Contacts of the strand formed by residues 24 - 29 (chain A) in PDB entry 3WYR
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 24 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 3.8 19.7 - - + -
13A TRP 3.9 8.3 - - - +
15A SER 3.4 24.5 - - - +
18A VAL* 4.2 10.8 - - + -
23A HIS* 1.3 76.9 - - - +
25A THR* 1.3 66.8 + - - +
26A LEU* 5.0 1.8 - - + -
59A PHE 4.0 0.7 - - - +
60A LEU* 3.6 2.4 - - - +
61A ILE* 2.8 53.1 + - + +
64A VAL* 3.8 17.0 - - + -
68A HIS* 6.2 0.7 - - + -
94A ILE* 4.2 21.1 - - + -
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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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12A ALA* 3.4 2.8 - - - -
13A TRP* 2.9 56.2 + - + -
23A HIS* 5.4 1.4 + - - -
24A VAL* 1.3 71.4 - - - +
26A LEU* 1.3 64.5 + - - +
27A ARG* 3.4 24.0 + - + +
58A SER* 3.9 18.2 - - - +
59A PHE 3.4 14.1 - - - +
60A LEU* 3.3 22.6 - - + +
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Residues in contact with LEU 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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11A SER 3.9 2.0 - - - -
12A ALA* 4.7 1.8 - - + -
24A VAL* 5.0 1.6 - - + -
25A THR* 1.3 71.4 - - - +
27A ARG* 1.3 59.5 + - - +
39A LEU* 3.6 34.5 - - + -
50A LEU* 4.9 2.7 - - + -
55A PHE* 4.0 12.5 - - + -
58A SER* 3.3 2.8 - - - -
59A PHE* 2.9 48.7 + - + +
61A ILE* 4.0 26.5 - - + -
72A TYR* 5.3 4.3 - - + -
92A LEU* 3.7 32.5 - - + -
94A ILE* 3.8 31.9 - - + -
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Residues in contact with ARG 27 (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 PHE* 4.5 3.4 - - - -
10A CYS* 3.2 7.2 - - - +
11A SER* 2.8 61.9 + - - +
12A ALA 5.2 1.0 + - - -
13A TRP* 3.5 46.4 - - - +
25A THR* 3.4 26.7 - - + +
26A LEU* 1.3 75.6 - - - +
28A CYS* 1.3 63.9 + - - +
55A PHE* 5.0 0.9 - - - -
57A ASN 4.0 3.8 - - - +
58A SER* 4.3 8.7 - - - -
92A LEU* 5.1 0.9 - - - +
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Residues in contact with CYS 28 (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 PRO* 3.6 13.9 - - - -
9A PHE 3.2 12.1 - - - -
10A CYS* 2.0 42.8 - - - -
27A ARG* 1.3 72.9 - - - +
29A HIS* 1.3 60.9 + - - +
35A ASN* 3.9 1.9 - - - +
37A PHE* 3.1 54.2 - - + -
55A PHE* 4.4 5.4 - - + -
57A ASN* 3.3 16.5 + - - +
74A CYS* 4.0 2.7 - - - -
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Residues in contact with HIS 29 (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 PRO* 3.5 0.9 - - - +
9A PHE* 2.9 41.6 + - + +
28A CYS* 1.3 77.0 + - - +
30A TYR* 1.3 64.7 + - - +
31A ARG* 4.3 24.5 + - + +
35A ASN* 3.0 29.6 + - - -
37A PHE* 3.8 1.6 - - - -
57A ASN* 5.3 2.2 + - - -
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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