Contacts of the strand formed by residues 222 - 226 (chain C) in PDB entry 6DVD
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 VAL 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C PHE* 5.2 0.7 - - + -
215C ASP 3.6 11.0 - - - +
216C VAL* 4.0 14.1 - - + -
221C THR* 1.3 79.1 - - - +
223C GLY* 1.3 63.8 + - - +
231C ARG* 4.1 1.8 - - - -
233C PRO* 3.8 3.6 - - - +
234C VAL* 3.0 50.2 + - + +
257C ILE* 4.4 16.4 - - + +
258C MET* 3.7 21.3 - - + -
261C THR* 3.4 14.5 + - - +
342C ILE* 4.7 7.9 - - + -
345C LEU* 4.2 18.2 - - + -
346C VAL* 5.6 3.1 - - + -
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Residues in contact with GLY 223 (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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214C PHE* 3.4 8.3 - - - +
215C ASP* 3.1 30.6 + - - +
222C VAL* 1.3 75.5 - - - +
224C VAL* 1.3 63.1 + - - +
231C ARG* 3.3 22.1 - - - +
232C GLN 3.2 13.5 - - - -
233C PRO* 4.3 0.9 - - - -
234C VAL* 3.7 4.9 - - - -
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Residues in contact with VAL 224 (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* 3.7 30.1 - - + -
213C GLU 3.5 7.9 - - - +
214C PHE* 3.5 27.4 - - + -
215C ASP* 4.9 0.2 - - - -
223C GLY* 1.3 75.5 - - - +
225C ARG* 1.3 66.0 + - - +
226C ILE* 3.9 13.3 + - + +
230C ARG 3.9 2.1 - - - +
231C ARG* 3.6 4.1 - - - +
232C GLN* 2.9 38.3 + - + +
233C PRO 4.0 4.3 - - - +
234C VAL* 4.0 16.4 - - - -
237C LEU* 4.4 16.4 - - + -
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Residues in contact with ARG 225 (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* 3.7 3.8 - - - -
213C GLU* 2.5 78.2 + - + +
215C ASP* 4.5 5.4 - - - +
224C VAL* 1.3 74.2 - - - +
226C ILE* 1.3 61.6 + - - +
227C ASP 3.9 0.9 + - - -
228C ARG* 3.1 48.3 + - - +
229C LYS 3.8 11.1 + - - +
230C ARG 4.2 1.3 - - - -
231C ARG* 3.6 35.1 - - + +
14H T 4.7 18.5 - - - +
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Residues in contact with ILE 226 (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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210C ALA* 5.7 0.2 - - + -
211C TRP 4.0 1.6 - - - -
212C LEU* 3.6 17.0 - - + -
224C VAL* 3.9 15.9 + - + +
225C ARG* 1.3 72.0 - - - +
227C ASP* 1.3 73.4 + - + +
229C LYS* 3.2 24.9 + - + +
230C ARG 4.5 3.9 + - - +
232C GLN* 5.8 6.5 - - + -
237C LEU* 4.3 25.1 - - + -
277C ILE* 4.5 23.3 - - + -
281C LEU* 4.2 18.4 - - + +
296C LEU* 6.3 0.2 - - + -
299C LEU* 5.9 0.7 - - + -
300C PHE* 3.6 34.5 - - + -
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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