Contacts of the helix formed by residues 361 - 369 (chain A) in PDB entry 2NVU
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 VAL 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A ILE* 4.8 4.7 - - + +
307A LEU* 4.7 11.4 - - + -
310A ALA* 3.2 27.8 - - + -
357A VAL 3.3 11.9 - - - +
358A GLY* 2.9 17.9 + - - +
360A HIS* 1.3 77.2 - - - +
362A ALA* 1.3 61.2 + - + +
363A LYS 3.0 1.3 - - - -
364A LEU* 2.8 7.8 + - - +
365A LEU* 2.6 42.7 + - + +
372A PRO 5.3 3.1 - - - +
375A ILE* 4.7 25.4 - - + +
380A LEU* 4.4 15.9 - - + -
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Residues in contact with ALA 362 (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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358A GLY 3.3 9.3 + - - +
359A ASN* 4.7 10.1 - - - +
361A VAL* 1.3 83.8 - - + +
363A LYS* 1.3 61.6 - - - +
365A LEU* 4.3 1.8 - - - +
366A GLN* 3.1 36.7 + - - +
372A PRO* 4.2 25.8 - - + +
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Residues in contact with LYS 363 (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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359A ASN 3.4 20.2 + - - +
360A HIS* 3.5 14.5 - - + +
362A ALA* 1.3 80.0 - - - +
364A LEU* 1.3 61.6 + - + +
366A GLN* 4.0 4.8 + - - +
367A SER* 3.0 22.9 + - - -
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Residues in contact with LEU 364 (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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297A ILE* 4.9 11.9 - - + -
306A ILE* 3.9 23.3 - - + +
309A ARG* 3.1 45.8 - - + +
310A ALA* 4.2 4.0 - - - +
313A GLU* 5.7 5.6 - - + -
360A HIS 3.3 15.3 - - - +
361A VAL* 2.8 8.8 + - - +
363A LYS* 1.3 84.6 - - + +
365A LEU* 1.3 65.7 + - - +
366A GLN 3.1 1.6 - - - -
367A SER* 2.7 29.4 + - - +
368A ILE* 2.9 25.8 + - + +
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Residues in contact with LEU 365 (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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306A ILE* 3.7 36.8 - - + -
361A VAL* 2.6 26.1 + - + +
362A ALA 3.5 1.1 + - - +
364A LEU* 1.3 72.6 - - - +
366A GLN* 1.3 56.8 + - - +
368A ILE* 4.4 0.7 - - - +
369A GLY 2.8 20.6 + - - -
370A GLN* 2.7 46.0 + - + +
371A ALA 3.0 22.2 - - - +
372A PRO* 3.1 26.9 - - + +
374A SER* 4.5 3.8 - - - +
375A ILE* 4.3 25.8 - - + +
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Residues in contact with GLN 366 (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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362A ALA* 3.1 24.3 + - - +
363A LYS* 4.2 5.3 - - - +
365A LEU* 1.3 75.2 - - - +
367A SER* 1.3 56.9 + - - +
368A ILE 3.5 0.4 - - - -
369A GLY* 4.2 4.8 + - - +
370A GLN 4.6 1.1 - - - -
372A PRO* 4.2 28.7 - - + +
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Residues in contact with SER 367 (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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363A LYS 3.0 10.2 + - - -
364A LEU* 2.7 38.0 + - - +
366A GLN* 1.3 78.9 - - - +
368A ILE* 1.3 73.4 + - - +
369A GLY 3.6 0.4 - - - -
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Residues in contact with ILE 368 (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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297A ILE* 3.7 30.5 - - + -
298A THR* 3.5 15.9 - - - +
299A LYS* 3.2 48.4 - - - +
301A THR 5.9 0.2 - - - +
306A ILE* 5.3 10.3 - - + -
364A LEU* 2.9 19.6 + - + +
365A LEU* 4.1 3.8 - - + +
367A SER* 1.3 105.4 - - - +
369A GLY* 1.3 56.0 + - - +
370A GLN* 3.4 27.1 + - + -
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Residues in contact with GLY 369 (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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299A LYS* 5.7 1.6 - - - -
365A LEU 2.8 5.7 + - - -
366A GLN* 4.2 4.6 - - - -
367A SER 3.6 2.2 - - - +
368A ILE* 1.3 79.2 - - - +
370A GLN* 1.3 70.7 + - - +
371A ALA 3.7 0.3 + - - -
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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