Contacts of the helix formed by residues 514 - 524 (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 ASN 514 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B MET* 3.4 34.4 - - + +
511B ASN 5.1 0.8 + - - -
512B ALA 3.1 0.6 + - - -
513B SER* 1.3 84.8 + - - +
515B LEU* 1.3 61.3 + - - +
516B ASP* 3.4 7.2 - - - -
517B LYS* 3.2 28.5 - - - +
518B VAL* 3.2 11.2 - - - +
654B VAL* 4.7 3.5 - - + +
656B HIS* 3.6 35.7 + - + -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B ALA* 2.9 21.4 + - + +
513B SER 3.3 1.0 - - - -
514B ASN* 1.3 74.5 - - - +
516B ASP* 1.3 67.8 + - - +
517B LYS 3.1 3.6 + - - -
518B VAL* 3.3 19.0 - - + +
519B LEU* 3.3 31.3 + - + +
535B SER* 4.0 18.6 - - - +
595B PRO* 4.3 10.1 - - + -
596B LYS* 4.0 28.9 - - + -
624B LEU* 4.1 26.9 - - + -
654B VAL* 3.9 24.7 - - + +
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Residues in contact with ASP 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B SER 3.9 14.5 + - - +
514B ASN* 3.9 2.9 - - - -
515B LEU* 1.3 76.0 - - - +
517B LYS* 1.3 75.1 + - - +
519B LEU* 3.8 3.8 + - - +
520B THR* 3.5 19.9 + - - +
596B LYS* 4.7 17.7 - - - +
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ASN* 3.2 25.6 - - + +
516B ASP* 1.3 88.8 + - - +
518B VAL* 1.3 66.5 + - - +
519B LEU 3.2 1.8 - - - -
520B THR* 3.3 9.6 - - + +
521B ASP* 3.0 38.0 + - - +
656B HIS* 3.3 38.4 + - - -
657B LEU 4.9 3.6 + - - -
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Residues in contact with VAL 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ASN 3.2 17.5 - - - +
515B LEU* 3.3 20.8 + - + +
517B LYS* 1.3 82.7 - - + +
519B LEU* 1.3 63.2 + - - +
521B ASP* 3.4 6.7 + - - +
522B ILE* 3.0 36.1 + - + +
535B SER* 3.6 29.8 - - - +
654B VAL* 4.5 2.7 - - + -
655B LEU 3.2 27.4 - - - +
656B HIS* 4.4 13.0 - - + -
657B LEU 5.6 0.2 - - - +
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Residues in contact with LEU 519 (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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515B LEU* 3.3 27.5 + - + +
516B ASP* 4.0 3.8 - - - +
517B LYS 3.2 0.4 - - - -
518B VAL* 1.3 83.3 - - - +
520B THR* 1.3 61.6 + - - +
522B ILE* 3.2 11.3 + - + +
523B LYS* 3.1 31.9 + - + +
535B SER* 3.5 27.6 - - - +
593B HIS* 3.6 12.3 - - + +
594B ASN* 3.8 31.2 - - + +
596B LYS* 3.7 33.0 - - + +
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Residues in contact with THR 520 (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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516B ASP 3.5 8.4 + - - +
517B LYS* 3.3 23.3 - - + +
519B LEU* 1.3 76.4 - - - +
521B ASP* 1.3 72.0 + - - +
523B LYS* 3.1 11.3 + - - +
524B ALA* 2.8 28.9 + - - +
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Residues in contact with ASP 521 (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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388B ARG* 6.3 0.4 - - - +
517B LYS* 3.0 27.5 + - - +
518B VAL* 3.5 7.8 - - - +
520B THR* 1.3 85.4 - - - +
522B ILE* 1.3 61.3 + - + +
524B ALA* 3.2 18.5 + - - +
525B ASP* 3.3 14.0 + - - +
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Residues in contact with ILE 522 (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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388B ARG* 4.1 14.1 - - - +
518B VAL* 3.0 19.6 + - + +
519B LEU* 3.4 12.3 - - + +
520B THR 3.1 0.4 - - - -
521B ASP* 1.3 78.8 - - + +
523B LYS* 1.3 66.7 + - + +
525B ASP* 3.2 25.0 + - - +
533B LEU* 4.0 33.0 - - + +
534B SER 3.6 33.2 - - - +
535B SER* 3.9 13.5 - - - +
593B HIS* 4.1 23.6 - - + +
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Residues in contact with LYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B LEU* 3.1 19.6 + - - +
520B THR* 3.1 11.5 + - - +
522B ILE* 1.3 76.6 - - + +
524B ALA* 1.3 57.0 + - - +
525B ASP 3.1 5.4 - - - -
526B LYS* 3.0 28.4 + - - +
593B HIS* 3.4 30.7 + - - -
594B ASN* 5.7 6.7 - - - +
597B ARG* 5.7 6.7 - - - +
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Residues in contact with ALA 524 (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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520B THR* 2.8 15.8 + - - +
521B ASP* 3.4 14.4 - - - +
522B ILE 3.1 0.8 - - - -
523B LYS* 1.3 76.3 - - - +
525B ASP* 1.3 57.0 + - - +
526B LYS* 4.1 7.6 + - - +
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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