Contacts of the helix formed by residues 500 - 517 (chain A) in PDB entry 2MV7
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 ASP 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A LYS* 1.3 72.7 + - + +
502A ALA* 3.0 10.7 + - - +
503A TYR* 3.6 24.0 + - - +
504A LEU* 3.9 8.8 - - - +
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Residues in contact with LYS 501 (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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500A ASP* 1.3 86.0 - - + +
502A ALA* 1.3 61.1 + - - +
504A LEU* 4.1 19.3 + - + +
505A ASP* 3.9 13.0 + - - +
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Residues in contact with ALA 502 (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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500A ASP* 3.0 4.2 - - - +
501A LYS* 1.3 78.3 - - - +
503A TYR* 1.3 70.0 + - - +
505A ASP* 2.9 24.3 + - - +
506A GLU* 3.1 12.2 + - + +
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Residues in contact with TYR 503 (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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500A ASP* 3.6 21.8 + - - +
502A ALA* 1.3 77.3 - - - +
504A LEU* 1.3 75.2 + - + +
506A GLU* 2.8 30.6 + - + +
507A LEU* 3.3 32.6 + - + +
547A LEU 4.7 1.2 + - - -
548A CYS* 5.0 7.5 + - - -
550A LEU* 3.5 15.9 + - - +
552A LYS* 3.2 40.2 + - + -
555A VAL* 3.3 38.8 - - + +
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Residues in contact with LEU 504 (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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500A ASP* 3.9 18.2 - - - +
501A LYS* 4.2 18.4 - - + +
502A ALA 3.3 0.4 - - - -
503A TYR* 1.3 83.0 - - + +
505A ASP* 1.3 54.0 + - - +
507A LEU* 2.6 40.4 + - + +
508A VAL* 2.9 18.0 + - + +
548A CYS* 5.7 4.0 - - - -
877B ASN* 4.5 22.4 - - + +
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Residues in contact with ASP 505 (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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501A LYS 3.9 7.0 + - - +
502A ALA* 2.9 20.6 + - - +
504A LEU* 1.3 76.7 - - - +
506A GLU* 1.3 71.6 + - - +
507A LEU 2.8 1.7 + - - -
508A VAL* 2.8 17.0 + - - +
509A GLU* 2.4 54.6 + - - +
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Residues in contact with GLU 506 (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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502A ALA* 3.4 16.8 - - + +
503A TYR* 2.8 24.8 + - + +
505A ASP* 1.3 81.8 - - - +
507A LEU* 1.3 62.8 + - + +
509A GLU* 4.6 3.5 - - - +
510A LEU* 3.2 36.1 + - - +
555A VAL* 5.2 3.4 - - + -
556A ARG* 5.0 5.2 + - - -
559A GLN* 2.9 30.5 + - - +
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Residues in contact with LEU 507 (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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503A TYR* 3.4 42.0 - - + +
504A LEU* 2.6 29.4 + - + +
506A GLU* 1.3 80.4 - - + +
508A VAL* 1.3 52.1 + - - +
510A LEU* 3.6 3.8 - - + +
511A HIS* 2.6 37.6 + - - +
547A LEU* 3.8 23.0 - - + +
548A CYS* 3.2 38.4 - - - -
550A LEU* 4.9 6.1 - - + -
555A VAL* 5.3 5.4 - - + -
879B LEU* 3.2 20.0 - - + +
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Residues in contact with VAL 508 (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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504A LEU* 2.9 19.5 + - + +
505A ASP* 2.8 12.3 + - - +
507A LEU* 1.3 75.2 - - - +
509A GLU* 1.3 69.3 + - - +
511A HIS* 3.0 8.1 + - + +
512A ARG* 2.7 38.4 + - + +
879B LEU* 4.4 15.5 - - + -
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Residues in contact with GLU 509 (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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505A ASP* 2.4 59.6 + - - +
