Contacts of the strand formed by residues 56 - 61 (chain A) in PDB entry 4OI0
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 ARG 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE 3.6 7.6 + - - +
20A ALA* 3.8 24.9 - - - +
39A PHE* 4.8 6.1 - - - -
54A LYS 3.2 7.8 + - - +
55A SER* 1.3 72.6 - - - +
57A VAL* 1.3 68.1 + - - +
74A GLU* 4.4 9.7 + - - -
75A SER* 4.5 7.3 + - - -
286A GLU* 3.5 45.6 + - - +
501A ADP 3.6 51.6 + - + +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.6 0.9 - - - +
18A ARG* 3.3 5.2 - - - +
19A PHE* 3.1 64.7 + - + +
29A LEU* 5.0 0.4 - - + -
38A ILE* 3.9 32.5 - - + -
39A PHE* 4.9 4.3 - - - -
51A PHE* 3.6 34.3 - - + -
55A SER* 4.3 5.8 - - - -
56A ARG* 1.3 87.2 - - - +
58A ALA* 1.3 67.0 + - - +
59A ALA 4.6 0.4 - - - +
501A ADP 4.4 4.6 - - - -
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.8 20.4 - - - +
17A LEU 3.3 5.6 - - - +
18A ARG* 4.3 1.6 - - + -
37A GLU 4.1 0.2 - - - +
38A ILE* 3.5 24.6 - - - +
39A PHE* 3.7 24.1 + - + -
57A VAL* 1.3 77.0 - - - +
59A ALA* 1.3 60.4 + - - +
60A PHE* 4.3 0.7 + - - +
501A ADP 3.3 30.3 - - + +
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Residues in contact with ALA 59 (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 LEU* 3.7 5.1 - - - +
16A GLU* 3.0 3.4 - - - -
17A LEU* 2.9 37.2 + - + +
19A PHE* 5.8 0.2 - - + -
29A LEU* 4.5 14.4 - - + -
36A ALA* 5.0 1.3 - - + -
37A GLU 3.4 6.1 - - - +
38A ILE* 3.9 16.4 - - + -
43A LEU* 4.6 5.6 - - + -
57A VAL* 4.2 1.2 - - + +
58A ALA* 1.3 72.8 - - - +
60A PHE* 1.3 59.1 + - - +
67A ILE* 3.9 24.9 - - + -
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Residues in contact with PHE 60 (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 LEU* 5.1 0.2 - - - -
14A ASP* 3.6 40.6 - - + -
15A CYS 3.5 10.5 - - - -
16A GLU* 3.8 20.0 - - + +
36A ALA* 3.2 4.6 - - - +
37A GLU* 2.8 42.5 + - + +
39A PHE 6.3 0.7 - - - +
58A ALA 4.2 0.9 - - - +
59A ALA* 1.3 73.9 - - - +
61A THR* 1.3 78.9 + - - +
62A TRP* 3.5 42.2 - + - -
82A THR* 3.4 21.1 - - + -
84A MET* 3.5 39.3 - - + -
85A VAL* 5.5 1.8 - - + -
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Residues in contact with THR 61 (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 LEU* 3.8 17.7 - - + -
12A LYS 3.5 21.3 - - - +
14A ASP* 2.8 34.7 + - - -
15A CYS 3.2 9.0 + - - +
35A TYR* 2.6 28.2 + - - +
36A ALA* 4.3 2.0 - - - +
60A PHE* 1.3 83.1 - - - +
62A TRP* 1.3 54.4 + - - +
63A LYS* 3.5 1.4 + - - +
64A GLY* 2.8 29.9 + - - -
65A ALA* 4.0 4.9 - - - +
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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