Contacts of the strand formed by residues 121 - 126 (chain C) in PDB entry 5GV2
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 ASP 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C LEU 4.0 0.3 - - - +
80C ASN* 3.2 16.9 - - - +
81C VAL 4.9 0.9 + - - -
90C GLN 4.1 5.0 - - - +
91C ALA 4.1 1.9 - - - -
92C ALA* 3.8 9.1 + - - -
93C GLY* 2.8 35.6 + - - -
94C VAL* 3.6 16.0 - - + +
97C ILE* 5.1 9.6 - - + -
114C MET* 5.0 5.6 - - + -
115C LEU 4.2 2.0 - - - -
116C SER* 2.7 32.1 + - - +
117C THR 4.7 0.2 + - - -
120C THR* 1.3 79.2 + - - +
122C PHE* 1.3 61.2 + - - +
123C ILE* 3.9 10.5 - - + +
296C TYR* 4.9 0.2 - - - -
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Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.8 22.4 - - + -
41C PHE* 4.7 2.0 - + + -
78C VAL* 3.5 28.5 - - + -
79C LEU 3.5 5.8 - - - -
80C ASN* 4.2 11.0 - - - -
114C MET* 3.7 6.4 - - - +
115C LEU* 2.9 51.8 + - + +
117C THR* 4.1 12.3 - - + -
120C THR* 3.3 29.8 - - + -
121C ASP* 1.3 73.1 - - - +
123C ILE* 1.3 62.8 + - - +
124C LEU* 4.1 9.9 - - + -
233C ILE* 3.8 46.4 - - + -
234C GLU* 5.6 2.7 - - - -
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 5.9 0.7 - - + -
79C LEU* 2.8 61.1 + - + +
80C ASN* 4.9 3.1 - - - -
81C VAL* 5.0 7.2 - - + -
97C ILE* 3.7 26.2 - - + -
101C VAL* 4.7 11.9 - - + -
102C ILE* 5.4 2.9 - - + -
105C LEU* 4.6 9.6 - - + -
112C VAL* 3.9 31.6 - - + -
113C LEU 3.7 2.0 - - - -
114C MET* 3.8 24.5 - - + -
121C ASP 3.9 9.6 - - - +
122C PHE* 1.3 77.5 - - - +
124C LEU* 1.3 63.0 + - - +
125C VAL* 4.5 6.7 - - + -
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.9 28.9 - - + -
12C VAL* 4.8 4.9 - - + -
41C PHE* 4.6 5.6 - - + -
54C MET* 3.9 20.9 - - - -
76C TRP* 3.9 16.6 - - + -
77C LEU 3.2 11.2 - - - +
78C VAL* 4.1 15.0 - - + -
112C VAL* 3.3 8.5 - - - +
113C LEU* 2.7 51.1 + - + +
115C LEU* 4.5 11.9 - - + -
122C PHE* 4.2 21.3 - - + -
123C ILE* 1.3 77.1 - - - +
125C VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C TRP* 3.4 8.6 - - - -
77C LEU* 2.7 45.8 + - + +
79C LEU* 4.0 31.6 - - + -
105C LEU* 4.4 3.1 - - + -
110C VAL* 3.9 27.1 - - + -
111C SER 4.1 3.4 - - - +
112C VAL* 4.1 13.5 - - + -
123C ILE* 4.5 1.1 - - + -
124C LEU* 1.3 80.1 - - - +
126C ARG* 1.3 68.9 + - - +
130C LEU* 5.5 4.5 - - + -
133C VAL* 4.2 17.0 - - + -
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Residues in contact with ARG 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ALA* 3.4 25.6 - - + +
75C THR 3.6 4.5 - - - -
76C TRP* 3.6 28.2 - - + -
109C HIS 5.8 1.4 + - - -
111C SER* 3.6 26.0 + - - +
125C VAL* 1.3 78.3 - - - +
127C GLU* 1.3 67.9 + - - +
128C GLN* 3.1 31.4 - - - +
129C ASP* 3.0 37.5 + - - +
130C LEU* 3.9 2.6 + - - +
275C PHE* 3.6 13.6 + - - +
276C ASP* 2.6 31.4 + - - +
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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