Contacts of the helix formed by residues 291 - 301 (chain A) in PDB entry 2VWK
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 TYR 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A LYS* 4.1 2.8 + - - -
290A VAL* 1.3 76.9 - - - +
292A ALA* 1.3 65.3 + - - +
293A GLU* 3.3 22.4 + - - +
294A GLU* 3.5 18.3 + - + +
295A ILE* 3.6 14.5 + - - +
663A TYR* 6.0 1.6 - - + -
698A VAL* 3.8 11.4 - - + +
700A SER* 4.0 16.8 - - - +
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Residues in contact with ALA 292 (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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291A TYR* 1.3 76.5 - - - +
293A GLU* 1.3 62.3 + - - +
294A GLU 3.4 0.2 - - - -
295A ILE* 3.2 27.0 - - + +
296A ALA* 3.3 13.0 + - - +
693A ILE* 3.6 22.8 - - + +
697A THR* 3.8 25.8 - - + +
698A VAL 3.6 15.6 + - - +
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Residues in contact with GLU 293 (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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291A TYR* 3.3 16.8 - - - +
292A ALA* 1.3 76.1 + - - +
294A GLU* 1.3 59.8 + - - +
296A ALA* 3.6 1.6 + - - +
297A GLN* 3.0 29.6 + - - +
682A VAL* 6.1 0.4 - - + -
686A LEU* 3.9 32.3 - - + -
689A ARG* 4.6 3.5 + - - +
691A ILE* 4.7 6.2 - - - +
693A ILE* 4.1 14.8 - - + -
698A VAL 3.5 0.2 - - - +
699A ILE* 3.2 24.2 - - + +
700A SER* 3.3 39.0 + - - +
716A PRO* 5.2 5.3 - - + +
717A PHE 5.0 2.4 + - - -
718A ASP* 4.8 13.7 + - - +
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Residues in contact with GLU 294 (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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290A VAL* 3.4 32.2 - - + +
291A TYR* 3.5 14.0 + - + +
292A ALA 3.4 0.2 - - - -
293A GLU* 1.3 79.0 + - - +
295A ILE* 1.3 58.7 + - + +
297A GLN* 3.3 11.8 - - + +
298A ALA* 3.3 21.0 + - - +
303A GLU 4.7 1.9 - - - +
304A GLY* 5.0 10.2 - - - +
307A ARG* 4.4 16.4 - - - +
308A VAL* 4.4 2.2 - - + +
718A ASP* 4.9 8.4 + - - +
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Residues in contact with ILE 295 (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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143A GLU* 3.7 24.9 - - + +
144A THR 5.9 3.1 - - - +
290A VAL* 3.6 27.6 - - + +
291A TYR 3.6 5.8 - - - +
292A ALA* 3.2 29.2 - - + +
294A GLU* 1.3 76.5 - - - +
296A ALA* 1.3 56.6 + - + +
297A GLN 3.1 4.5 - - - -
298A ALA* 3.0 17.0 + - - +
299A TRP* 3.1 17.6 + - - -
308A VAL* 3.5 37.3 - - + +
311A TYR* 4.8 9.6 - - + +
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Residues in contact with ALA 296 (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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145A LEU* 6.3 3.8 - - + -
292A ALA 3.3 11.5 + - - +
295A ILE* 1.3 80.3 - - + +
297A GLN* 1.3 61.8 + - - +
299A TRP* 3.5 22.8 + - + +
300A GLU* 3.7 6.6 + - - +
690A GLY 5.0 0.7 - - - +
691A ILE* 3.4 40.3 - - + +
692A LYS 4.8 7.4 - - - +
693A ILE* 5.2 0.9 - - + -
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Residues in contact with GLN 297 (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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293A GLU 3.0 20.5 + - - +
294A GLU* 3.3 13.0 - - + +
295A ILE 3.1 0.2 - - - -
296A ALA* 1.3 77.4 - - - +
298A ALA* 1.3 61.5 + - - +
300A GLU* 3.8 0.7 + - - +
301A THR* 3.3 47.5 + - - +
303A GLU* 4.2 15.1 + - - +
689A ARG* 3.6 35.6 + - - +
691A ILE* 3.8 10.9 - - - +
718A ASP* 5.4 2.9 - - - +
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Residues in contact with ALA 298 (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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174A ARG* 4.5 1.0 - - - -
294A GLU 3.3 4.1 + - - +
295A ILE 3.0 10.7 + - - +
297A GLN* 1.3 76.9 - - - +
299A TRP* 1.3 64.9 + - + +
300A GLU 3.5 0.2 - - - -
302A GLY* 3.2 21.7 + - - +
303A GLU 3.7 19.1 - - - +
304A GLY 3.8 5.4 - - - +
305A LEU* 3.4 26.2 - - + +
308A VAL* 3.8 24.7 - - + -
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Residues in contact with TRP 299 (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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144A THR 5.9 0.4 - - - -
145A LEU* 4.8 11.4 - - + -
158A LEU* 3.8 37.0 - - + -
174A ARG* 2.9 31.9 + - - +
295A ILE 3.1 17.2 + - - -
296A ALA* 3.6 15.0 - - - +
297A GLN 3.2 1.0 - - - -
298A ALA* 1.3 80.7 - - - +
300A GLU* 1.3 61.6 + - - +
302A GLY 4.9 0.2 + - - -
305A LEU* 5.2 0.9 - - + -
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Residues in contact with GLU 300 (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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174A ARG* 5.7 1.4 + - - -
296A ALA 3.7 9.6 + - - +
297A GLN 4.8 0.7 - - - +
299A TRP* 1.3 80.7 - - - +
301A THR* 1.3 69.2 + - - +
689A ARG 5.4 4.7 - - - +
690A GLY 5.1 10.1 - - - +
691A ILE* 5.6 1.6 - - + -
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Residues in contact with THR 301 (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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297A GLN* 3.3 34.2 + - - +
300A GLU* 1.3 82.2 - - - +
302A GLY* 1.3 58.6 + - - +
303A GLU* 3.7 24.2 - - + +
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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