Contacts of the helix formed by residues 296 - 302 (chain X) in PDB entry 3A40
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 ARG 296 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X ARG* 5.8 3.0 - - - +
283X ASP* 4.5 10.5 + - - +
284X MET 5.0 2.9 - - - +
285X SER* 4.1 16.1 - - - +
286X TRP* 4.8 6.7 - - - -
291X GLN* 5.1 11.3 + - - +
294X LYS* 3.1 44.0 + - + +
295X TYR* 1.3 78.6 - - - +
297X VAL* 1.3 69.1 + - + +
298X SER* 3.1 17.0 - - - +
299X ASP* 2.9 25.7 + - - +
300X VAL* 3.5 7.4 + - - +
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Residues in contact with VAL 297 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284X MET 5.2 4.2 + - - +
286X TRP* 4.9 2.8 - - + -
296X ARG* 1.3 73.6 - - + +
298X SER* 1.3 67.0 + - - +
300X VAL* 3.1 21.9 + - + +
301X THR* 3.1 15.2 + - - -
310X ILE* 3.5 24.6 - - + +
314X ILE* 3.5 38.8 - - + -
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Residues in contact with SER 298 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X ARG* 3.9 17.4 - - - +
297X VAL* 1.3 82.8 - - - +
299X ASP* 1.3 62.8 + - - +
301X THR* 3.4 11.9 - - - -
302X LYS* 3.1 47.2 + - - +
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Residues in contact with ASP 299 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X ARG* 2.8 53.6 + - - +
226X MET* 3.6 26.8 - - + +
230X LEU* 3.7 9.1 - - + +
294X LYS 3.4 1.9 - - - +
295X TYR* 3.3 9.0 - - + -
296X ARG* 2.9 33.1 + - - +
298X SER* 1.3 81.2 + - - +
300X VAL* 1.3 64.2 + - + +
302X LYS* 3.2 14.3 + - - +
303X ALA 3.2 8.8 + - - -
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Residues in contact with VAL 300 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X 23R 3.8 52.3 - - + +
230X LEU* 4.5 5.8 - - + -
286X TRP* 4.8 9.9 - - + -
296X ARG 3.9 11.7 - - - +
297X VAL* 3.1 13.1 + - + +
299X ASP* 1.3 74.1 - - + +
301X THR* 1.3 66.9 + - - +
303X ALA* 3.0 13.8 + - - +
304X GLY 3.4 0.3 + - - -
305X HIS* 3.4 29.9 + - + +
309X LEU* 5.2 0.9 - - + -
310X ILE* 3.7 24.7 - - + -
313X LEU* 5.3 2.9 - - + -
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Residues in contact with THR 301 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161X ASP* 4.1 4.9 - - - +
164X GLY* 4.8 5.2 - - - -
220X GLU* 2.9 52.1 - - + +
297X VAL 3.1 13.2 + - - -
298X SER* 3.4 16.0 - - - +
300X VAL* 1.3 77.0 - - - +
302X LYS* 1.3 56.8 + - - +
304X GLY* 3.0 16.8 + - - -
305X HIS 3.6 13.3 + - - +
310X ILE* 3.6 11.8 - - - +
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Residues in contact with LYS 302 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X ARG* 4.0 24.9 - - + -
159X VAL* 3.0 36.6 - - + +
161X ASP* 4.3 26.8 + - - +
220X GLU* 4.4 9.2 - - + +
224X LEU* 3.5 6.3 - - - -
225X SER* 3.3 39.6 + - - +
226X MET* 3.4 14.7 + - + -
298X SER* 3.1 32.3 + - - +
299X ASP* 3.2 12.4 + - - +
301X THR* 1.3 76.5 - - - +
303X ALA* 1.3 56.3 + - - +
304X GLY 3.4 1.6 - - - -
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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