Contacts of the strand formed by residues 74 - 78 (chain E) in PDB entry 5ITX
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 ALA 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E ARG* 4.8 9.0 - - + -
58E LEU 3.3 7.0 - - - +
59E ILE* 5.6 3.4 - - + -
73E LEU* 1.3 86.4 - - - +
75E LEU* 1.3 63.3 + - - +
126E GLY* 3.7 10.0 + - - -
127E GLY* 3.5 36.2 + - - +
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Residues in contact with LEU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E VAL* 4.3 22.7 - - + -
56E LEU 3.8 0.5 - - - +
57E ARG* 3.2 6.9 - - - +
58E LEU* 2.8 41.4 + - + +
60E LEU* 4.2 26.7 - - + -
73E LEU* 5.7 4.5 - - + -
74E ALA* 1.3 76.6 - - - +
76E VAL* 1.3 62.7 + - - +
77E PHE* 3.9 23.6 + - + -
99E LEU* 4.8 0.4 - - + -
101E PHE* 4.5 14.4 - - + -
123E TRP* 3.7 31.9 - - + +
124E ASP 3.9 14.4 - - - +
125E LEU* 5.2 6.3 - - + +
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Residues in contact with VAL 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLU* 4.8 9.9 - - + +
56E LEU 3.4 9.0 - - - +
57E ARG* 4.7 3.6 - - - +
75E LEU* 1.3 72.2 - - - +
77E PHE* 1.3 66.2 + - - +
78E ARG* 4.0 15.0 + - - +
122E ARG 3.5 4.9 - - - +
124E ASP* 3.3 36.2 + - + +
126E GLY 3.2 24.7 - - - +
127E GLY* 3.5 7.6 - - - -
128E LYS 3.1 35.7 - - - +
129E TRP* 4.6 12.3 - - + -
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Residues in contact with PHE 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 5.2 0.2 - - - +
55E GLU* 3.7 6.2 - - - +
56E LEU* 2.9 52.9 + - + +
58E LEU* 3.7 23.8 - - + -
75E LEU* 3.9 26.2 - - + -
76E VAL* 1.3 76.8 - - - +
78E ARG* 1.3 62.4 + - - +
79E PHE* 4.3 13.8 - - + -
85E PHE* 4.1 10.3 - + - -
99E LEU* 3.8 23.3 - - + -
101E PHE* 4.8 2.0 - + - -
114E PHE* 3.6 49.6 - + + -
122E ARG 3.7 3.4 - - - -
123E TRP* 3.7 23.6 - + + +
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Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LYS 4.0 17.5 - - - +
55E GLU* 4.3 12.6 + - + +
76E VAL* 4.0 15.9 + - - +
77E PHE* 1.3 75.2 + - - +
79E PHE* 1.3 64.6 + - - +
80E GLY 3.5 3.6 - - - +
114E PHE* 4.5 7.1 - - - -
121E GLY* 3.2 19.6 - - - -
122E ARG* 2.9 48.8 + - + +
124E ASP* 3.4 35.5 + - - +
130E GLN* 2.9 26.3 + - - -
133E ARG* 4.0 14.1 - - - +
299F T 4.8 3.8 - - - +
300F C 3.1 26.2 + - - -
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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