Contacts of the helix formed by residues 465 - 470 (chain B) in PDB entry 5J3V
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 TYR 465 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B LEU* 2.3 50.5 + - + +
424B ILE* 4.3 1.0 - - - +
425B ALA* 3.6 26.0 + - + -
429B MET* 3.7 29.4 - - + -
432B MET* 4.1 18.9 - - + +
436B LEU* 3.7 29.4 - - + -
440B ILE* 4.1 23.8 - - + -
443B LEU* 5.3 0.4 - - + -
461B THR* 3.1 36.1 - - + -
462B LEU* 3.4 7.2 + - - +
463B SER 3.3 0.4 - - - -
464B ARG* 1.3 76.9 - - - +
466B ALA* 1.3 61.3 + - - +
467B HIS 3.2 3.1 - - - +
468B TRP* 3.3 11.6 + - + +
469B VAL* 3.2 16.3 + - - +
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Residues in contact with ALA 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B LEU 3.6 5.0 + - - +
463B SER* 3.5 23.5 + - - +
464B ARG 3.4 2.4 - - - -
465B TYR* 1.3 78.2 - - - +
467B HIS* 1.3 61.9 + - - +
469B VAL* 3.8 6.8 - - - +
470B VAL* 3.4 28.4 + - - +
506B THR* 4.5 3.4 - - + -
507B LEU* 4.0 26.4 - - + +
510B GLU* 4.0 17.2 - - + +
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Residues in contact with HIS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B MET* 6.2 7.6 - - + -
464B ARG 5.3 1.1 + - - +
465B TYR* 3.2 1.7 - - - -
466B ALA* 1.3 79.9 - - - +
468B TRP* 1.3 53.2 + - - +
470B VAL* 3.3 12.9 - - + +
471B SER* 2.7 36.8 + - - -
510B GLU* 3.8 28.9 + - - +
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Residues in contact with TRP 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B MET* 5.2 8.2 - - - -
433B ILE* 3.6 31.8 - - + +
436B LEU* 3.4 32.8 - - + -
437B PRO* 3.9 30.3 - - + -
440B ILE* 3.7 26.0 - - + -
465B TYR* 3.3 10.3 + - + +
467B HIS* 1.3 78.3 - - - +
469B VAL* 1.3 73.1 + - + +
471B SER* 3.1 18.0 + - - -
472B GLN* 3.1 48.5 - - + +
477B TYR* 3.6 41.7 - + - -
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ILE* 4.4 19.1 - - + -
462B LEU* 4.9 1.8 - - + +
465B TYR 3.2 18.6 + - - +
466B ALA* 3.8 8.1 - - - +
467B HIS 3.4 0.4 - - - -
468B TRP* 1.3 94.0 - - + +
470B VAL* 1.3 58.8 + - + +
471B SER 3.1 0.2 - - - -
472B GLN* 3.2 25.3 + - - +
477B TYR* 3.8 11.0 - - + +
478B LEU* 3.7 39.4 + - + +
481B LEU* 3.9 27.1 - - + -
507B LEU* 4.9 0.9 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ALA 3.4 13.7 - - - +
467B HIS* 3.3 22.4 - - - +
469B VAL* 1.3 73.6 - - - +
471B SER* 1.3 59.4 + - - +
472B GLN 3.1 10.4 + - - +
478B LEU* 3.9 24.7 - - + -
507B LEU* 4.1 7.0 - - + -
510B GLU* 3.9 23.3 - - + +
511B ALA* 3.7 28.3 - - + +
514B GLU* 3.9 22.6 - - - +
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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