Contacts of the helix formed by residues 292 - 302 (chain A) in PDB entry 3QV2
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 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A GLY 4.4 6.1 - - - +
291A LEU* 1.3 76.7 - - - +
293A ASP* 1.3 65.8 + - - +
294A LYS* 3.8 10.7 + - - +
295A GLN* 2.9 36.0 + - - +
296A GLN* 3.2 22.1 + - - +
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Residues in contact with ASP 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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202A SER* 5.6 0.5 + - - -
203A TYR* 2.7 41.3 + - - -
271A PRO* 3.9 10.4 - - + +
287A GLN* 4.9 5.9 + - - +
292A THR* 1.3 74.4 - - - +
294A LYS* 1.3 54.5 + - + +
296A GLN* 3.1 16.0 + - - +
297A TYR* 2.7 57.2 + - + -
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Residues in contact with LYS 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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234A TYR 4.7 3.6 - - - +
235A THR* 3.4 36.6 + - - +
236A LYS* 3.3 35.3 - - + +
292A THR* 3.2 10.2 + - - +
293A ASP* 1.3 78.4 - - + +
295A GLN* 1.3 59.0 + - + +
297A TYR* 3.2 6.8 + - + +
298A GLN* 2.9 48.5 + - + +
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Residues in contact with GLN 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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41A ILE* 4.3 25.8 - - + +
290A GLY 4.0 2.8 - - - +
291A LEU* 3.1 29.9 - - + +
292A THR* 2.9 38.5 + - - +
294A LYS* 1.3 79.8 - - + +
296A GLN* 1.3 62.4 + - - +
298A GLN* 3.5 16.7 + - - +
299A CYS* 3.3 29.4 + - - -
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Residues in contact with GLN 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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45A ILE* 5.1 2.0 - - + -
271A PRO* 3.4 23.9 - - + +
286A THR* 2.8 54.4 + - - +
287A GLN* 3.0 27.9 + - - +
291A LEU* 3.0 33.9 + - + +
292A THR 3.2 12.5 + - - +
293A ASP* 3.1 10.1 + - - +
295A GLN* 1.3 73.4 - - - +
297A TYR* 1.3 61.0 + - - +
299A CYS* 3.3 5.6 + - - +
300A LEU* 2.9 37.2 + - - +
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Residues in contact with TYR 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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203A TYR* 3.4 25.1 - + - -
231A THR 4.1 2.4 - - - +
232A LYS 3.8 7.6 - - - +
234A TYR* 3.7 28.4 - + + +
235A THR* 3.5 34.6 - - + +
268A TYR* 4.3 0.3 - - - +
269A PHE 2.7 28.1 + - - -
271A PRO* 3.5 23.3 - - + +
274A ILE* 3.7 19.8 - - + +
293A ASP* 2.7 45.7 + - + +
294A LYS* 3.4 9.4 - - + +
296A GLN* 1.3 72.9 - - - +
298A GLN* 1.3 52.8 + - - +
300A LEU* 3.4 3.9 + - - +
301A GLY* 2.7 33.4 + - - -
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Residues in contact with GLN 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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232A LYS* 3.3 47.2 + - + +
233A SER* 5.6 0.7 - - - -
294A LYS* 2.9 36.8 + - + +
295A GLN* 3.7 14.5 - - - +
297A TYR* 1.3 76.6 - - - +
299A CYS* 1.3 62.5 + - - +
301A GLY 3.4 0.2 + - - -
302A ASN* 3.1 30.8 + - - -
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Residues in contact with CYS 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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15A ILE* 3.6 22.7 - - + +
39A ASN* 4.9 2.2 - - - -
41A ILE* 3.7 24.7 - - - -
42A ALA* 4.2 17.0 - - - -
45A ILE* 4.0 15.5 - - + -
286A THR* 5.8 0.2 - - + -
295A GLN 3.3 15.5 + - - +
296A GLN 3.3 6.5 + - - +
298A GLN* 1.3 78.4 - - - +
300A LEU* 1.3 64.5 + - + +
302A ASN* 3.1 16.6 + - - +
303A SER* 3.1 12.8 + - - -
323A SAH 4.6 2.6 - - - +
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Residues in contact with LEU 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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15A ILE* 4.0 13.0 - - + -
271A PRO* 3.2 42.8 - - + +
274A ILE* 4.1 21.3 - - + -
275A LYS* 4.0 24.0 - - + +
278A HIS* 3.3 12.6 - - - +
280A PHE* 4.9 3.8 - - + -
286A THR* 3.7 28.5 - - + +
296A GLN 2.9 21.9 + - - +
297A TYR* 3.8 5.6 - - - +
299A CYS* 1.3 75.1 - - - +
301A GLY* 1.3 62.0 + - - +
303A SER* 2.6 27.5 + - - +
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Residues in contact with GLY 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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165A ARG* 2.8 20.4 + - - -
167A ARG* 4.8 1.4 + - - -
230A PHE* 3.5 16.4 - - - +
231A THR* 3.4 31.0 - - - -
232A LYS 3.7 3.7 + - - -
274A ILE* 6.1 0.4 - - - +
297A TYR 2.7 17.4 + - - -
298A GLN 3.8 1.1 - - - -
299A CYS 3.3 0.2 - - - -
300A LEU* 1.3 73.9 - - - +
302A ASN* 1.3 61.2 + - - +
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Residues in contact with ASN 302 (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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81A CYS* 5.5 6.6 - - - -
165A ARG* 4.0 0.9 - - - +
232A LYS* 3.2 42.6 + - - +
298A GLN 3.1 19.3 + - - +
299A CYS* 3.1 9.5 + - - +
301A GLY* 1.3 77.1 - - - +
303A SER* 1.3 65.9 + - - +
304A VAL* 5.1 0.2 - - - +
323A SAH 3.7 35.6 + - + +
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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