Contacts of the helix formed by residues 514 - 525 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A MET* 4.2 17.0 - - - +
511A ASN 4.9 1.0 + - - -
512A ALA 3.1 0.6 - - - -
513A SER* 1.3 104.8 + - - +
515A LEU* 1.3 65.5 + - - +
516A ASP* 3.3 7.4 - - - -
517A LYS* 3.1 28.6 - - + +
518A VAL* 3.3 9.3 - - + +
654A VAL* 4.7 4.5 - - + +
656A HIS* 3.1 40.0 + - + +
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ALA* 3.2 19.4 + - + +
513A SER 3.6 0.2 - - - -
514A ASN* 1.3 78.2 - - - +
516A ASP* 1.3 64.5 + - - +
517A LYS 3.2 0.2 + - - -
518A VAL* 3.2 4.7 + - + +
519A LEU* 3.1 42.3 + - + +
535A SER* 3.8 23.1 - - - +
595A PRO* 4.1 12.8 - - + -
596A LYS* 3.8 29.6 - - + -
624A LEU* 4.0 26.5 - - + -
654A VAL* 4.2 22.2 - - + +
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Residues in contact with ASP 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ALA 4.9 0.6 + - - -
513A SER 4.1 5.7 - - - +
514A ASN* 3.6 13.5 - - - -
515A LEU* 1.3 75.5 - - - +
517A LYS* 1.3 79.5 + - - +
519A LEU* 3.6 10.6 + - - +
520A THR* 3.3 27.4 + - - +
596A LYS* 6.0 4.3 - - - +
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Residues in contact with LYS 517 (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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514A ASN* 3.1 26.0 - - + +
516A ASP* 1.3 84.4 + - - +
518A VAL* 1.3 71.8 + - - +
519A LEU 3.2 1.8 - - - -
520A THR* 2.8 21.1 + - - +
521A ASP* 3.0 32.1 + - - +
656A HIS* 3.2 38.7 + - - -
657A LEU* 3.6 15.9 + - - +
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Residues in contact with VAL 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 6.2 2.7 - - - +
514A ASN 3.3 18.8 - - - +
515A LEU* 3.2 14.3 + - + +
517A LYS* 1.3 91.9 - - + +
519A LEU* 1.3 61.8 + - - +
521A ASP* 3.6 8.6 - - - +
522A ILE* 2.9 34.1 + - + +
535A SER* 3.4 38.6 - - - +
654A VAL* 4.6 2.9 - - + -
655A LEU 3.5 22.0 - - - +
656A HIS* 4.8 4.3 - - - +
657A LEU 5.9 0.2 - - - +
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Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LEU* 3.1 38.7 + - + +
516A ASP* 3.8 8.7 - - - +
517A LYS 3.2 0.2 - - - -
518A VAL* 1.3 82.2 - - - +
520A THR* 1.3 60.4 + - + +
522A ILE* 3.4 11.7 + - + +
523A LYS* 3.1 20.3 + - - +
535A SER* 3.7 24.5 - - - +
593A HIS 4.0 5.8 - - - +
594A ASN* 3.8 27.6 - - + +
596A LYS* 3.8 27.6 - - + +
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Residues in contact with THR 520 (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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516A ASP 3.3 13.2 + - - +
517A LYS* 2.8 26.6 + - - +
519A LEU* 1.3 73.9 - - + +
521A ASP* 1.3 63.7 + - - +
523A LYS* 3.0 14.6 + - + +
524A ALA* 2.8 29.6 + - - +
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Residues in contact with ASP 521 (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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388A ARG* 6.0 3.6 - - - +
517A LYS* 3.0 33.0 + - - +
518A VAL* 3.6 8.3 - - - +
520A THR* 1.3 78.0 + - - +
522A ILE* 1.3 60.4 + - + +
524A ALA* 3.2 6.0 + - - +
525A ASP* 2.8 33.0 + - - +
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Residues in contact with ILE 522 (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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388A ARG* 4.4 12.1 - - - +
518A VAL* 2.9 22.3 + - + +
519A LEU* 3.5 11.7 - - + +
520A THR 3.3 0.2 - - - -
521A ASP* 1.3 76.6 - - + +
523A LYS* 1.3 62.8 + - - +
525A ASP* 3.4 20.8 - - - +
533A LEU* 4.0 33.4 - - + +
534A SER 3.6 38.4 - - - +
535A SER* 3.7 14.6 - - - +
593A HIS 4.4 4.5 - - - +
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Residues in contact with LYS 523 (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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519A LEU 3.1 12.9 + - - +
520A THR* 3.0 15.1 + - + +
522A ILE* 1.3 81.1 - - - +
524A ALA* 1.3 60.3 + - - +
525A ASP 3.7 0.9 + - - +
526A LYS* 3.4 19.9 - - - +
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Residues in contact with ALA 524 (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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520A THR 2.8 14.6 + - - +
521A ASP* 3.9 6.5 - - - +
523A LYS* 1.3 75.6 - - - +
525A ASP* 1.3 66.8 + - - +
526A LYS* 3.2 18.8 + - - +
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Residues in contact with ASP 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 6.1 0.7 - - - -
390A HIS* 3.4 27.1 + - - -
441A VAL* 4.4 0.9 - - - +
502A ARG* 5.4 5.7 + - - -
504A GLU* 4.9 2.6 - - - +
521A ASP 2.8 17.9 + - - +
522A ILE 3.4 15.7 - - - +
523A LYS 3.4 1.1 - - - +
524A ALA* 1.3 75.8 - - - +
526A LYS* 1.3 63.3 + - - +
527A ASP* 3.6 28.6 + - - +
533A LEU* 4.0 22.3 - - + +
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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
------------------------------------------------------------
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