Contacts of the helix formed by residues 369 - 373 (chain X) in PDB entry 2XB2
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 GLY 369 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X SER 4.5 0.5 - - - +
248X LEU* 3.8 16.8 - - - +
251X ILE* 4.2 11.4 - - - -
346X VAL 4.1 6.3 + - - -
368X SER* 1.3 78.7 + - - +
370X ARG* 1.3 65.7 + - - +
371X TYR 3.3 3.1 + - - -
372X GLY 3.6 8.0 + - - -
373X ARG* 3.1 32.9 + - - +
374X LYS 4.3 1.4 + - - -
375X GLY* 4.2 6.3 - - - -
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Residues in contact with ARG 370 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X SER 4.1 0.4 - - - -
85X GLY* 3.5 22.0 - - - +
340X GLY 4.5 1.2 + - - -
341X LEU 3.9 15.1 + - - -
342X ASP* 2.2 44.3 + - - +
343X VAL 4.3 1.6 - - - +
344X PRO* 3.8 30.5 + - + +
346X VAL 5.1 0.2 - - - +
366X GLY 2.8 30.5 + - - -
367X ARG* 3.1 29.2 - - - +
368X SER* 4.2 1.3 + - - -
369X GLY* 1.3 75.0 - - - +
371X TYR* 1.3 67.4 + - + +
373X ARG* 2.9 35.4 + - - +
1413X ANP 3.3 54.7 + - - -
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Residues in contact with TYR 371 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X LYS 3.6 6.9 + - - -
62X SER* 3.7 19.9 + - - -
85X GLY 2.9 31.8 + - - +
86X THR* 4.0 6.3 - - - -
369X GLY 3.3 1.6 + - - -
370X ARG* 1.3 74.2 - - + +
372X GLY* 1.3 58.4 + - - +
373X ARG* 3.5 9.7 + - - +
1413X ANP 3.2 85.7 + + - +
146Y ILE* 3.2 44.1 - - + +
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Residues in contact with GLY 372 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85X GLY 4.5 0.4 + - - -
86X THR* 5.8 0.6 - - - +
248X LEU* 5.7 7.0 - - - +
250X GLY* 5.1 6.5 - - - -
369X GLY 3.6 5.5 + - - -
370X ARG 3.4 0.2 - - - -
371X TYR* 1.3 75.1 - - - +
373X ARG* 1.3 67.1 + - - +
374X LYS* 3.8 2.4 + - - +
146Y ILE* 3.4 12.7 - - - +
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Residues in contact with ARG 373 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250X GLY* 4.2 9.2 - - - +
251X ILE* 4.9 0.2 - - - +
344X PRO* 3.3 51.8 + - - +
345X GLN* 4.5 14.2 - - - +
346X VAL 6.0 0.4 - - - +
369X GLY* 3.1 26.5 + - - +
370X ARG* 2.9 24.6 + - - +
371X TYR* 3.3 8.8 + - - +
372X GLY* 1.3 83.0 - - - +
374X LYS* 1.3 63.0 + - - +
375X GLY 3.7 0.9 + - - -
1413X ANP 4.1 10.7 + - - -
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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