Contacts of the helix formed by residues 476 - 483 (chain B) in PDB entry 4NPJ
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 476 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387B LEU* 3.6 37.2 - - + -
420B VAL* 4.2 13.5 - - + -
446B VAL* 4.3 12.8 - - + -
452B GLN* 3.2 55.8 + - + +
453B GLU 4.1 5.4 - - - +
454B LEU* 3.9 20.0 - - + +
474B ILE 3.3 1.0 + - - +
475B ASP* 1.3 69.5 - - - +
477B ILE* 1.3 60.6 + - + +
479B VAL* 2.8 13.4 + - + +
480B GLU* 2.8 42.6 + - + +
505B TRP* 5.5 2.5 - - + -
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Residues in contact with ILE 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B LYS* 5.3 7.0 - - - +
449B HIS 5.4 7.6 - - - +
451B GLY* 5.5 8.7 - - - +
452B GLN* 5.7 4.9 - - + +
475B ASP* 4.4 13.0 - - + +
476B LEU* 1.3 78.9 - - + +
478B GLU* 1.3 73.4 + - + +
480B GLU* 3.4 20.8 + - - +
481B LYS* 3.0 27.0 + - - +
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Residues in contact with GLU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B ILE* 5.8 2.1 - - + +
475B ASP* 3.2 32.4 + - + +
476B LEU 3.1 0.6 - - - -
477B ILE* 1.3 84.3 - - + +
479B VAL* 1.3 61.2 + - + +
481B LYS* 3.2 7.0 + - - +
482B GLU* 2.8 48.6 + - + +
485B LEU* 6.4 0.2 - - + -
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Residues in contact with VAL 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.7 28.9 - - + -
454B LEU* 6.0 0.2 - - + -
474B ILE* 3.8 20.9 - - + -
475B ASP 3.5 13.9 - - - +
476B LEU* 2.8 18.0 + - + +
478B GLU* 1.3 74.4 - - + +
480B GLU* 1.3 54.9 + - + +
482B GLU* 3.5 0.6 - - - +
483B ARG* 2.6 36.4 + - - +
485B LEU* 4.1 16.2 - - + -
503B LEU* 3.9 28.5 - - + +
505B TRP* 4.2 8.9 - - + +
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Residues in contact with GLU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B LYS* 3.7 31.5 + - - +
446B VAL* 4.3 4.9 - - - +
476B LEU* 2.8 27.7 + - - +
477B ILE* 3.5 18.9 + - - +
479B VAL* 1.3 75.4 - - - +
481B LYS* 1.3 61.3 + - - +
483B ARG* 3.0 32.4 + - - -
505B TRP* 3.5 58.1 - - + +
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Residues in contact with LYS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B ILE 3.0 15.1 + - - +
478B GLU* 3.5 10.1 - - - +
480B GLU* 1.3 79.7 - - - +
482B GLU* 1.3 68.8 + - + +
483B ARG* 3.5 10.9 + - - +
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Residues in contact with GLU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B GLU* 2.8 36.6 + - + +
479B VAL 4.0 1.8 - - - +
481B LYS* 1.3 78.8 - - + +
483B ARG* 1.3 58.1 + - - +
484B LEU* 2.7 29.1 + - - +
485B LEU* 3.2 37.4 - - + +
487B GLU* 4.5 2.6 - - - +
659B LYS* 5.8 0.7 - - - +
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Residues in contact with ARG 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B VAL* 2.6 23.4 + - - -
480B GLU* 3.0 22.7 + - - +
481B LYS* 3.5 9.6 + - - +
482B GLU* 1.3 74.3 - - - +
484B LEU* 1.3 56.0 + - - +
503B LEU 3.9 0.6 - - - +
504B GLU* 3.7 0.9 - - - -
505B TRP* 2.9 52.7 + - - +
507B THR* 3.4 23.0 + - - -
657B LEU* 3.3 8.4 - - + +
658B GLU* 3.1 42.5 + - - +
659B LYS* 4.1 20.2 - - + +
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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