Contacts of the helix formed by residues 281 - 291 (chain B) in PDB entry 6QVC
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 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B VAL* 4.1 8.3 + - - +
276B GLY* 3.4 8.6 + - - -
279B PHE* 3.3 32.2 - - + +
280B GLY* 1.3 74.9 - - - +
282B PRO* 1.3 60.3 - - - +
283B LEU 3.6 1.6 - - - -
285B GLY* 2.8 23.8 + - - -
545B ILE* 3.4 29.0 - - + +
548B GLU* 3.3 36.8 - - + +
549B LEU* 4.2 10.3 - - + -
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Residues in contact with PRO 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 6.0 4.9 - - + -
560A MET* 3.9 22.2 - - - -
276B GLY* 4.9 0.7 - - - -
280B GLY 3.4 7.6 - - - +
281B THR* 1.3 84.2 - - - +
283B LEU* 1.3 59.0 + - - +
285B GLY* 2.9 14.9 + - - -
286B VAL* 2.9 20.3 + - - +
306B PHE* 4.7 5.4 - - + -
309B ALA* 3.7 13.9 - - + +
310B THR* 3.8 29.4 - - - +
313B ALA* 3.6 19.3 - - + -
548B GLU* 3.2 17.5 - - - +
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Residues in contact with LEU 283 (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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283A LEU* 4.3 18.4 - - + -
287A LEU* 4.6 9.4 - - + -
544A VAL* 3.9 28.0 - - + -
547A PHE* 4.2 17.9 - - + -
556A ILE* 5.6 0.4 - - + -
560A MET* 3.7 20.0 - - + -
282B PRO* 1.3 75.8 - - - +
284B GLY* 1.3 63.0 + - - +
286B VAL* 3.3 12.8 - - + +
287B LEU* 3.0 34.0 + - + +
306B PHE* 3.8 18.2 - - + -
544B VAL* 3.9 13.7 - - + -
547B PHE* 5.3 3.1 - - + -
548B GLU* 3.3 29.6 - - - +
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 5.2 0.2 - - - -
281B THR 3.7 2.9 + - - -
282B PRO 3.3 0.2 - - - -
283B LEU* 1.3 86.3 - - - +
285B GLY* 1.3 55.6 + - - +
287B LEU* 3.9 2.8 - - - +
288B PHE* 2.9 32.2 + - - +
541B SER* 4.5 2.1 - - - -
544B VAL* 3.6 22.2 - - - +
545B ILE* 3.6 22.9 - - - +
548B GLU* 4.1 1.6 + - - -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA* 3.8 11.1 - - - -
275B VAL* 3.6 25.9 - - - +
276B GLY* 4.2 2.7 - - - -
281B THR 2.8 21.0 + - - -
282B PRO 2.9 5.5 + - - -
284B GLY* 1.3 74.7 - - - +
286B VAL* 1.3 58.5 + - - +
288B PHE 3.3 1.9 + - - -
289B SER* 2.9 27.5 + - - -
309B ALA* 5.2 0.7 - - - -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 6.0 1.3 - - + -
272B ALA* 4.3 5.8 - - + -
282B PRO 2.9 10.6 + - - +
283B LEU* 3.3 24.7 - - + +
285B GLY* 1.3 76.5 - - - +
287B LEU* 1.3 62.4 + - + +
289B SER* 3.2 7.7 + - - -
290B ILE* 3.0 30.7 + - - +
302B TYR* 4.2 27.9 - - + +
305B GLY* 3.5 33.4 - - - +
306B PHE* 3.7 21.5 - - + +
309B ALA* 4.2 2.7 - - + -
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Residues in contact with LEU 287 (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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283A LEU* 4.7 12.8 - - + -
286A VAL* 6.1 0.2 - - + -
287A LEU* 4.2 27.6 - - + -
302A TYR* 3.3 37.9 - - + +
306A PHE* 6.2 0.9 - - + -
283B LEU* 3.0 24.3 + - + +
284B GLY 4.1 1.1 - - - +
286B VAL* 1.3 84.3 - - + +
288B PHE* 1.3 55.6 + - - +
290B ILE* 3.4 9.4 - - + +
291B GLU* 2.9 35.9 + - - +
302B TYR* 5.5 1.8 - - + -
541B SER* 3.6 17.3 - - - -
544B VAL* 3.9 28.3 - - + -
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Residues in contact with PHE 288 (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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191B ILE* 5.2 11.9 - - + -
232B GLU* 4.2 24.5 - - - -
236B VAL* 5.2 3.6 - - + -
271B CYS* 4.1 12.8 - - - -
275B VAL* 3.7 34.5 - - + -
284B GLY 2.9 20.1 + - - +
285B GLY 3.8 2.9 - - - +
287B LEU* 1.3 75.1 - - - +
289B SER* 1.3 58.9 + - - +
291B GLU* 2.8 35.1 - - - +
292B VAL* 4.4 9.6 - - + +
293B THR* 4.8 1.0 + - - +
484B PHE* 6.3 4.3 - + + -
537B SER* 5.4 7.9 - - - -
539B THR* 4.9 8.3 - - + -
541B SER* 3.6 13.6 - - - +
542B THR* 5.1 7.2 - - - -
545B ILE* 5.8 6.5 - - + -
578B TYR* 5.5 9.4 - + - -
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Residues in contact with SER 289 (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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268B THR* 2.7 41.5 + - - +
271B CYS* 3.6 11.1 - - - +
272B ALA* 3.5 21.3 + - - +
285B GLY 2.9 17.1 + - - -
286B VAL* 3.5 6.1 - - - -
287B LEU 3.1 0.2 - - - -
288B PHE* 1.3 79.6 - - - +
290B ILE* 1.3 57.7 + - - +
293B THR* 2.3 32.1 + - - +
294B SER* 5.0 0.2 + - - -
297B PHE* 6.5 0.2 - - - -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 4.4 17.7 - - + -
297A PHE* 5.2 5.2 - - + +
299A VAL* 4.5 16.3 - - + +
302A TYR* 5.4 10.8 - - + -
268B THR* 5.5 1.8 - - - -
286B VAL 3.0 20.7 + - - +
287B LEU* 3.4 23.6 - - + +
289B SER* 1.3 76.6 - - - +
291B GLU* 1.3 66.8 + - + +
292B VAL 2.9 10.4 + - - -
293B THR 3.3 9.4 + - - -
294B SER* 4.0 14.7 + - - +
297B PHE* 3.5 50.7 - - + -
302B TYR* 5.9 5.6 - - + -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 4.4 17.2 - - - +
302A TYR* 4.3 25.1 - - + -
303A TRP* 4.1 22.6 + - - +
287B LEU 2.9 17.3 + - - +
288B PHE* 2.8 35.0 - - - +
290B ILE* 1.3 76.9 - - + +
292B VAL* 1.3 80.2 + - + +
539B THR* 3.0 32.3 + - - +
541B SER* 2.9 19.1 + - - +
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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