Contacts of the helix formed by residues 519 - 530 (chain A) in PDB entry 6WLY
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 PRO 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A ASN 4.5 2.2 - - - +
518A GLU* 1.3 97.7 - - + +
520A PRO* 1.3 76.2 - - + +
521A LEU* 3.3 3.4 - - + +
522A LYS* 2.9 20.9 + - + +
523A ALA* 2.9 19.4 + - - +
505B LYS* 5.9 0.4 - - + -
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Residues in contact with PRO 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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479A PRO* 3.7 27.6 - - + +
480A TYR* 3.4 28.3 - - + +
519A PRO* 1.3 86.0 - - + +
521A LEU* 1.3 59.0 + - + +
523A ALA* 3.3 2.8 + - - +
524A MET* 3.0 33.6 + - - +
505B LYS* 4.3 16.6 - - + +
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Residues in contact with LEU 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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519A PRO* 3.3 3.0 - - + +
520A PRO* 1.3 77.3 - - + +
522A LYS* 1.3 66.2 + - - +
524A MET* 3.4 25.0 + - + +
525A LYS* 3.2 21.1 + - - +
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Residues in contact with LYS 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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518A GLU* 3.2 33.9 + - + +
519A PRO* 2.9 26.9 + - + +
521A LEU* 1.3 78.4 - - - +
523A ALA* 1.3 61.6 + - - +
525A LYS* 3.3 9.1 + - + +
526A MET* 3.1 49.2 + - + +
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Residues in contact with ALA 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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480A TYR* 3.5 40.4 - - + +
515A TYR* 3.7 24.2 - - + +
518A GLU* 4.4 1.3 - - + +
519A PRO 2.9 8.2 + - - +
520A PRO 3.3 5.4 + - - +
522A LYS* 1.3 76.2 - - - +
524A MET* 1.3 56.6 + - - +
526A MET* 3.2 6.6 + - - +
527A ILE* 2.9 38.9 + - + +
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Residues in contact with MET 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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475A LEU* 4.5 18.2 - - + -
479A PRO* 3.8 39.5 - - + +
482A MET* 4.0 18.8 - - + +
487A ILE* 3.7 35.5 - - + +
520A PRO 3.0 21.6 + - - +
521A LEU* 3.7 26.7 - - + +
522A LYS 3.2 0.2 - - - -
523A ALA* 1.3 73.7 - - - +
525A LYS* 1.3 60.7 + - - +
527A ILE* 3.3 3.1 + - - +
528A ARG* 2.9 30.5 + - - +
509B VAL* 5.7 2.0 - - + -
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Residues in contact with LYS 525 (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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487A ILE* 5.5 0.2 - - - -
521A LEU 3.2 11.2 + - - +
522A LYS* 3.3 11.2 + - - +
524A MET* 1.3 78.0 - - - +
526A MET* 1.3 58.6 + - + +
528A ARG* 3.3 29.4 - - - +
529A ASP* 2.9 46.8 + - - +
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Residues in contact with MET 526 (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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515A TYR* 3.5 46.1 + - + -
518A GLU* 4.3 15.7 - - + +
522A LYS* 3.1 41.6 + - + +
523A ALA 3.2 5.1 + - - +
525A LYS* 1.3 75.7 - - + +
527A ILE* 1.3 62.1 + - - +
529A ASP* 5.0 0.2 - - - -
530A ASN* 2.9 57.1 + - - +
531A LEU 5.1 0.3 - - - +
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Residues in contact with ILE 527 (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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479A PRO 3.5 25.1 - - - +
480A TYR* 3.8 20.4 - - + +
482A MET 3.5 20.4 - - - +
484A PRO* 3.9 13.5 - - + +
487A ILE* 3.6 10.5 - - + -
499A TRP* 4.3 18.9 - - + +
503A ILE* 6.1 1.6 - - + -
514A PRO* 5.8 1.1 - - + +
515A TYR* 4.0 19.7 - - + -
523A ALA* 2.9 26.7 + - + +
524A MET* 3.6 7.0 - - - +
526A MET* 1.3 78.4 - - - +
528A ARG* 1.3 60.9 + - - +
530A ASN 3.8 3.2 - - - +
531A LEU 6.1 0.4 - - - -
533A PRO* 6.0 6.1 - - + -
555A ARG* 3.1 17.0 + - - -
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Residues in contact with ARG 528 (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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484A PRO* 4.4 7.4 - - - -
487A ILE* 3.9 20.6 + - + +
488A SER* 3.3 35.0 - - - +
524A MET 2.9 16.8 + - - +
525A LYS* 3.3 30.1 - - - +
527A ILE* 1.3 80.0 - - - +
529A ASP* 1.3 89.0 + - - +
555A ARG* 2.8 29.3 + - - +
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Residues in contact with ASP 529 (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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525A LYS* 2.9 32.4 + - + +
528A ARG* 1.3 116.6 + - - +
530A ASN* 1.3 70.3 + - - +
555A ARG* 4.6 2.8 + - - -
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Residues in contact with ASN 530 (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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515A TYR* 4.2 8.9 + - - +
526A MET* 2.9 49.6 + - - +
527A ILE 3.8 4.3 - - - +
529A ASP* 1.3 88.9 - - - +
531A LEU* 1.3 76.6 + - + +
532A PRO* 4.6 0.2 - - - +
555A ARG* 3.0 23.5 + - - -
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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