Contacts of the strand formed by residues 206 - 210 (chain C) in PDB entry 3IKH
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 ALA 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C VAL* 4.7 1.1 - - + -
199C ILE 3.3 12.6 - - - +
200C THR* 3.9 7.4 - - + -
201C GLN* 4.4 0.4 - - - +
205C GLY* 1.3 75.5 - - - +
207C TRP* 1.3 63.6 + - - +
215C GLN 3.9 0.3 - - - +
216C PHE* 3.6 5.9 - - - -
217C CYS* 2.7 41.7 + - + +
234C PHE* 3.7 32.3 - - + -
254C LEU* 4.1 6.6 - - + +
900C ATP 3.9 6.3 - - - +
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Residues in contact with TRP 207 (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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197C LEU 3.8 0.3 - - - +
198C VAL* 3.3 10.0 - - - +
199C ILE* 2.8 50.0 + - + +
201C GLN* 3.1 34.3 + - - +
206C ALA* 1.3 73.4 - - - +
208C LEU* 1.3 59.3 + - - +
209C VAL* 4.0 11.4 - - + +
214C ARG* 4.0 34.1 - - + -
215C GLN 3.4 20.2 - - - -
216C PHE* 3.7 35.7 - + + -
254C LEU* 4.1 2.7 - - - -
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Residues in contact with LEU 208 (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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196C THR* 4.0 13.9 - - + -
197C LEU 3.6 8.5 - - - +
198C VAL* 4.1 9.0 - - + -
207C TRP* 1.3 73.0 - - - +
209C VAL* 1.3 64.2 + - - +
210C GLN* 3.7 34.8 - - + +
213C GLN 3.6 1.6 - - - +
214C ARG* 3.3 3.1 - - - -
215C GLN* 2.7 58.5 + - + +
249C PRO* 3.9 2.9 - - + +
250C ASP* 3.6 39.7 - - - +
251C ALA* 3.9 1.6 - - - +
254C LEU* 3.7 19.5 - - + +
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Residues in contact with VAL 209 (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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194C VAL 4.8 1.2 - - - +
195C LYS 3.9 2.1 - - - +
196C THR 3.9 0.5 - - - -
197C LEU* 2.7 67.3 + - + +
199C ILE* 4.6 8.5 - - + -
207C TRP* 4.4 17.3 - - + +
208C LEU* 1.3 75.5 - - - +
210C GLN* 1.3 66.2 + - - +
212C GLY 5.5 4.5 - - - +
213C GLN 3.4 7.6 - - - +
214C ARG* 4.4 22.9 - - + +
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Residues in contact with GLN 210 (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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194C VAL 5.7 0.4 - - - -
195C LYS 3.7 13.9 + - - +
196C THR* 2.9 26.8 + - - +
208C LEU* 3.7 26.2 - - + +
209C VAL* 1.3 80.4 - - - +
211C GLU* 1.3 59.3 + - + +
212C GLY 3.2 2.0 - - - -
213C GLN* 2.5 46.5 + - + +
215C GLN* 5.0 2.1 - - - +
248C ALA* 4.2 10.5 - - - +
249C PRO 3.0 28.3 + - - +
250C ASP* 5.0 1.0 - - - -
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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