Contacts of the strand formed by residues 73 - 77 (chain A) in PDB entry 4I93
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 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 3.3 5.9 - - - +
62A VAL* 2.8 47.7 + - + -
63A SER* 2.9 20.3 + - - -
71A ASN* 3.8 18.6 - - - +
72A VAL* 1.3 77.4 - - - +
74A TYR* 1.3 61.2 + - - +
85A ALA* 4.0 14.4 - - + -
86A VAL 3.2 9.0 - - - +
87A LYS* 4.1 5.8 - - + -
186A ARG* 5.5 4.0 - - - +
200A PHE* 3.9 36.1 - - + -
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Residues in contact with TYR 74 (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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53A THR* 4.1 12.1 - - + -
56A PHE* 3.4 55.3 + + + -
57A ALA 3.6 15.0 - - - -
58A ALA* 4.8 0.2 - - - -
60A ASN* 3.2 7.4 - - + +
61A ILE* 3.4 27.5 - - + +
62A VAL* 4.4 4.3 - - - -
67A GLU* 4.2 12.8 + - - +
72A VAL* 3.6 28.5 - - + +
73A VAL* 1.3 75.6 - - - +
75A LYS* 1.3 69.5 + - - +
76A GLY 3.9 0.2 + - - -
85A ALA* 3.4 2.8 - - - -
86A VAL* 2.7 48.8 + - + +
88A ARG* 4.0 30.8 + - + -
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Residues in contact with LYS 75 (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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53A THR* 3.8 8.6 - - - +
59A GLU 4.6 9.2 - - - -
60A ASN* 2.8 54.4 + - - +
61A ILE 5.4 0.4 - - - -
62A VAL* 3.6 24.7 - - + +
74A TYR* 1.3 75.2 - - - +
76A GLY* 1.3 59.2 + - - +
84A ILE 3.5 5.6 - - - +
85A ALA* 4.7 0.9 - - - +
134A PHE* 3.8 37.0 - - + -
138A GLU* 5.9 0.6 + - - -
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Residues in contact with GLY 76 (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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52A ALA 3.0 17.0 - - - -
53A THR* 4.2 3.5 - - - +
60A ASN* 5.6 0.2 - - - -
74A TYR 3.9 0.8 + - - -
75A LYS* 1.3 75.8 - - - +
77A LYS* 1.3 61.9 + - - +
83A ARG* 3.3 9.9 - - - +
84A ILE* 2.9 42.1 + - - +
134A PHE* 5.6 0.2 - - - -
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Residues in contact with LYS 77 (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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52A ALA* 2.9 27.5 + - - +
76A GLY* 1.3 76.5 - - - +
78A LEU* 1.3 68.2 + - - +
79A GLU* 4.8 4.0 - - - +
81A GLN* 2.8 42.4 + - - +
82A ARG 3.4 5.8 - - - +
83A ARG* 3.7 43.3 - - + +
84A ILE* 4.8 0.2 - - - -
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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