Contacts of the helix formed by residues 520 - 528 (chain B) in PDB entry 4DBG
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 520 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509B PHE* 4.9 0.9 - - + -
518B GLU* 4.1 10.9 - - - +
519B VAL* 1.4 92.0 - - + +
521B LEU* 1.3 64.0 + - - +
522B GLN* 4.5 3.1 - - + +
523B TRP* 3.3 28.9 + - + +
524B LEU* 3.5 13.9 + - - +
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Residues in contact with LEU 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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505B PRO* 3.7 40.4 - - + +
506B GLU* 3.7 24.9 - - - +
509B PHE* 3.8 34.0 - - + -
519B VAL 3.1 3.6 + - - -
520B PRO* 1.3 68.8 - - - +
522B GLN* 1.3 79.0 + - + +
523B TRP 3.3 0.2 + - - -
524B LEU* 3.4 5.6 + - + +
525B ARG* 3.2 21.9 + - + +
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Residues in contact with GLN 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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520B PRO* 3.3 4.1 - - + +
521B LEU* 1.3 95.0 - - + +
523B TRP* 1.3 58.8 + - - +
525B ARG* 3.4 32.3 + - - +
526B SER* 3.0 28.1 + - - -
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Residues in contact with TRP 523 (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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495B ILE* 5.7 5.2 - - + -
519B VAL* 4.3 14.6 - - + -
520B PRO* 3.3 27.5 + - + +
521B LEU 3.2 0.6 - - - -
522B GLN* 1.3 76.9 - - - +
524B LEU* 1.3 85.3 + - + +
526B SER* 3.1 12.2 + - - -
527B GLU* 3.0 63.3 + - + +
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Residues in contact with LEU 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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495B ILE* 4.6 13.9 - - + -
505B PRO* 3.7 31.9 - - + +
508B ILE* 4.1 19.7 - - + -
509B PHE* 3.9 18.2 - - + +
519B VAL* 3.8 26.9 - - + -
520B PRO 3.5 9.6 + - - +
521B LEU* 3.4 8.0 + - - +
523B TRP* 1.3 97.6 - - + +
525B ARG* 1.3 67.1 + - - +
527B GLU* 3.2 5.2 + - + +
528B LEU* 3.0 35.4 + - + +
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Residues in contact with ARG 525 (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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505B PRO* 4.1 21.9 - - + +
521B LEU* 3.2 13.4 + - + +
522B GLN* 3.4 36.1 + - - +
524B LEU* 1.3 78.4 - - - +
526B SER* 1.3 58.9 + - - +
528B LEU* 3.1 24.5 + - - +
529B PRO 4.8 0.9 - - - +
530B TYR* 5.1 4.0 + - - -
533B GLU* 3.2 42.5 + - - +
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Residues in contact with SER 526 (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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522B GLN 3.0 13.7 + - - -
523B TRP* 3.1 19.6 + - - -
524B LEU 3.2 0.2 - - - -
525B ARG* 1.3 76.9 - - - +
527B GLU* 1.3 64.4 + - - +
528B LEU 4.0 3.5 - - - +
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Residues in contact with GLU 527 (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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495B ILE* 5.2 12.2 - - + +
523B TRP* 3.0 64.2 + - + +
524B LEU* 3.2 6.7 + - + +
526B SER* 1.3 81.0 + - - +
528B LEU* 1.3 67.2 + - + +
529B PRO* 4.0 1.7 - - - +
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Residues in contact with LEU 528 (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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494B MET 4.9 0.4 - - - +
495B ILE* 3.7 34.5 - - + -
503B ALA* 3.8 35.4 - - + +
505B PRO* 3.7 42.2 - - + -
508B ILE* 5.0 3.6 - - + -
524B LEU* 3.0 21.3 + - + +
525B ARG 3.1 14.6 + - - +
526B SER 4.0 4.0 - - - +
527B GLU* 1.3 80.3 - - + +
529B PRO* 1.3 82.0 - - + +
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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