Contacts of the strand formed by residues 73 - 79 (chain J) in PDB entry 3A13
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 73 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J TYR* 3.6 37.3 + - - +
12J TYR* 3.6 8.2 - - - +
14J ASP* 3.8 29.8 - - + +
17J TYR* 4.5 33.0 - - + -
68J ALA 5.0 1.6 + - - -
71J SER* 3.5 30.3 + - - +
72J ALA* 1.3 89.4 + - - +
74J ALA* 1.3 61.2 + - - +
75J TYR* 3.5 4.5 + - - -
89J ILE* 3.2 5.6 - - - -
90J ALA* 2.8 37.9 + - + +
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Residues in contact with ALA 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J TYR 2.8 17.3 + - - +
13J VAL* 3.7 5.9 - - + -
14J ASP 2.9 26.4 + - - +
43J ALA* 4.2 21.3 - - + +
47J ALA* 4.3 1.7 - - + +
73J LYS* 1.3 69.3 - - - +
75J TYR* 1.3 58.7 + - - +
76J ASP 3.9 0.7 - - - -
77J PHE* 3.7 26.5 - - + -
87J VAL* 4.2 1.3 - - + -
88J ARG 3.6 6.1 - - - -
89J ILE* 4.0 16.6 - - + +
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Residues in contact with TYR 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ASP 3.3 15.7 - - - +
15J LYS* 3.5 25.7 - - - +
17J TYR* 3.6 31.8 - + + +
19J PRO* 3.6 32.1 - - + +
26J ILE* 3.7 16.9 - - + +
73J LYS 3.8 12.1 - - - +
74J ALA* 1.3 75.2 - - - +
76J ASP* 1.3 73.3 + - + +
77J PHE* 4.4 2.5 - - - -
88J ARG* 2.9 61.1 + - + +
89J ILE 4.0 3.1 - - - -
90J ALA* 3.8 22.0 - - + -
352J LEU* 4.9 1.7 - - - +
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Residues in contact with ASP 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74J ALA 3.9 0.2 - - - -
75J TYR* 1.3 103.1 - - + +
77J PHE* 1.3 74.1 + - - +
78J HIS* 4.7 5.0 + - - +
86J ILE* 3.5 2.6 - - - +
87J VAL* 3.2 6.6 - - - +
88J ARG* 2.9 65.0 + - + +
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Residues in contact with PHE 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J VAL* 3.8 18.6 - - + -
15J LYS* 4.0 34.3 - - + +
39J ILE* 3.7 37.5 - - + -
40J GLU* 4.3 5.8 - - + -
43J ALA* 3.5 33.2 - - + -
74J ALA* 3.7 28.7 - - + -
76J ASP* 1.3 88.0 + - - +
78J HIS* 1.3 61.0 + - - +
79J ASP 4.2 0.6 + - - -
85J TRP* 4.1 15.1 - - + -
86J ILE 3.6 2.9 - - - -
87J VAL* 4.0 9.0 - - + -
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Residues in contact with HIS 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J ASP* 5.0 5.8 - - - +
77J PHE* 1.3 74.4 - - - +
79J ASP* 1.3 77.2 + - - +
80J MET* 3.4 28.2 + - - -
85J TRP* 3.1 10.7 - - - -
86J ILE* 2.9 50.1 + - + +
88J ARG* 6.3 0.7 - - - +
349J VAL* 4.0 27.5 - - + +
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Residues in contact with ASP 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J HIS* 1.3 88.6 + - - +
80J MET* 1.3 61.3 + - - +
81J GLY* 2.9 27.7 + - - -
83J GLY 5.3 1.2 + - - -
84J SER 4.1 1.7 - - - +
85J TRP* 3.5 43.5 + - + -
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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