Contacts of the strand formed by residues 222 - 227 (chain L) in PDB entry 6VEN
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216L TRP* 4.0 3.6 - - - -
217L ASP* 3.0 31.2 + - - +
220L GLY* 3.1 10.6 - - - +
221L GLY* 1.3 79.7 - - - +
223L VAL* 1.3 73.6 + - - +
224L VAL* 3.7 11.8 + - - +
389M ILE* 6.2 2.9 - - - -
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Residues in contact with VAL 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L LYS* 4.1 14.8 - - + -
215L ILE 3.6 8.1 - - - +
216L TRP* 3.4 45.0 - - + +
222L CYS* 1.3 79.7 - - - +
224L VAL* 1.3 66.6 + - - +
225L ARG 3.5 22.9 - - - +
226L THR* 3.7 14.4 - - - +
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Residues in contact with VAL 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203L TYR* 4.5 5.4 - - + -
215L ILE* 3.0 29.1 + - + +
217L ASP* 4.2 14.6 - - + +
222L CYS* 3.8 18.4 - - - +
223L VAL* 1.3 79.5 - - - +
225L ARG* 1.3 81.4 + - + +
387M GLU* 3.4 26.1 - - - +
389M ILE* 5.2 17.3 - - + -
391M ILE* 3.7 32.5 - - + -
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Residues in contact with ARG 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L VAL 3.9 0.6 - - - +
214L LYS* 3.4 2.1 - - - -
215L ILE* 2.9 42.5 + - + -
223L VAL* 3.5 3.3 - - - +
224L VAL* 1.3 101.3 + - + +
226L THR* 1.3 65.7 + - - +
227L PHE* 4.2 16.6 - - + -
270L SER 3.0 19.0 + - - +
271L ASP* 2.4 48.1 + - - +
273L LYS* 4.3 18.8 - - - +
387M GLU* 4.7 4.7 - - - -
388M GLU* 3.9 15.3 - - - +
389M ILE* 3.2 38.5 + - - +
391M ILE* 3.8 17.4 - - + +
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Residues in contact with THR 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L VAL* 3.6 27.6 - - + -
213L VAL 3.4 3.8 - - - -
214L LYS* 4.0 9.4 - - - +
223L VAL* 3.7 14.0 - - - +
225L ARG* 1.3 76.1 + - - +
227L PHE* 1.3 65.8 + - - +
228L GLN* 4.3 8.3 + - + +
273L LYS* 3.1 31.6 + - - +
387M GLU* 4.8 2.6 + - - -
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Residues in contact with PHE 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L GLY 4.3 0.5 - - - +
212L VAL* 3.8 3.6 - - - +
213L VAL* 2.8 57.8 + - + +
215L ILE* 4.0 23.6 - - + -
225L ARG* 4.2 15.7 - - + -
226L THR* 1.3 73.4 - - - +
228L GLN* 1.3 65.4 + - - +
256L VAL* 3.9 15.3 - - + -
268L TRP* 3.6 43.5 - + + +
269L ASN 3.8 7.4 - - - -
270L SER* 3.5 30.3 - - - -
273L LYS* 3.7 37.2 - - + +
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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