Contacts of the helix formed by residues 472 - 481 (chain C) 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 SER 472 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231C TYR* 3.3 12.3 - - - -
232C GLY 3.7 11.0 - - - -
471C TYR* 1.3 74.5 - - - +
473C PHE* 1.3 62.9 + - - +
474C ASP* 3.4 12.2 + - - +
475C GLU* 2.7 45.1 + - - +
476C ILE* 3.1 19.3 + - - +
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Residues in contact with PHE 473 (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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60C TYR* 3.8 14.1 - + - -
209C SER 3.2 26.7 - - - -
212C LEU 3.4 7.6 - - - -
213C VAL* 3.6 21.1 - - + -
227C ILE* 3.5 38.8 - - + -
231C TYR* 3.7 12.7 + + + +
232C GLY 2.8 18.1 + - - +
233C THR* 3.4 21.1 - - + -
238C PRO* 4.3 0.7 - - + -
472C SER* 1.3 73.2 - - - +
474C ASP* 1.3 56.8 + - - +
476C ILE* 3.4 16.5 + - + +
477C ARG* 3.0 66.0 + - + +
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Residues in contact with ASP 474 (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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232C GLY 4.4 0.3 - - - +
233C THR* 3.4 17.4 - - - +
234C LYS* 2.7 44.3 + - - +
235C ASP* 5.1 1.4 + - - +
472C SER* 3.1 10.6 + - - +
473C PHE* 1.3 76.5 - - - +
475C GLU* 1.3 60.3 + - + +
477C ARG* 3.7 12.3 + - - +
478C LYS* 3.1 27.7 + - - +
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Residues in contact with GLU 475 (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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121C GLU 4.8 0.2 - - - -
469C LYS* 5.8 1.7 - - - -
470C SER 4.4 2.8 - - - +
471C TYR* 3.5 28.2 - - + -
472C SER* 2.7 40.6 + - - +
474C ASP* 1.3 75.3 - - + +
476C ILE* 1.3 56.9 + - - +
478C LYS* 3.3 5.9 + - - +
479C ASN* 2.8 46.7 + - - +
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Residues in contact with ILE 476 (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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60C TYR* 3.9 22.9 - - + -
121C GLU* 3.7 24.2 - - + +
122C GLY* 3.4 22.8 - - - +
213C VAL* 4.0 19.5 - - + -
231C TYR* 3.4 40.6 - - + -
471C TYR* 4.4 6.7 - - + +
472C SER 3.1 13.9 - - - +
473C PHE* 3.5 13.0 - - + +
475C GLU* 1.3 73.3 - - - +
477C ARG* 1.3 66.8 + - - +
479C ASN* 3.0 3.8 + - - +
480C ALA* 2.8 22.7 + - - +
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Residues in contact with ARG 477 (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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212C LEU* 2.7 27.7 + - - +
213C VAL* 3.5 25.9 + - + +
214C ASN 5.8 0.4 - - - -
215C PHE 3.3 12.4 + - - -
216C LYS* 3.9 22.5 - - - +
233C THR* 5.0 4.9 - - - +
235C ASP* 5.7 2.0 + - - -
237C VAL 5.2 0.4 + - - -
238C PRO* 2.7 40.6 + - - +
473C PHE* 3.0 44.6 + - + +
474C ASP* 4.0 11.5 + - - +
476C ILE* 1.3 75.9 - - - +
478C LYS* 1.3 63.3 + - - +
480C ALA* 3.1 3.0 + - - +
481C GLN* 3.1 26.1 + - - +
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Residues in contact with LYS 478 (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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474C ASP 3.1 19.9 + - - +
475C GLU* 3.3 9.9 - - - +
476C ILE 3.1 0.2 - - - -
477C ARG* 1.3 77.8 - - - +
479C ASN* 1.3 67.7 + - - +
480C ALA 3.2 0.9 + - - -
481C GLN* 2.9 51.1 + - - +
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Residues in contact with ASN 479 (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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120C PRO* 4.2 4.9 - - - +
121C GLU 3.4 13.3 - - - +
122C GLY* 3.0 24.8 - - - +
123C PHE* 3.5 29.6 - - + +
124C VAL* 3.5 13.3 + - - +
471C TYR* 5.0 3.6 - - - -
475C GLU* 2.8 31.2 + - - +
476C ILE 3.0 4.7 + - - +
478C LYS* 1.3 80.0 - - - +
480C ALA* 1.3 58.2 + - - +
481C GLN 3.5 1.1 + - - +
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Residues in contact with ALA 480 (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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58C VAL* 4.2 10.3 - - + -
122C GLY 3.3 12.3 - - - +
124C VAL* 3.8 6.3 - - + -
166C ARG* 2.9 22.5 + - - +
213C VAL* 3.8 24.2 - - + +
214C ASN* 4.6 8.2 - - - +
476C ILE 2.8 15.1 + - - +
477C ARG* 3.1 4.7 + - - +
479C ASN* 1.3 77.6 - - - +
481C GLN* 1.3 67.5 + - - +
482C LEU* 4.9 1.0 - - - +
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Residues in contact with GLN 481 (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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124C VAL* 4.7 1.4 - - - +
166C ARG* 3.4 10.6 + - - -
169C LYS* 5.9 4.0 - - - +
477C ARG 3.1 13.9 + - - +
478C LYS* 2.9 58.9 + - - +
479C ASN 3.5 1.5 - - - +
480C ALA* 1.3 86.5 - - - +
482C LEU* 1.3 67.3 + - - +
483C ASN* 5.4 1.4 + - - -
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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