Contacts of the strand formed by residues 294 - 298 (chain C) in PDB entry 4CKG
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 GLN 294 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C THR 3.3 5.7 - - - +
290C ILE* 3.4 3.4 - - - +
291C GLN 2.9 35.6 + - - +
292C SER* 4.1 6.6 + - - +
293C ASN* 1.3 82.7 - - - +
295C LEU* 1.4 59.7 + - - +
296C VAL* 3.6 22.9 + - + +
307C VAL* 3.7 16.6 - - + +
309C VAL 4.0 7.6 - - - +
310C ASP 3.5 26.3 + - - +
311C ASP* 4.3 9.5 + - - +
312C LEU* 4.9 1.0 + - - +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 6.1 0.4 - - + -
288C PHE* 3.8 26.7 - - + -
289C THR 3.9 11.0 - - - +
290C ILE* 4.5 10.5 - - + +
293C ASN 4.0 2.4 + - - -
294C GLN* 1.4 68.8 + - - +
296C VAL* 1.3 63.1 + - - +
307C VAL* 3.5 2.6 - - - +
308C VAL* 2.8 53.4 + - + +
309C VAL* 4.1 8.6 + - + +
312C LEU* 4.7 21.6 - - + +
331C VAL* 5.0 9.4 - - + -
340C LEU* 4.8 16.6 - - + -
351C TRP* 4.4 15.5 - - + -
355C VAL* 4.4 24.0 - - + -
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Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C PHE* 3.3 8.5 - - - -
289C THR* 2.8 51.2 + - + +
291C GLN* 5.4 3.1 - - + +
294C GLN* 3.6 28.9 - - + +
295C LEU* 1.3 81.9 - - - +
297C TYR* 1.4 56.3 + - - +
305C VAL* 3.7 35.7 - - + -
306C THR 3.1 16.2 - - - +
307C VAL* 3.8 10.3 - - + +
308C VAL* 3.8 4.7 - - - -
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Residues in contact with TYR 297 (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 LYS* 4.2 23.9 + - + -
286C ARG* 3.7 42.4 - - + -
287C TRP 3.3 13.5 - - - +
288C PHE* 3.9 14.6 - + + -
296C VAL* 1.4 72.0 - - - +
298C GLN* 1.3 66.8 + - - +
299C LYS* 5.1 12.1 - - + -
305C VAL* 3.6 3.3 - - - -
306C THR* 3.1 62.7 + - + +
307C VAL 4.2 10.1 - - - -
308C VAL* 3.7 18.4 - - + -
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Residues in contact with GLN 298 (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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286C ARG* 4.1 4.8 - - - -
287C TRP* 3.3 58.9 + - + +
289C THR* 4.9 4.3 + - - +
297C TYR* 1.3 81.1 - - - +
299C LYS* 1.4 63.4 + - - +
300C LYS 2.7 28.0 + - - +
301C TYR 2.8 23.0 + - - -
303C ASP* 3.3 29.9 + - - +
304C PRO 5.0 0.2 - - - -
305C VAL* 3.3 25.8 - - + +
306C THR* 5.5 1.6 - - - -
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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