Contacts of the strand formed by residues 114 - 118 (chain F) in PDB entry 2GVG
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 ILE 114 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112F LEU* 2.8 12.2 + - + +
113F PRO* 1.3 77.5 - - - +
115F GLU* 1.3 63.7 + - - +
116F ILE* 3.8 16.8 - - + -
134F VAL* 3.6 23.6 - - + -
135F GLU 3.4 13.7 - - - +
136F ASN* 3.7 9.2 - - - +
137F THR* 3.9 4.0 - - - -
144F LEU* 3.4 38.1 - - + -
145F THR* 4.1 14.4 - - - +
148F ILE* 4.2 15.3 - - + -
462F PHE* 3.6 15.5 - - + +
463F LYS* 3.1 5.2 - - - -
464F ASN* 3.0 23.9 + - - +
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Residues in contact with GLU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ILE* 1.3 75.2 - - - +
116F ILE* 1.3 64.7 + - - +
117F LYS* 3.5 21.7 + - + +
133F THR 3.8 1.0 - - - +
134F VAL* 3.4 4.0 - - - -
135F GLU* 2.8 52.0 + - + +
137F THR* 3.9 15.0 - - + +
460F THR* 2.7 32.7 + - + +
462F PHE 3.2 8.5 - - - +
463F LYS* 4.0 27.2 + - + +
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Residues in contact with ILE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F LEU* 4.3 15.3 - - + -
66F LEU* 3.8 23.8 - - + -
70F LEU* 4.1 15.9 - - + -
114F ILE* 3.8 17.0 - - + -
115F GLU* 1.3 78.5 - - - +
117F LYS* 1.3 68.3 + - - +
132F PHE* 4.3 9.4 - - + -
133F THR 3.2 10.5 - - - +
134F VAL* 3.9 8.1 - - + -
148F ILE* 4.8 0.7 - - + -
152F LEU* 4.3 16.8 - - + -
460F THR* 3.5 2.8 - - - -
461F VAL* 2.9 38.6 + - + +
462F PHE* 2.8 28.1 + - + +
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Residues in contact with LYS 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F TYR* 6.4 1.1 - - + -
115F GLU* 3.5 29.4 - - + +
116F ILE* 1.3 75.0 - - - +
118F ALA* 1.3 60.3 + - - +
132F PHE* 2.9 4.2 - - - +
133F THR* 2.8 50.5 + - - +
135F GLU* 5.0 9.9 + - - +
456F ASP* 5.4 4.8 + - - +
458F LEU* 4.1 21.0 - - + +
459F HIS 3.3 8.5 - - - +
460F THR* 3.5 22.2 - - - +
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F PHE* 4.0 4.0 - - + -
62F LEU* 3.8 21.5 - - + -
117F LYS* 1.3 74.1 - - - +
119F VAL* 1.3 68.9 + - - +
120F PRO 3.8 1.2 - - - -
131F LEU 3.3 7.0 - - - +
132F PHE* 3.4 18.4 - - + -
457F LEU 3.9 0.5 - - - +
458F LEU* 3.6 8.7 - - - -
459F HIS* 2.9 31.5 + - - +
461F VAL* 4.2 13.0 - - + +
471F TYR* 5.2 1.6 + - - -
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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