Contacts of the helix formed by residues 515 - 522 (chain B) in PDB entry 6WCZ
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 ARG 515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508B VAL* 5.9 0.2 - - - +
511B LEU* 3.6 33.0 - - + +
514B GLN* 1.3 102.1 + - + +
516B LEU* 1.3 64.0 + - - +
517B GLY 3.3 2.9 - - - -
518B TYR* 3.2 30.9 + - + +
519B ILE* 3.6 5.7 + - - +
818B VAL* 3.0 30.1 + - - +
819B TRP* 5.8 1.2 - - - -
822B GLU* 2.6 43.4 + - - +
823B ASN* 3.1 25.1 - - - +
824B ASP* 4.3 5.9 + - - +
825B HIS* 4.7 22.0 + - + -
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Residues in contact with LEU 516 (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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508B VAL* 3.7 37.5 - - + -
511B LEU* 3.7 7.0 - - + -
512B GLY 3.4 23.3 - - - +
513B LEU* 3.7 16.4 - - + -
514B GLN 3.7 1.2 - - - -
515B ARG* 1.3 78.5 - - - +
517B GLY* 1.3 54.6 + - - +
519B ILE* 2.6 32.6 + - + +
520B LEU* 3.1 11.6 + - - +
710B PHE* 4.2 19.0 - - + -
711B CYS* 6.2 3.4 - - + -
715B PHE* 3.6 24.7 - - + -
800B HIS* 3.8 19.7 - - + +
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Residues in contact with GLY 517 (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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514B GLN 5.4 1.0 + - - -
515B ARG 3.3 0.8 - - - -
516B LEU* 1.3 78.4 - - - +
518B TYR* 1.3 57.7 + - - +
520B LEU* 3.5 10.2 + - - +
521B GLU* 2.9 30.3 + - - +
705B TRP* 5.0 0.7 - - - -
715B PHE* 3.6 24.6 - - - -
727B VAL* 3.6 24.0 - - - +
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Residues in contact with TYR 518 (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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514B GLN 4.9 3.8 - - - -
515B ARG* 3.2 28.1 + - - +
516B LEU 3.2 0.4 - - - -
517B GLY* 1.3 75.5 - - - +
519B ILE* 1.3 60.9 + - + +
521B GLU* 3.8 14.8 - - - +
522B GLU* 2.9 32.7 + - - +
725B SER* 2.9 31.6 + - - -
726B ILE* 3.5 5.0 - - - +
727B VAL* 3.1 46.2 + - + -
819B TRP* 5.6 3.4 - + - -
823B ASN* 5.5 5.2 - - - -
825B HIS* 3.8 56.6 + + + +
826B MET* 5.4 1.6 + - - +
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Residues in contact with ILE 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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501B ARG* 3.5 31.6 - - + +
508B VAL* 4.0 30.7 - - + -
515B ARG 3.6 3.2 + - - +
516B LEU* 2.6 34.6 + - + +
518B TYR* 1.3 74.8 - - - +
520B LEU* 1.3 59.0 + - + +
522B GLU* 3.3 26.3 - - + +
523B MET* 3.0 30.8 + - + +
661B ALA* 4.3 16.8 - - + -
710B PHE* 6.1 2.2 - - + -
825B HIS* 5.6 5.2 - - + +
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Residues in contact with LEU 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 LEU 3.1 7.9 + - - +
517B GLY* 3.7 14.4 - - - +
519B ILE* 1.3 80.3 - - + +
521B GLU* 1.3 62.9 + - - +
523B MET* 2.9 19.0 + - + +
524B ASN* 2.9 23.7 + - - +
531B MET* 5.3 10.9 - - - +
668B VAL* 5.6 9.2 - - + -
705B TRP* 3.5 45.1 - - + +
708B VAL* 4.5 15.3 - - + +
710B PHE* 3.7 33.7 - - + -
715B PHE* 4.0 15.9 - - + -
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Residues in contact with GLU 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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517B GLY 2.9 21.4 + - - +
518B TYR* 3.9 18.7 - - + +
520B LEU* 1.3 81.0 - - - +
522B GLU* 1.3 59.3 + - - +
524B ASN* 3.2 21.4 + - + +
525B ARG* 3.6 18.6 + - - -
705B TRP* 3.6 36.1 - - + -
717B LYS* 4.3 15.2 + - - +
727B VAL* 5.1 7.2 - - + -
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Residues in contact with GLU 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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518B TYR 2.9 19.7 + - - +
519B ILE* 3.3 28.3 - - + +
521B GLU* 1.3 77.5 + - - +
523B MET* 1.3 63.7 + - + +
524B ASN 3.1 0.9 - - - +
525B ARG* 4.0 18.1 + - + +
526B ALA 5.1 0.7 + - - -
825B HIS* 4.7 16.8 + - - -
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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