Contacts of the strand formed by residues 290 - 296 (chain B) in PDB entry 2QI8
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 THR 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B THR* 3.4 3.0 - - - +
286B TRP* 2.8 61.8 + - + +
287B ASN* 4.9 1.9 + - - -
289B THR* 1.3 84.2 + - - +
291B ARG* 1.3 70.4 + - - +
292B VAL* 4.4 0.2 - - - -
326B TYR* 4.0 22.7 - - + +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLU* 4.1 14.5 + - - -
283B MET* 2.7 46.7 - - - +
284B GLY 3.5 11.6 + - - +
285B THR* 4.5 6.3 + - - +
289B THR 3.5 4.6 + - - -
290B THR* 1.3 79.1 - - - +
292B VAL* 1.3 69.2 + - - +
326B TYR* 4.4 5.0 - - - -
340B TYR* 3.6 43.7 + - + +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.7 0.4 - - + -
283B MET* 3.7 4.5 - - - +
284B GLY 2.9 49.1 + - - -
285B THR 3.7 13.2 - - - +
286B TRP* 3.7 17.9 - - + -
290B THR 3.8 2.5 - - - +
291B ARG* 1.3 85.7 - - - +
293B ALA* 1.3 58.8 + - - +
294B ILE* 3.8 19.7 - - + -
326B TYR* 3.7 19.3 - - + -
337B VAL* 3.5 28.0 - - + -
338B MET 3.6 4.0 - - - +
340B TYR* 3.8 12.3 - - - -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 5.9 1.8 - - + -
281B VAL* 5.1 9.2 - - + -
282B TRP 3.4 7.4 - - - +
292B VAL* 1.3 73.8 - - - +
294B ILE* 1.3 62.4 + - - +
295B LYS 4.2 0.4 - - - -
336B ILE 3.7 0.7 - - - +
337B VAL* 3.4 4.0 - - - +
338B MET* 2.8 45.4 + - + +
339B GLU 3.7 20.6 - - - +
340B TYR* 4.1 11.7 - - + +
341B MET 5.4 0.4 - - - +
393B LEU* 6.4 2.5 - - + -
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LEU* 4.4 13.2 - - + -
268B ARG 3.8 17.0 - - - +
269B LEU* 3.8 28.7 - - + -
280B GLU 3.6 1.7 - - - +
281B VAL* 3.2 7.1 - - - +
282B TRP* 2.8 45.8 + - + +
283B MET 4.8 0.9 - - - +
284B GLY* 4.0 7.2 - - - +
285B THR 4.6 0.4 - - - +
292B VAL* 3.8 24.9 - - + -
293B ALA* 1.3 78.1 - - - +
295B LYS* 1.3 62.8 + - - +
296B THR* 4.3 2.9 - - + -
335B TYR* 3.7 33.4 - - + -
336B ILE 3.4 7.9 - - - +
337B VAL* 4.5 7.9 - - + -
338B MET* 4.9 0.2 - - - -
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B GLU 3.3 11.0 - - - +
281B VAL* 4.0 18.6 - - + +
293B ALA 4.2 0.6 - - - -
294B ILE* 1.3 73.5 - - - +
296B THR* 1.3 67.7 + - - +
335B TYR* 3.4 2.9 - - - -
336B ILE* 2.7 58.3 + - + +
338B MET* 3.7 19.1 - - + +
404B ASP* 2.8 35.3 + - - +
407B LEU* 4.2 20.0 - - + -
408B ALA* 5.3 6.2 - - - +
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B LEU* 4.3 12.3 - - + -
279B GLY* 3.1 21.8 - - - -
280B GLU* 2.9 43.5 + - - +
282B TRP* 4.9 3.6 - - + +
294B ILE* 4.3 4.7 - - + +
295B LYS* 1.3 83.3 - - - +
297B LEU* 1.3 62.9 + - - +
334B ILE 3.5 6.7 - - - -
335B TYR* 3.5 39.7 - - + -
336B ILE* 4.9 2.9 - - - -
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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