506A GLU* 4.7 5.2 - - - +
508A VAL* 1.3 87.0 - - - +
510A LEU* 1.3 70.0 + - + +
512A ARG* 3.3 5.0 + - - +
513A ARG* 2.8 39.6 + - - +
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Residues in contact with LEU 510 (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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506A GLU* 3.2 25.0 + - - +
507A LEU* 3.4 4.5 + - + +
508A VAL 3.2 0.6 - - - -
509A GLU* 1.3 81.8 - - + +
511A HIS* 1.3 53.7 + - - +
513A ARG* 3.2 21.5 + - - +
514A LEU* 2.6 47.9 + - + +
547A LEU* 4.2 10.1 - - + -
550A LEU* 5.2 2.9 - - + -
555A VAL* 5.7 1.6 - - + -
558A LEU* 3.9 28.7 - - + -
559A GLN* 3.4 37.7 - - + +
562A LEU* 3.6 17.3 - - + -
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Residues in contact with HIS 511 (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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507A LEU 2.6 23.1 + - - +
508A VAL* 3.2 4.9 - - + +
510A LEU* 1.3 73.9 - - - +
512A ARG* 1.3 68.6 + - + +
514A LEU* 3.1 9.7 + - - +
515A MET* 2.9 47.2 + - + +
547A LEU* 4.3 3.7 - - + +
879B LEU* 3.3 43.9 - - + +
880B PRO* 3.3 20.0 - - - +
881B VAL* 2.9 35.3 - - + +
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Residues in contact with ARG 512 (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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508A VAL* 2.7 25.2 + - + +
509A GLU* 3.6 6.1 - - - +
511A HIS* 1.3 78.3 - - + +
513A ARG* 1.3 70.0 + - + +
515A MET* 3.1 21.3 + - - +
516A THR* 2.9 40.5 + - - +
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Residues in contact with ARG 513 (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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509A GLU* 2.8 33.5 + - - +
510A LEU* 3.6 21.5 - - - +
512A ARG* 1.3 75.9 - - + +
514A LEU* 1.3 53.5 + - + +
516A THR* 2.9 10.8 + - - -
517A LEU* 2.6 42.5 + - + +
559A GLN 5.8 0.2 + - - -
562A LEU* 3.3 43.9 + - + +
563A GLU* 3.8 22.5 + - - +
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Residues in contact with LEU 514 (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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510A LEU* 2.6 41.4 + - + +
511A HIS* 3.4 7.4 - - - +
513A ARG* 1.3 72.4 - - - +
515A MET* 1.3 64.2 + - - +
517A LEU* 3.1 36.5 + - + +
523A LEU* 4.6 11.6 - - + +
526A ILE* 3.9 28.3 - - + -
545A PHE* 4.5 15.0 - - + -
547A LEU* 3.7 29.2 - - + -
558A LEU* 5.1 3.8 - - + -
562A LEU* 4.2 11.4 - - + -
881B VAL* 4.5 16.7 - - + +
883B ILE* 5.9 0.2 - - + -
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Residues in contact with MET 515 (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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511A HIS* 2.9 41.9 + - + +
512A ARG* 3.3 17.7 - - - +
514A LEU* 1.3 78.3 - - - +
516A THR* 1.3 62.7 + - + +
517A LEU 4.4 2.1 - - - +
880B PRO 4.6 5.4 - - - +
881B VAL* 5.0 14.1 - - - +
882B SER* 5.7 4.9 - - - +
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Residues in contact with THR 516 (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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512A ARG* 2.9 36.7 + - - +
513A ARG* 2.9 16.1 + - - -
515A MET* 1.3 79.5 - - + +
517A LEU* 1.3 67.9 + - - +
518A ARG* 3.3 7.1 + - - +
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Residues in contact with LEU 517 (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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513A ARG* 2.6 25.2 + - + +
514A LEU* 3.1 22.7 + - + +
515A MET 4.4 2.1 - - - +
516A THR* 1.3 77.0 + - - +
518A ARG* 1.3 68.3 + - - +
519A GLU* 4.0 16.8 - - + +
522A ILE* 3.7 23.8 - - + -
523A LEU* 3.8 24.9 - - + +
562A LEU* 3.6 32.3 - - + -
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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