Contacts of the helix formed by residues 513 - 525 (chain I) in PDB entry 6NZD
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 513 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510I GLN* 4.9 7.4 - - + +
511I LYS 3.1 7.9 + - - +
512I ASP* 1.3 80.1 - - - +
514I VAL* 1.3 61.5 + - - +
515I GLN 3.2 1.5 - - - +
516I ARG* 3.3 7.8 + - - +
517I ILE* 2.9 29.0 + - - +
1001I THR* 6.3 3.1 - - - -
1004I TRP* 6.1 6.1 - - + -
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Residues in contact with VAL 514 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506I VAL 4.8 11.5 - - - +
509I LYS* 5.6 7.6 - - + -
510I GLN 4.3 12.9 + - - +
512I ASP 4.7 0.6 - - - +
513I LEU* 1.3 78.3 - - - +
515I GLN* 1.3 57.5 + - - +
517I ILE* 3.4 6.9 + - - +
518I LEU* 2.9 30.0 + - - +
951I TYR* 3.7 31.6 - - + +
963I GLY* 5.3 4.3 - - - -
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Residues in contact with GLN 515 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512I ASP* 5.3 7.5 - - - +
513I LEU 3.2 4.1 - - - +
514I VAL* 1.3 79.9 - - - +
516I ARG* 1.3 56.8 + - - +
518I LEU* 3.3 6.4 + - - +
519I TYR* 2.9 41.5 + - + -
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Residues in contact with ARG 516 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420I GLU* 5.4 2.7 - - + +
424I LEU* 3.9 28.7 - - + +
434I PHE* 6.3 0.7 - - - -
512I ASP 4.6 6.0 + - - +
513I LEU* 3.3 16.1 + - - +
515I GLN* 1.3 76.0 - - - +
517I ILE* 1.3 60.7 + - - +
519I TYR* 3.3 8.2 + - - +
520I VAL* 2.9 29.1 + - - +
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Residues in contact with ILE 517 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434I PHE* 6.1 1.8 - - - -
506I VAL* 4.3 26.4 - - + +
513I LEU 2.9 17.0 + - - +
514I VAL* 3.8 7.0 - - - +
516I ARG* 1.3 76.7 - - - +
518I LEU* 1.3 58.0 + - - +
520I VAL* 3.4 6.6 + - - +
521I LEU* 2.9 30.1 + - - +
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Residues in contact with LEU 518 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395I ILE* 5.3 8.3 - - + -
514I VAL 2.9 18.3 + - - +
515I GLN* 3.6 8.1 - - - +
516I ARG 3.3 0.2 - - - -
517I ILE* 1.3 75.2 - - - +
519I TYR* 1.3 62.0 + - + +
521I LEU* 3.8 4.7 - - - +
522I THR* 2.9 31.7 + - - -
949I ALA* 5.2 14.8 - - + -
950I GLY 6.1 1.6 - - - +
961I LEU* 6.0 3.6 - - + -
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Residues in contact with TYR 519 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395I ILE* 5.6 8.7 - - + -
396I ALA 5.0 5.7 + - - -
397I GLU 4.7 13.4 + - - -
398I PRO* 6.3 1.6 - - + -
399I VAL* 4.4 11.1 - - + +
416I ARG 6.3 0.4 - - - -
417I PHE* 4.1 33.4 - + + -
420I GLU* 4.9 16.8 - - + -
515I GLN* 2.9 29.5 + - + +
516I ARG* 3.3 8.3 + - - +
518I LEU* 1.3 79.3 - - + +
520I VAL* 1.3 56.5 + - - +
522I THR* 3.4 5.0 + - - -
523I TYR* 2.9 29.6 + - - +
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Residues in contact with VAL 520 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421I PHE* 4.9 12.6 - - + -
434I PHE* 3.7 32.3 - - + -
516I ARG 2.9 16.5 + - - +
517I ILE* 3.8 5.8 - - - +
519I TYR* 1.3 76.3 - - - +
521I LEU* 1.3 59.4 + - - +
523I TYR* 3.4 4.5 + - - +
524I PHE* 2.9 39.7 + - + +
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Residues in contact with LEU 521 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441I VAL* 5.9 4.0 - - - -
445I HIS* 5.3 4.5 + - + -
504I THR* 5.9 4.9 - - - -
506I VAL* 6.0 4.7 - - + -
517I ILE 2.9 18.9 + - - +
518I LEU* 4.0 4.5 - - - +
520I VAL* 1.3 75.8 - - - +
522I THR* 1.3 57.4 + - - +
524I PHE* 3.8 3.3 - - - -
525I LEU* 2.9 33.1 + - - +
961I LEU* 4.2 24.7 - - + -
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Residues in contact with THR 522 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398I PRO* 3.9 27.4 - - - +
399I VAL* 4.2 6.7 - - - -
400I TRP* 3.6 14.7 + - - +
518I LEU 2.9 20.5 + - - -
519I TYR* 3.9 5.2 - - - -
521I LEU* 1.3 75.5 - - - +
523I TYR* 1.3 61.1 + - - +
525I LEU* 3.6 14.9 - - - +
948I LEU* 5.7 8.5 - - - -
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Residues in contact with TYR 523 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399I VAL* 3.8 16.6 - - + +
400I TRP* 4.2 34.2 - + - +
403I MET* 5.6 4.0 - - + -
417I PHE* 3.5 38.8 - + + -
421I PHE* 5.0 6.5 - + + -
519I TYR 2.9 16.7 + - - +
520I VAL* 3.9 4.5 - - - +
522I THR* 1.3 77.8 - - - +
524I PHE* 1.3 87.0 + + - +
525I LEU 3.3 11.4 - - - +
1052I ILE* 4.8 15.6 + - + +
1055I LEU* 5.1 12.9 - - + +
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Residues in contact with PHE 524 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421I PHE* 4.4 24.7 - + - -
434I PHE* 5.0 8.5 - + - -
438I LEU* 4.1 31.4 - - + -
441I VAL* 4.6 18.1 - - + +
442I LEU* 5.4 13.2 - - + +
445I HIS* 4.5 12.9 - - - +
448I TRP* 4.6 18.9 - - - +
520I VAL* 2.9 23.4 + - + +
521I LEU* 3.8 2.5 - - - +
523I TYR* 1.3 103.3 - + - +
525I LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 525 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400I TRP* 3.9 8.0 - - - +
445I HIS* 3.9 26.2 - - + +
491I LEU* 5.7 5.4 - - - +
521I LEU 2.9 19.4 + - - +
522I THR* 3.6 13.4 - - - +
523I TYR 3.2 12.8 - - - +
524I PHE* 1.3 78.8 - - - +
526I ARG* 1.3 64.7 + - - +
960I VAL* 6.4 1.3 - - + -
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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