Contacts of the helix formed by residues 230 - 236 (chain C) in PDB entry 2V1C
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 HIS 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C ALA* 3.9 16.9 - - + +
222C VAL* 3.5 23.1 + - + +
223C THR* 3.7 24.5 - - + -
226C VAL* 2.9 38.3 + - + -
227C GLY 3.7 9.5 + - - -
228C GLY* 3.4 21.3 + - - -
229C VAL* 1.3 67.5 - - - +
231C SER* 1.3 62.1 + - - +
232C TRP* 3.1 33.2 + + - +
233C ARG* 2.9 48.0 + - - +
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Residues in contact with SER 231 (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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114A MET* 3.3 32.0 + - - +
97C GLU* 4.7 7.4 + - - -
101C ALA* 5.8 0.4 - - - +
229C VAL* 2.5 20.6 + - - -
230C HIS* 1.3 68.2 - - - +
232C TRP* 1.3 59.0 + - - +
233C ARG 3.0 11.3 + - - -
234C GLN* 3.1 26.6 + - - +
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Residues in contact with TRP 232 (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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114A MET 5.0 0.4 - - - -
94C LEU* 2.8 33.9 - - + +
97C GLU* 3.6 18.8 - - + +
98C PHE* 3.7 34.8 - + - +
101C ALA* 3.6 25.6 - - + +
215C TRP* 5.2 0.7 - + - -
218C LEU* 4.3 14.8 - - + -
219C GLU* 4.0 27.1 - - + -
222C VAL* 3.9 21.2 - - + +
223C THR* 5.5 0.2 - - + -
230C HIS* 3.1 30.5 + - + +
231C SER* 1.3 79.3 + - - +
233C ARG* 1.3 67.1 + - + +
234C GLN 3.1 2.5 - - - -
235C LEU* 2.2 63.5 - - + +
236C VAL* 3.8 20.2 - - + -
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Residues in contact with ARG 233 (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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219C GLU* 3.6 37.7 + - + +
223C THR* 3.8 23.3 - - - +
229C VAL* 4.7 3.0 - - - +
230C HIS* 2.9 53.4 + - - +
231C SER 3.0 1.8 + - - +
232C TRP* 1.3 86.5 - - + +
234C GLN* 1.3 62.6 + - - +
235C LEU 2.8 6.8 + - - -
236C VAL* 3.3 19.0 + - - +
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Residues in contact with GLN 234 (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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114A MET 4.0 0.2 - - - +
115A ASN* 2.1 72.0 + - + +
116A GLY* 3.1 21.6 + - - +
121A LYS* 5.8 3.6 - - - +
231C SER* 3.1 11.9 + - - +
232C TRP 3.1 0.6 - - - -
233C ARG* 1.3 79.3 - - - +
235C LEU* 1.4 57.2 + - - +
236C VAL 3.3 6.1 + - - +
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Residues in contact with LEU 235 (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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112A SER* 5.7 1.1 - - - -
113A PRO 4.2 1.6 - - - +
115A ASN* 4.1 20.2 - - - +
116A GLY* 5.0 0.4 - - - +
90C ALA 4.3 8.9 - - - +
91C PHE* 5.6 1.2 - - - -
93C HIS* 3.2 35.4 - - + -
94C LEU* 2.6 50.8 - - + +
97C GLU* 3.0 17.5 - - + -
232C TRP* 2.2 53.4 - - + +
234C GLN 1.4 77.6 - - - +
236C VAL* 1.3 59.5 + - - +
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Residues in contact with VAL 236 (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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91C PHE* 6.5 1.1 - - - -
94C LEU* 3.7 23.8 - - + -
215C TRP* 3.6 46.0 - - + -
216C ARG* 6.5 0.7 - - - -
219C GLU* 3.7 18.2 - - - +
232C TRP* 3.8 17.3 - - + -
233C ARG* 3.3 19.5 + - - +
234C GLN 4.3 5.5 - - - +
235C LEU* 1.3 86.1 - - - +
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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