Contacts of the strand formed by residues 70 - 74 (chain V) in PDB entry 5GAG
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 70 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A C 4.5 3.6 + - - -
336A C 5.6 1.6 - - - +
5V ILE* 4.5 9.9 - - + +
11V VAL* 4.3 20.2 - - + -
12V ILE 3.4 11.0 - - - +
13V VAL* 4.3 8.5 - - + -
14V LEU* 3.5 6.6 - - - +
34V VAL* 4.3 12.1 - - + -
36V VAL* 4.7 8.5 - - + -
65V ILE* 3.7 24.7 - - + -
66V GLN 4.2 1.8 - - - +
67V VAL* 3.4 39.7 - - + +
68V SER 3.3 0.7 - - - +
69V ASN* 1.3 87.2 - - - +
71V ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A C 6.0 2.9 - - - +
5V ILE* 5.2 0.2 - - - -
11V VAL* 3.3 7.3 - - - -
12V ILE* 2.9 30.1 + - - +
14V LEU* 3.7 25.1 - - + +
70V VAL* 1.3 76.5 - - - +
72V ILE* 1.3 65.6 + - - +
80V ALA* 3.8 15.5 - - + -
81V ASP 3.7 17.5 - - - +
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Residues in contact with ILE 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V ILE* 3.6 22.0 - - + +
9V ASP* 3.8 31.4 - - + +
10V GLU 3.3 22.7 - - - +
11V VAL* 4.2 0.9 - - - -
71V ALA* 1.3 71.0 - - - +
73V PHE* 1.3 64.4 + - - +
80V ALA* 3.8 0.9 - - - -
81V ASP* 2.9 51.0 + - + +
82V ARG 4.4 0.2 - - - +
83V VAL* 3.5 26.7 - - + -
94V ARG* 6.0 0.2 - - - +
96V PHE* 3.8 24.9 - - + -
103V ILE* 4.4 11.0 - - + -
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Residues in contact with PHE 73 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V GLU* 2.9 50.5 + - - +
11V VAL 4.1 2.9 - - - -
12V ILE* 3.8 31.6 - - + -
22V ARG* 3.6 42.0 - - - -
71V ALA 3.3 0.8 + - - -
72V ILE* 1.3 82.3 - - - +
74V ASN* 1.3 57.9 + - - +
75V ALA* 3.5 27.2 + - + +
78V GLY* 3.6 37.7 - - - -
79V LYS* 3.5 12.1 - - - -
80V ALA 4.6 0.2 - - - -
96V PHE* 4.8 3.3 - - - -
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Residues in contact with ASN 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72V ILE 3.7 2.2 + - - -
73V PHE* 1.3 73.8 - - - +
75V ALA* 1.3 58.9 + - - +
76V ALA* 3.3 19.6 + - - +
77V THR* 3.6 12.4 - - - +
78V GLY* 3.0 22.3 + - - -
79V LYS 2.9 18.7 + - - +
81V ASP* 3.1 31.7 + - + +
96V PHE* 3.4 28.0 - - + -
99V ASN* 3.0 34.8 + - - +
101V GLU* 4.0 1.2 - - - +
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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