Contacts of the strand formed by residues 289 - 294 (chain C) in PDB entry 6RKU
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 ILE 289 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C ILE* 4.9 9.9 - - + -
281C VAL* 3.7 47.3 - - + +
286C VAL* 3.9 23.8 - - + -
287C GLU 3.3 6.4 - - - +
288C GLY* 1.3 81.5 - - - +
290C SER* 1.3 63.9 + - - +
291C ALA 3.7 19.3 - - - +
292C LEU* 5.9 2.5 - - + -
305C ILE* 4.3 22.0 - - + -
306C GLU 4.1 2.7 - - - -
308C LYS* 4.2 4.6 - - - +
316C VAL* 4.3 11.0 - - + -
320C LEU* 4.4 17.9 - - + -
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Residues in contact with SER 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL* 5.2 4.8 - - - +
288C GLY 4.0 1.2 + - - -
289C ILE* 1.3 75.9 - - - +
291C ALA* 1.3 70.3 + - - +
306C GLU* 2.9 44.1 + - - +
307C VAL 4.6 0.7 - - - -
308C LYS* 4.4 16.8 - - - +
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Residues in contact with ALA 291 (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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289C ILE* 3.7 17.1 - - - +
290C SER* 1.3 82.0 + - - +
292C LEU* 1.3 67.2 + - - +
293C ARG* 5.6 4.7 - - + -
305C ILE* 4.3 2.6 - - - +
306C GLU* 4.0 31.7 + - + +
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Residues in contact with LEU 292 (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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274C ILE* 3.8 44.4 - - + +
277C ILE* 4.0 29.8 - - + -
278C ALA* 4.9 7.6 - - + +
281C VAL* 6.2 0.7 - - + -
289C ILE* 5.9 2.2 - - + -
291C ALA* 1.3 81.3 - - - +
293C ARG* 1.3 83.2 + - - +
294C ASP* 5.9 0.9 - - + -
303C ILE* 5.5 1.3 - - + -
304C VAL 4.3 7.4 - - - +
305C ILE* 4.9 13.5 - - + +
306C GLU 5.3 0.7 - - - +
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Residues in contact with ARG 293 (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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411B GLN* 4.9 13.5 - - - +
258C THR* 5.5 2.4 - - - +
274C ILE* 5.6 0.3 - - - +
291C ALA* 5.6 4.9 - - + +
292C LEU* 1.3 93.1 - - - +
294C ASP* 1.3 65.9 + - - +
295C GLU* 5.2 11.3 + - + -
303C ILE* 4.1 5.7 - - - +
304C VAL* 3.3 54.9 + - + +
306C GLU* 4.9 22.4 + - - +
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Residues in contact with ASP 294 (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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411B GLN* 3.0 28.1 + - - +
438B ARG* 2.5 39.8 + - + +
270C LYS* 4.4 5.6 + - - -
274C ILE* 6.6 0.9 - - + -
292C LEU* 5.9 1.1 - - + -
293C ARG* 1.3 79.0 - - - +
295C GLU* 1.3 85.5 + - - +
296C SER* 2.8 16.7 + - - -
302C ARG 3.0 11.0 - - - +
303C ILE* 4.5 7.8 - - - +
304C VAL 4.9 2.5 - - - +
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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