Contacts of the helix formed by residues 222 - 231 (chain A) in PDB entry 5VZH
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 CYS 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ARG* 3.8 21.1 - - - -
212A VAL* 3.9 21.5 - - + +
215A GLU* 3.6 17.7 - - + +
216A LEU* 3.8 21.3 - - + +
221A VAL* 1.3 77.0 - - - +
223A GLU* 1.3 66.3 + - - +
224A GLU* 3.8 1.1 - - - -
225A VAL* 3.1 33.5 + - + +
226A GLU* 3.0 24.3 + - - +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLU* 3.4 12.5 + - - +
221A VAL* 4.1 3.9 + - - +
222A CYS* 1.3 70.8 - - - +
224A GLU* 1.3 59.1 + - - +
226A GLU* 3.2 6.7 + - - +
227A ARG* 2.8 45.7 + - - +
230A ARG* 4.9 9.8 + - - +
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Residues in contact with GLU 224 (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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163A LEU* 4.0 23.6 - - + +
175A ARG* 4.7 5.0 + - - -
179A PHE* 5.5 0.3 - - - -
208A HIS* 2.7 40.0 + - - -
211A ARG* 2.9 30.4 + - - +
215A GLU* 4.8 0.2 + - - -
222A CYS* 3.3 4.0 - - - -
223A GLU* 1.3 77.4 - - - +
225A VAL* 1.3 63.0 + - - +
227A ARG* 3.3 29.1 + - - +
228A VAL* 3.1 32.8 + - + +
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Residues in contact with VAL 225 (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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159A ALA* 3.8 31.4 - - + +
162A ILE* 4.2 15.2 - - + +
163A LEU* 3.9 24.7 - - + -
212A VAL* 4.2 1.6 - - + -
216A LEU* 6.3 0.7 - - + -
222A CYS* 3.1 31.6 + - + +
224A GLU* 1.3 77.4 - - - +
226A GLU* 1.3 62.5 + - - +
228A VAL* 3.2 4.8 + - - +
229A ARG* 2.9 56.0 + - - +
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A VAL* 3.1 36.4 - - + +
222A CYS 3.0 12.3 + - - +
223A GLU* 3.7 7.0 - - + +
225A VAL* 1.3 78.5 - - - +
227A ARG* 1.3 63.7 + - - +
229A ARG* 3.1 42.5 + - - +
230A ARG* 3.2 46.4 + - - +
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Residues in contact with ARG 227 (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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223A GLU* 2.8 43.7 + - - +
224A GLU* 3.6 29.2 - - - +
225A VAL 3.3 0.2 - - - -
226A GLU* 1.3 78.6 - - - +
228A VAL* 1.3 64.0 + - + +
230A ARG* 3.5 22.3 + - - +
231A SER* 3.2 23.0 + - - -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ILE* 3.9 14.1 - - + -
163A LEU* 4.1 15.3 - - + -
166A ALA* 3.7 20.9 - - + -
224A GLU* 3.1 20.3 + - + +
225A VAL 3.5 6.5 - - - +
227A ARG* 1.3 77.7 - - + +
229A ARG* 1.3 65.3 + - - +
231A SER* 2.9 25.3 + - - +
234A TYR* 3.2 37.7 - - + +
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A GLU* 5.5 5.1 - - - +
159A ALA* 4.9 8.9 - - - +
162A ILE* 3.6 33.4 - - + +
225A VAL* 2.9 31.6 + - - +
226A GLU* 3.1 42.4 + - - +
228A VAL* 1.3 78.0 - - - +
230A ARG* 1.3 58.4 + - + +
234A TYR* 3.8 14.5 - - + -
235A GLN* 3.1 22.9 - - - +
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Residues in contact with ARG 230 (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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223A GLU* 4.9 10.3 + - - +
226A GLU* 3.3 39.2 + - - +
227A ARG* 3.6 28.1 - - - +
229A ARG* 1.3 75.7 - - + +
231A SER* 1.3 64.9 + - - +
232A GLU* 3.5 1.9 + - - -
235A GLN* 3.0 18.5 - - - +
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Residues in contact with SER 231 (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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227A ARG* 3.2 18.0 + - - -
228A VAL* 2.9 18.6 + - - -
230A ARG* 1.3 78.3 - - - +
232A GLU* 1.3 65.8 + - - +
233A ARG* 4.2 6.4 - - - +
234A TYR* 3.1 19.1 + - - +
235A GLN* 3.1 19.6 + - - +
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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