Contacts of the helix formed by residues 281 - 291 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A VAL* 4.1 8.1 + - - +
276A GLY* 3.4 9.2 + - - -
279A PHE* 3.3 33.3 - - + +
280A GLY* 1.3 75.5 - - - +
282A PRO* 1.3 62.2 - - - +
283A LEU 3.6 1.3 - - - -
284A GLY* 4.9 0.2 - - - -
285A GLY* 2.8 24.0 + - - -
545A ILE* 3.4 29.1 - - + +
548A GLU* 3.3 36.3 - - + +
549A LEU* 4.2 10.1 - - + -
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Residues in contact with PRO 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLY* 4.9 0.7 - - - -
280A GLY 3.4 7.6 - - - +
281A THR* 1.3 83.1 - - - +
283A LEU* 1.3 56.9 + - - +
285A GLY* 2.9 14.4 + - - -
286A VAL* 2.9 21.0 + - - +
306A PHE* 4.7 5.2 - - + -
309A ALA* 3.7 14.6 - - + +
310A THR* 3.8 32.1 - - - +
313A ALA* 3.6 19.7 - - + -
548A GLU* 3.2 18.6 - - - +
557B LEU* 6.0 4.0 - - + -
560B MET* 4.0 19.7 - - - -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PRO* 1.3 76.2 - - - +
284A GLY* 1.3 61.9 + - - +
286A VAL* 3.3 12.9 - - + +
287A LEU* 3.0 34.7 + - + +
306A PHE* 3.8 19.1 - - + -
544A VAL* 3.9 12.8 - - + -
547A PHE* 5.3 3.1 - - + -
548A GLU* 3.3 29.8 - - + +
283B LEU* 4.3 18.2 - - + -
287B LEU* 4.7 8.7 - - + -
544B VAL* 3.9 27.6 - - + -
547B PHE* 4.2 18.8 - - + -
556B ILE* 5.6 0.9 - - + -
560B MET* 3.8 19.1 - - + -
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 5.2 0.2 - - - -
281A THR 3.7 2.9 + - - -
283A LEU* 1.3 87.5 - - - +
285A GLY* 1.3 55.9 + - - +
287A LEU* 4.1 2.8 - - - +
288A PHE* 2.9 32.1 + - - +
541A SER* 4.5 2.6 - - - -
544A VAL* 3.6 22.0 - - - -
545A ILE* 3.6 24.3 - - - +
548A GLU* 4.1 1.2 + - - -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA* 3.8 11.5 - - - -
275A VAL* 3.6 26.4 - - - +
276A GLY* 4.2 2.5 - - - -
281A THR* 2.8 19.7 + - - -
282A PRO 2.9 6.8 + - - -
284A GLY* 1.3 73.9 - - - +
286A VAL* 1.3 58.4 + - - +
288A PHE 3.3 2.1 + - - -
289A SER* 2.9 27.4 + - - -
309A ALA* 5.2 0.2 - - - -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA* 4.3 5.4 - - + -
282A PRO 2.9 11.5 + - - +
283A LEU* 3.3 24.7 - - + +
285A GLY* 1.3 76.1 - - - +
287A LEU* 1.3 61.7 + - + +
289A SER* 3.2 8.7 + - - -
290A ILE* 3.0 30.0 + - - +
302A TYR* 4.2 27.3 - - + +
305A GLY* 3.5 33.7 - - - +
306A PHE* 3.7 21.5 - - + +
309A ALA* 4.2 2.2 - - + -
287B LEU* 6.1 1.1 - - + -
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Residues in contact with LEU 287 (chain A).
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* 3.0 25.3 + - + +
284A GLY* 4.1 1.3 - - - +
286A VAL* 1.3 82.7 - - + +
288A PHE* 1.3 56.5 + - - +
290A ILE* 3.4 10.5 - - + +
291A GLU* 2.9 36.0 + - - +
302A TYR* 5.5 2.2 - - + -
541A SER* 3.6 16.4 - - - -
544A VAL* 3.9 26.9 - - + -
283B LEU* 4.6 14.1 - - + -
286B VAL* 6.0 0.2 - - + -
287B LEU* 4.2 26.7 - - + -
302B TYR* 3.3 35.0 - - + +
306B PHE* 6.2 1.1 - - + -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 5.2 13.0 - - + -
232A GLU* 4.2 23.8 - - - -
236A VAL* 5.2 3.6 - - + -
271A CYS* 4.1 13.2 - - - -
275A VAL* 3.7 33.7 - - + -
284A GLY 2.9 19.5 + - - +
285A GLY 3.8 2.7 - - - +
287A LEU* 1.3 74.3 - - - +
289A SER* 1.3 58.7 + - - +
291A GLU* 2.8 34.2 - - - +
292A VAL* 4.4 11.2 - - + +
293A THR* 4.8 1.0 + - - +
484A PHE* 6.3 3.8 - + + -
537A SER* 5.4 8.1 - - - -
539A THR* 4.9 8.5 - - + -
541A SER* 3.6 13.0 - - - +
542A THR* 5.1 7.0 - - - -
545A ILE* 5.8 6.3 - - + -
578A TYR* 5.5 9.0 - + - -
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A THR* 2.7 41.1 + - - +
271A CYS* 3.6 11.0 - - - +
272A ALA* 3.5 21.3 + - - +
285A GLY 2.9 16.6 + - - -
286A VAL* 3.5 6.3 - - - -
287A LEU 3.1 0.4 - - - -
288A PHE* 1.3 79.1 - - - +
290A ILE* 1.3 58.3 + - - +
293A THR* 2.3 32.1 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A THR* 5.5 1.6 - - - -
286A VAL 3.0 20.3 + - - +
287A LEU* 3.4 23.3 - - + +
289A SER* 1.3 77.6 - - - +
291A GLU* 1.3 67.7 + - + +
292A VAL 2.9 10.2 + - - -
293A THR 3.3 9.9 + - - -
294A SER* 4.0 15.1 + - - +
297A PHE* 3.5 51.1 - - + -
302A TYR* 5.9 5.8 - - + -
290B ILE* 4.4 18.6 - - + -
297B PHE* 5.2 5.6 - - + -
299B VAL* 4.4 16.1 - - + +
302B TYR* 5.4 11.0 - - + -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU 2.9 16.4 + - - +
288A PHE* 2.8 34.2 - - - +
290A ILE* 1.3 77.9 - - + +
292A VAL* 1.3 77.8 + - + +
539A THR* 3.0 33.4 + - - +
540A VAL 5.0 0.4 - - - +
541A SER* 2.9 19.3 + - - +
299B VAL* 4.3 16.6 - - - +
302B TYR* 4.2 26.5 - - + +
303B TRP* 3.9 23.2 + - - +
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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