Contacts of the helix formed by residues 183 - 189 (chain A) in PDB entry 4GV1
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 LYS 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A LEU 3.5 1.8 + - - -
182A LYS* 1.3 70.5 - - - +
184A GLU* 1.3 61.9 + - - +
185A VAL 3.3 0.2 + - - -
186A ILE* 3.3 8.3 + - - +
187A VAL* 3.0 28.2 + - - +
218A GLN* 2.9 27.5 + - - -
219A THR 2.8 27.0 + - - -
220A HIS* 3.6 20.2 + - - +
221A ASP 2.9 17.9 + - - +
222A ARG 3.7 11.2 - - - +
223A LEU* 3.9 17.0 - - + -
461A VAL 5.3 2.4 + - - -
465A ARG 3.7 2.2 - - - +
466A ARG* 4.0 20.1 + - + -
467A PRO* 2.9 28.8 + - + +
468A HIS* 4.3 3.0 + - - +
469A PHE* 4.1 12.5 - - + -
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 3.2 4.5 - - + +
183A LYS* 1.3 78.8 - - - +
185A VAL* 1.3 69.7 + - + +
187A VAL* 3.5 1.6 + - - +
188A ALA* 3.0 36.4 + - - +
221A ASP 4.7 0.8 + - - -
465A ARG* 3.3 28.9 + - + +
466A ARG* 3.4 40.2 - - - +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A THR 3.7 22.7 - - - +
161A PHE* 4.2 16.4 - - + +
182A LYS* 3.1 34.6 + - + +
184A GLU* 1.3 86.9 - - + +
186A ILE* 1.3 65.3 + - - +
188A ALA* 3.2 4.5 + - - +
189A LYS* 3.0 46.3 + - + +
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 4.0 18.8 - - + +
181A LEU* 4.0 23.8 - - + -
182A LYS 3.1 13.3 + - - +
183A LYS* 3.6 10.3 - - - +
185A VAL* 1.3 75.3 - - - +
187A VAL* 1.3 61.7 + - + +
189A LYS 3.6 0.2 + - - -
190A ASP 3.2 2.1 + - - -
191A GLU* 2.9 44.4 + - + +
192A VAL* 3.4 35.8 + - + +
195A THR* 3.5 24.2 - - + +
223A LEU* 5.2 4.7 - - + -
469A PHE* 5.3 4.7 - - + -
503A GOL 3.5 11.4 - - - +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS 3.0 20.3 + - - +
184A GLU 3.9 3.8 - - - +
186A ILE* 1.3 76.6 - - - +
188A ALA* 1.3 63.4 + - - +
190A ASP* 3.2 13.5 + - - +
192A VAL* 3.9 21.0 - - + +
464A GLU 3.8 15.5 - - - +
465A ARG* 3.7 23.3 - - + +
467A PRO* 3.8 23.1 - - + -
469A PHE* 4.5 2.5 - - + -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A GLU* 3.0 32.6 + - - +
185A VAL* 3.2 6.5 + - - +
187A VAL* 1.3 79.5 - - - +
189A LYS* 1.3 67.4 + - + +
190A ASP* 3.4 1.4 + - - +
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A THR* 5.9 6.3 - - - +
161A PHE* 3.7 32.9 - - + -
185A VAL* 3.0 31.3 + - + +
186A ILE 4.4 1.8 - - - +
187A VAL 3.2 0.2 - - - -
188A ALA* 1.3 82.2 - - + +
190A ASP* 1.3 70.3 + - - +
191A GLU* 3.2 4.7 + - + +
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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