Contacts of the helix formed by residues 353 - 359 (chain A) in PDB entry 1XV9
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 LEU 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 3.5 24.0 - - + -
311A ALA* 4.6 3.1 - - - -
314A SER* 3.0 32.3 - - - +
349A VAL* 2.8 18.9 + - + +
352A GLU* 1.3 79.4 - - + +
354A VAL* 1.3 57.9 + - - +
356A LYS* 3.0 5.5 + - - +
357A MET* 2.7 49.5 + - + +
421A ARG* 4.5 14.4 - - + +
424A ALA* 4.7 1.6 - - + -
425A LEU* 3.8 27.8 - - + +
428A ILE* 3.6 27.8 - - + -
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 3.2 36.3 - - - +
317A SER* 3.8 27.8 - - - +
318A ILE* 4.1 9.7 - - - +
320A VAL 5.2 0.2 - - - +
323A GLY 5.6 0.4 - - - +
324A ILE* 4.7 4.5 - - + -
349A VAL* 3.4 16.4 + - + +
350A LEU* 3.8 19.1 - - + +
353A LEU* 1.3 73.3 - - - +
355A SER* 1.3 73.4 + - - +
357A MET* 3.0 15.8 + - - +
358A ARG* 3.0 30.1 + - - +
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Residues in contact with SER 355 (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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350A LEU 2.7 25.0 + - - -
351A THR* 3.9 16.6 + - - +
354A VAL* 1.3 78.9 - - - +
356A LYS* 1.3 63.8 + - - +
358A ARG* 3.1 14.3 + - - +
359A ASP* 2.9 38.3 + - - +
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Residues in contact with LYS 356 (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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350A LEU 4.4 0.2 + - - -
351A THR 4.0 10.9 + - - +
352A GLU 3.3 19.1 - - - +
353A LEU 3.0 9.5 + - - +
355A SER* 1.3 82.3 + - - +
357A MET* 1.3 63.8 + - - +
359A ASP* 3.6 14.6 + - + +
360A MET* 3.5 17.7 - - - +
421A ARG* 3.7 35.8 - - + +
278B ARG* 3.7 13.0 - - - +
282B ASP* 3.1 37.3 + - - -
286B GLU* 4.6 10.7 + - - -
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Residues in contact with MET 357 (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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311A ALA* 3.9 17.0 - - + +
314A SER* 3.6 26.9 - - - +
315A HIS* 3.3 36.6 - - + +
318A ILE* 3.9 13.9 - - + -
353A LEU* 2.7 34.0 + - + +
354A VAL 3.5 4.3 - - - +
356A LYS* 1.3 72.7 - - + +
358A ARG* 1.3 63.6 + - - +
360A MET* 3.0 12.1 + - - +
361A GLN 3.0 19.1 + - - -
362A MET* 3.8 36.3 + - + -
367A LEU* 4.7 0.9 - - + -
421A ARG* 5.8 6.3 - - + -
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Residues in contact with ARG 358 (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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318A ILE* 3.3 36.3 + - + +
320A VAL 2.9 28.5 + - - -
321A LYS* 3.7 33.5 - - - +
322A ASP 4.9 1.4 - - - +
354A VAL* 3.0 26.7 + - - +
355A SER* 3.3 15.9 + - - +
357A MET* 1.3 72.1 - - - +
359A ASP* 1.3 67.8 + - - +
360A MET 2.8 11.3 + - - -
361A GLN* 3.3 15.2 + - - +
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Residues in contact with ASP 359 (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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355A SER* 2.9 28.5 + - - +
356A LYS* 3.7 14.2 - - + +
357A MET 3.3 0.4 - - - -
358A ARG* 1.3 87.2 + - - +
360A MET* 1.3 61.6 + - - +
417A LYS* 5.9 1.4 + - - -
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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