4.0 3.1 - - - -
44A ALA* 3.3 14.6 - - + +
45A ALA 4.5 0.9 - - - -
46A THR* 3.7 24.5 - - + +
77A ILE* 4.5 7.2 - - + -
88A ILE* 3.8 24.9 - - + -
89A LEU 2.9 10.0 + - - +
90A CYS* 3.3 3.0 - - + +
91A MET* 3.2 30.0 + - - +
95A ASN* 4.4 1.3 - - + -
99A LEU* 4.0 19.7 - - + -
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Residues in contact with CYS 12 (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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0A MES 3.1 26.2 - - - +
11A VAL* 1.3 76.7 - - - +
13A LEU* 1.3 65.1 + - - +
15A ASN* 3.3 20.0 - - - -
18A ARG* 3.9 11.4 - - + +
19A SER* 3.1 37.4 + - - +
44A ALA 3.3 5.3 + - - -
45A ALA* 3.2 4.2 - - - -
46A THR* 3.1 20.1 + - - -
91A MET* 3.7 17.5 - - + -
95A ASN* 3.5 13.9 - - - -
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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