Contacts of the helix formed by residues 498 - 503 (chain A) in PDB entry 2V4L
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 ASN 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A GLN* 4.2 8.7 + - - -
497A PHE* 1.3 83.0 - - - +
499A ALA* 1.3 64.1 + - - +
500A ASP* 3.1 24.5 + - - +
501A LYS* 3.3 25.1 + - - +
502A LEU* 4.2 2.2 - - - +
669A PHE* 5.8 0.2 - - - -
1036A MET* 3.5 21.8 - - - +
1039A MET 4.0 7.2 + - - +
1040A PRO* 3.9 16.3 + - - +
1041A GLN* 3.2 25.3 + - - +
1042A LEU* 3.6 12.6 - - + -
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Residues in contact with ALA 499 (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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498A ASN* 1.3 70.0 - - - +
500A ASP* 1.3 67.4 + - - +
502A LEU* 3.1 18.8 + - - +
668A LYS* 4.2 27.4 - - + +
669A PHE* 3.8 24.9 - - + -
709A TYR* 2.8 23.7 + - - -
1036A MET* 2.9 22.4 + - - +
1037A THR* 4.4 2.2 - - + -
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Residues in contact with ASP 500 (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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463A TYR* 3.4 24.3 + - - +
498A ASN* 3.1 17.4 + - - +
499A ALA* 1.3 80.5 - - - +
501A LYS* 1.3 55.1 + - - +
502A LEU 3.0 5.4 + - - -
503A THR* 3.4 17.8 + - - +
668A LYS* 5.2 6.1 + - - -
706A SER* 5.3 4.0 - - - -
708A HIS* 3.5 39.1 + - + +
709A TYR* 3.9 11.4 - - - -
1036A MET 4.8 0.2 + - - -
1039A MET 5.7 0.9 - - - +
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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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388A GLN* 5.7 4.1 - - - +
391A GLN* 5.1 5.6 - - - +
430A ASN* 4.6 5.3 + - - +
432A GLN* 2.9 29.1 + - - +
460A LEU* 4.1 14.5 - - + +
463A TYR* 3.5 32.4 - - + +
465A ASN* 3.0 20.1 + - - +
487A ILE* 4.6 7.0 - - + -
497A PHE* 4.2 26.5 - - + +
498A ASN* 3.3 15.6 + - - +
499A ALA 3.2 1.2 - - - -
500A ASP* 1.3 76.5 - - - +
502A LEU* 1.3 61.8 + - + +
503A THR 3.6 0.4 - - - -
1041A GLN* 3.9 22.7 - - - +
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Residues in contact with LEU 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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388A GLN* 4.6 11.0 - - - +
391A GLN* 3.6 37.2 - - + +
428A LEU* 3.9 25.3 - - + +
465A ASN* 3.5 5.7 + - - +
498A ASN 4.2 2.9 - - - +
499A ALA* 3.4 17.0 - - - +
500A ASP 3.0 1.2 - - - -
501A LYS* 1.3 83.2 - - + +
503A THR* 1.3 65.1 + - - +
504A SER 3.7 0.5 + - - -
633A CYS* 4.0 18.6 - - + +
668A LYS 4.5 4.9 - - - +
669A PHE* 3.9 33.4 - - + +
709A TYR* 3.8 4.9 - - - +
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Residues in contact with THR 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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463A TYR* 5.1 0.4 - - + -
465A ASN* 2.7 30.7 + - - +
485A TRP* 3.7 17.2 + - + +
500A ASP 3.4 15.0 + - - +
501A LYS 3.6 0.4 - - - -
502A LEU* 1.3 78.2 - - - +
504A SER* 1.3 62.1 + - - +
505A ALA* 3.1 24.5 + - - +
708A HIS* 2.6 35.0 + - + +
709A TYR* 3.5 28.1 + - - -
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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