Contacts of the helix formed by residues 504 - 512 (chain B) in PDB entry 2JI8
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 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A GLU 5.9 0.4 - - - +
511A ALA* 2.9 35.9 + - - +
512A PHE* 5.2 0.7 - - - -
502B ARG 5.5 1.8 - - - +
503B GLY* 1.3 68.9 - - - -
505B TYR* 1.3 60.1 + - - +
506B ASP* 2.9 36.7 + - - +
507B MET* 3.0 47.1 + - + +
508B MET 3.3 0.3 + - - -
510B GLU* 5.8 0.4 + - - -
518B VAL* 3.9 14.1 - - - +
542B ASN* 3.8 5.2 - - - +
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Residues in contact with TYR 505 (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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54A ARG* 3.3 27.9 + - - -
460A MET* 3.9 5.2 - - + -
512A PHE* 3.6 29.9 - + - -
452B ASP* 4.1 11.3 + - + +
455B PHE* 3.6 34.5 - + - -
476B ILE* 3.8 19.7 - - + -
478B ASN* 3.6 24.0 - - - -
500B LEU* 5.2 1.2 - - - +
501B THR 4.1 10.5 + - - -
503B GLY 3.1 27.4 + - - -
504B ARG* 1.3 74.6 - - - +
506B ASP* 1.3 55.5 + - - +
508B MET* 3.3 11.0 + - - +
509B MET 3.0 23.2 + - - -
540B LEU* 3.5 31.5 - - + +
542B ASN* 3.6 7.9 - - - +
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Residues in contact with ASP 506 (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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504B ARG* 2.9 52.9 + - - -
505B TYR* 1.3 78.3 - - - +
507B MET* 1.3 58.1 + - - +
509B MET* 3.4 3.7 + - - +
510B GLU* 3.1 39.0 + - - +
516B GLY* 3.8 6.6 - - - -
517B TYR 3.6 32.7 - - - +
518B VAL* 3.4 13.5 - - - +
540B LEU* 3.7 11.2 - - + +
542B ASN* 3.4 10.3 + - + +
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Residues in contact with MET 507 (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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507A MET* 3.2 56.5 - - + +
510A GLU* 3.6 29.2 - - + +
511A ALA* 3.7 15.5 - - + +
504B ARG* 3.0 45.1 + - + +
506B ASP* 1.3 78.3 - - - +
508B MET* 1.3 61.3 + - - +
510B GLU* 3.4 8.6 + - - +
511B ALA* 3.0 24.6 + - - +
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Residues in contact with MET 508 (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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460A MET* 3.8 16.4 - - - +
508A MET* 3.2 52.3 - - + +
511A ALA* 3.9 6.6 - - + +
512A PHE* 3.9 17.9 - - + -
455B PHE* 4.6 5.6 - - - -
459B GLY 3.8 24.9 - - - +
460B MET* 4.1 7.2 - - - -
462B LEU* 4.1 14.4 - - + -
504B ARG 3.3 5.3 + - - +
505B TYR* 3.3 14.3 + - - +
507B MET* 1.3 76.9 - - - +
509B MET* 1.3 64.7 + - - +
511B ALA* 3.2 12.6 + - - +
512B PHE* 3.2 32.3 - - + -
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Residues in contact with MET 509 (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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462B LEU* 3.7 32.9 - - + +
465B ILE* 4.8 7.2 - - + -
466B CYS* 3.5 21.5 - - - -
472B VAL 4.8 0.7 - - - +
474B VAL* 5.3 1.3 - - + -
505B TYR 3.0 8.8 + - - +
506B ASP* 3.6 9.0 - - - +
507B MET 3.3 0.2 - - - -
508B MET* 1.3 74.8 - - - +
510B GLU* 1.3 62.0 + - - +
512B PHE* 3.2 12.6 + - - +
513B GLY 3.6 0.2 + - - -
514B GLY* 3.2 22.0 + - - -
515B LYS 3.7 20.2 - - - +
538B PRO* 3.4 19.1 - - + +
539B CYS 3.4 38.1 - - - +
540B LEU* 3.7 22.0 - - + -
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Residues in contact with GLU 510 (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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504A ARG* 5.7 0.5 - - - +
507A MET* 4.1 15.6 - - + +
504B ARG* 5.8 0.3 + - - -
506B ASP* 3.1 24.3 + - - +
507B MET* 3.9 10.6 - - - +
508B MET 3.2 0.4 - - - -
509B MET* 1.3 71.6 - - - +
511B ALA* 1.3 64.2 + - - +
512B PHE 3.1 2.9 + - - -
513B GLY* 3.2 10.8 + - - -
514B GLY 3.2 21.5 - - - +
515B LYS* 4.3 7.4 + - - +
516B GLY* 3.3 29.9 + - - +
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Residues in contact with ALA 511 (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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503A GLY* 3.5 3.5 - - - -
504A ARG* 2.8 62.3 + - - +
507A MET* 3.8 10.1 - - + +
508A MET* 4.0 7.9 - - + +
507B MET 3.0 13.4 + - - +
508B MET* 3.2 15.5 + - - +
510B GLU* 1.3 77.6 - - - +
512B PHE* 1.3 64.6 + - + +
513B GLY 3.5 0.2 - - - -
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Residues in contact with PHE 512 (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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501A THR* 3.7 21.3 + - + +
503A GLY* 4.2 12.1 - - - -
505A TYR* 3.7 28.3 - + - -
508A MET* 3.8 15.5 - - + -
460B MET* 3.6 25.4 - - + -
462B LEU* 4.6 4.7 - - + -
463B GLU* 3.5 46.7 - - + -
466B CYS* 3.4 20.0 - - - +
508B MET* 3.2 47.8 - - + -
509B MET 3.2 6.2 + - - +
510B GLU 3.1 0.8 - - - -
511B ALA* 1.3 86.3 - - + +
513B GLY* 1.3 58.7 + - - +
514B GLY 3.5 1.8 - - - -
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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