Contacts of the strand formed by residues 289 - 293 (chain C) in PDB entry 4QGC
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 GLY 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267C ILE 3.3 3.4 + - - -
268C ILE* 3.7 16.8 - - - +
269C SER 3.0 19.6 + - - -
287C SER* 3.4 12.3 - - - -
288C ASP* 1.3 82.3 - - - +
290C ILE* 1.3 65.0 + - - +
322C LYS* 4.7 3.6 - - - -
323C PRO* 3.3 16.4 - - - -
465C LEU* 6.5 0.2 - - - -
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Residues in contact with ILE 290 (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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268C ILE* 3.5 6.0 - - - +
269C SER* 3.5 19.7 - - - +
271C ILE* 3.9 14.6 - - + -
280C PHE* 3.7 30.1 - - + -
283C ILE* 4.2 13.2 - - + -
284C LEU* 3.7 22.2 - - + -
287C SER* 4.3 1.1 - - - +
289C GLY* 1.3 82.2 - - - +
291C MET* 1.3 62.3 + - - +
292C VAL* 4.3 11.0 - - + -
317C CYS* 3.6 28.3 - - - -
323C PRO 2.9 6.7 + - - -
324C VAL* 3.2 3.2 - - + +
325C ILE* 2.6 34.5 + - - +
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Residues in contact with MET 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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113C ASP* 4.6 0.4 - - - +
241C PHE* 3.5 44.0 - - + -
268C ILE* 3.5 7.8 - - + +
269C SER 2.8 9.3 + - - -
270C LYS* 3.4 38.6 - - + -
271C ILE* 2.9 30.5 + - - +
290C ILE* 1.3 75.0 - - - +
292C VAL* 1.3 65.5 + - - +
293C ALA* 3.6 3.9 + - + +
325C ILE* 3.3 21.1 - - + +
327C ALA* 3.8 23.1 - - + -
328C THR* 6.2 0.2 - - - -
360C MET* 3.6 21.5 - - - +
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Residues in contact with VAL 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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271C ILE* 4.4 3.4 - - - -
290C ILE* 4.3 4.9 - - + -
291C MET* 1.3 73.0 - - - +
293C ALA* 1.3 59.5 + - - +
294C ARG* 3.4 18.2 + - + -
297C LEU* 3.9 11.0 - - + -
306C VAL* 6.4 0.2 - - + -
310C GLN* 4.5 14.8 - - + +
313C MET* 3.7 43.7 - - + -
314C ILE* 4.8 7.4 - - + -
324C VAL* 4.0 23.8 - - + -
325C ILE 2.7 12.2 + - - +
326C CYS* 4.8 4.9 - - + -
327C ALA 3.0 27.8 + - - +
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Residues in contact with ALA 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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270C LYS* 5.3 5.8 - - + -
271C ILE 3.4 18.3 + - - +
272C GLU* 4.1 14.6 - - + +
291C MET* 3.6 9.2 + - + +
292C VAL* 1.3 69.1 - - - +
294C ARG* 1.3 65.3 + - - +
295C GLY 3.3 2.2 + - - -
296C ASP* 3.4 20.1 + - - +
297C LEU* 3.0 25.6 + - - +
327C ALA* 4.0 2.9 - - + -
328C THR* 3.8 14.4 - - + -
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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