Contacts of the helix formed by residues 506 - 511 (chain A) in PDB entry 4V1M
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 ALA 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A ASP* 5.7 1.8 - - + +
457A ALA* 3.5 13.7 - - + +
501A LEU 3.0 5.5 + - - +
502A SER* 3.5 26.0 - - - +
504A LEU 3.6 2.2 - - - -
505A CYS* 1.3 78.1 - - - +
507A VAL* 1.3 66.4 + - - +
508A PRO* 3.3 11.7 - - + -
509A LEU* 2.9 28.2 + - + +
510A GLN* 3.4 4.1 + - - -
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Residues in contact with VAL 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 3.8 27.8 - - + +
362A ASP* 3.9 9.0 - - + -
456A MET* 4.0 19.3 - - + -
457A ALA 3.2 15.4 + - - +
458A HIS* 3.3 38.1 - - + +
474A VAL* 3.6 24.2 - - + -
505A CYS 3.4 2.0 + - - -
506A ALA* 1.3 67.6 - - - +
508A PRO* 1.4 69.4 - - + +
510A GLN* 3.1 13.0 + - - +
511A ILE* 3.4 10.2 + - - +
521A MET* 4.0 6.0 - - + +
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Residues in contact with PRO 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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362A ASP* 3.6 26.0 - - + +
506A ALA* 3.4 13.5 - - + -
507A VAL* 1.4 91.4 - - + +
509A LEU* 1.4 63.7 + - + +
511A ILE* 3.2 32.7 + - + +
634A THR* 4.8 0.5 - - - +
639A PRO* 3.4 37.4 - - + +
640A GLN* 4.3 13.2 - - + +
643A ALA* 3.8 18.2 - - + -
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Residues in contact with LEU 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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502A SER 3.9 8.1 - - - +
503A GLN 3.4 34.8 - - - +
504A LEU* 3.6 22.0 - - - +
506A ALA* 2.9 25.2 + - + +
508A PRO* 1.4 75.7 - - + +
510A GLN* 1.3 64.2 + - - +
511A ILE 3.3 1.0 + - - -
512A VAL 4.0 10.6 + - - +
639A PRO* 3.9 25.8 - - + +
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Residues in contact with GLN 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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452A LYS* 3.2 32.0 + - - +
453A MET* 4.0 11.7 - - + +
456A MET* 3.6 37.2 - - + -
504A LEU 3.2 25.7 + - - -
505A CYS* 3.8 4.6 - - - +
506A ALA 3.4 10.3 + - - +
507A VAL 3.1 4.6 + - - +
509A LEU* 1.3 75.9 - - - +
511A ILE* 1.4 60.7 + - - +
512A VAL 3.6 8.5 + - - +
513A SER* 4.1 3.3 + - - -
520A CYS* 3.3 16.1 - - - -
521A MET* 3.8 3.8 - - - -
1141B HIS* 3.3 27.0 + - - -
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Residues in contact with ILE 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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361A LEU* 4.0 23.1 - - + -
507A VAL 3.4 8.8 + - - +
508A PRO* 3.2 28.9 + - + +
509A LEU 3.3 0.4 + - - -
510A GLN* 1.4 74.4 - - - +
512A VAL* 1.3 57.3 + - - +
519A PRO* 3.2 4.6 - - + +
520A CYS* 2.7 32.4 + - - -
521A MET* 3.9 15.3 - - + +
630A ILE* 3.6 31.2 - - + -
634A THR* 3.8 13.0 - - + +
639A PRO 3.9 14.1 - - - +
642A CYS* 4.1 10.8 - - + -
643A ALA 4.0 9.6 - - - +
646A PHE* 4.1 9.6 - - + -
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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
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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