Contacts of the helix formed by residues 496 - 508 (chain C) in PDB entry 3QI2
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 ASP 496 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A ASN* 5.6 3.8 + - - +
497C ILE* 1.3 63.1 + - - +
498C GLU* 4.2 14.5 - - + +
499C GLY* 3.4 28.9 + - - -
500C LEU* 3.8 10.9 + - - +
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Residues in contact with ILE 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ARG* 3.7 25.8 - - - +
212A ILE* 4.3 19.7 - - + -
215A PHE* 5.9 2.2 - - + -
256A ASN* 5.0 11.7 - - - +
258A TRP* 4.4 34.1 - - + -
496C ASP* 1.3 72.9 - - - +
498C GLU* 1.3 61.7 + - - +
499C GLY 3.2 1.6 - - - -
500C LEU* 3.0 15.8 + - + +
501C VAL* 2.8 42.5 + - + +
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Residues in contact with GLU 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ARG* 3.5 25.2 - - + +
496C ASP* 4.2 13.1 - - + +
497C ILE* 1.3 78.8 - - - +
499C GLY* 1.3 56.8 + - - +
501C VAL* 3.3 7.3 + - + +
502C GLU* 2.8 38.6 + - + +
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Residues in contact with GLY 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C ASP* 3.4 24.6 + - - -
497C ILE 3.2 0.6 - - - -
498C GLU* 1.3 77.0 - - - +
500C LEU* 1.3 58.0 + - - +
502C GLU* 3.3 15.3 + - - +
503C LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 4.9 4.5 - - + -
249A LEU* 4.7 4.7 - - + -
252A SER* 4.5 20.6 - - - -
253A ILE* 3.8 25.4 - - + +
256A ASN* 3.6 28.5 - - + +
258A TRP* 6.2 0.9 - - + -
259A PHE* 3.7 21.8 - - + -
496C ASP 3.8 9.6 + - - +
497C ILE* 3.0 21.1 + - + +
499C GLY* 1.3 73.2 - - - +
501C VAL* 1.3 61.7 + - + +
503C LEU* 3.0 9.1 + - + +
504C LEU* 2.8 44.6 + - + +
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Residues in contact with VAL 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ARG* 4.1 33.2 - - + +
211A TRP* 3.5 36.8 - - + -
212A ILE* 5.5 0.4 - - + -
215A PHE* 5.2 4.7 - - + -
497C ILE* 2.8 36.1 + - + +
498C GLU* 3.7 6.1 - - + +
500C LEU* 1.3 73.1 - - + +
502C GLU* 1.3 63.2 + - - +
504C LEU* 3.4 9.4 + - - +
505C ASN* 3.0 35.2 + - - +
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Residues in contact with GLU 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C GLU* 2.8 24.1 + - + +
499C GLY* 3.3 13.5 - - - +
501C VAL* 1.3 76.7 - - - +
503C LEU* 1.3 63.7 + - - +
505C ASN* 3.2 10.1 + - - +
506C ARG* 3.2 39.0 + - - +
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Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A GLU 5.4 0.4 - - - +
248A LYS* 3.9 26.7 - - + +
249A LEU* 3.7 33.7 - - + +
252A SER* 4.0 15.9 - - - +
499C GLY 2.9 13.8 + - - +
500C LEU* 3.4 11.4 - - + +
502C GLU* 1.3 76.3 - - - +
504C LEU* 1.3 64.0 + - - +
506C ARG* 3.3 38.3 + - - +
507C VAL* 3.0 50.1 + - + +
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Residues in contact with LEU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.1 16.6 - - + -
211A TRP* 3.6 26.6 - - + -
215A PHE* 3.4 33.7 - - + -
249A LEU* 3.6 24.0 - - + -
253A ILE* 4.6 1.3 - - + -
500C LEU* 2.8 35.9 + - + +
501C VAL* 3.6 11.2 - - - +
503C LEU* 1.3 72.9 - - - +
505C ASN* 1.3 63.1 + - - +
507C VAL* 4.8 1.3 - - - -
508C GLN* 3.0 52.9 + - - +
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Residues in contact with ASN 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLY 5.2 1.6 - - - +
204A GLN 4.9 0.2 - - - +
205A ARG* 3.8 31.6 - - + +
206A SER 3.4 25.3 + - - +
211A TRP* 3.1 25.5 + - - -
501C VAL* 3.0 29.6 + - - +
502C GLU* 3.2 8.8 + - - +
504C LEU* 1.3 76.5 - - - +
506C ARG* 1.3 57.0 + - + +
508C GLN* 4.2 1.0 - - - -
509C SER* 3.0 28.9 + - - -
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Residues in contact with ARG 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.3 7.3 + - - -
239A GLU* 4.1 15.1 + - - -
245A GLU* 4.8 2.0 - - - +
248A LYS* 3.3 28.7 - - - +
502C GLU* 3.2 26.9 + - + +
503C LEU* 3.3 38.8 - - - +
505C ASN* 1.3 76.7 - - + +
507C VAL* 1.3 65.6 + - + +
508C GLN 3.5 0.2 - - - -
509C SER* 3.7 13.5 + - - -
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Residues in contact with VAL 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 3.5 24.5 - - + -
42A ARG* 2.7 34.7 + - - +
245A GLU* 4.3 33.7 - - + +
246A SER 5.0 0.4 - - - +
249A LEU* 3.8 25.8 - - + -
503C LEU* 3.0 44.9 + - + +
504C LEU 4.2 1.6 - - - +
506C ARG* 1.3 81.7 - - + +
508C GLN* 1.3 58.1 + - - +
509C SER 3.3 1.8 - - - -
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Residues in contact with GLN 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU 4.9 2.6 + - - -
39A LEU* 3.6 19.6 - - - +
40A GLY 3.1 39.4 + - - +
41A ALA* 4.4 0.2 - - - -
42A ARG* 3.8 14.8 - - - +
46A LYS* 3.9 12.2 + - - +
201A VAL* 2.9 28.8 + - - +
203A GLY* 3.5 17.2 + - - +
211A TRP* 4.1 17.6 - - + -
249A LEU* 4.7 1.5 - - + +
504C LEU* 3.0 25.8 + - + +
505C ASN* 4.2 1.1 - - - -
507C VAL* 1.3 79.9 - - + +
509C SER* 1.3 58.5 + - - +
510C SER* 2.9 11.6 + - - -
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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