Contacts of the helix formed by residues 500 - 505 (chain A) in PDB entry 4Y2P
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 VAL 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A ASN 5.2 1.7 - - - +
361A PRO* 5.6 0.7 - - - +
380A VAL* 6.0 1.3 - - + -
496A ASP 3.4 14.6 - - - +
497A PHE* 3.8 24.7 - - + +
498A VAL 3.3 4.9 + - - +
499A LEU* 1.3 73.6 - - - +
501A PRO* 1.4 77.8 - - + +
502A GLN* 3.6 29.6 - - + +
503A MET* 3.1 38.8 + - + +
504A SER* 4.1 1.0 + - - -
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Residues in contact with PRO 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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492A THR* 3.7 28.3 - - + +
493A ALA 3.4 29.2 - - - +
494A GLU* 3.8 23.1 - - - +
496A ASP 4.1 2.2 - - - +
499A LEU 3.8 1.3 - - - +
500A VAL* 1.4 85.4 - - + +
502A GLN* 1.3 57.5 + - - +
504A SER* 2.8 31.9 + - - -
505A GLN* 4.3 0.7 + - - -
518A HIS* 4.0 9.6 - - + -
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Residues in contact with GLN 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 VAL* 3.1 18.3 + - + +
501A PRO* 1.3 77.3 - - - +
503A MET* 1.3 61.8 + - - +
505A GLN* 3.0 56.1 + - - +
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Residues in contact with MET 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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361A PRO* 3.7 36.1 - - + +
363A ILE* 3.8 29.5 - - + +
378A ASN* 5.0 4.7 - - - +
381A PHE* 3.7 27.1 - - + -
498A VAL 3.8 22.9 - - - +
499A LEU* 4.2 8.7 - - + -
500A VAL* 3.1 29.2 + - + +
502A GLN* 1.3 80.7 - - + +
504A SER* 1.3 58.2 + - - +
505A GLN* 3.3 1.9 + - - +
506A HIS* 4.9 1.6 + - - -
507A MET* 5.2 0.5 - - - +
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Residues in contact with SER 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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361A PRO* 3.8 13.4 - - - +
490A MET* 4.1 9.9 - - - -
492A THR* 3.5 9.5 - - - +
500A VAL 4.1 0.6 + - - -
501A PRO* 2.8 21.1 + - - -
503A MET* 1.3 76.7 - - - +
505A GLN* 1.3 56.9 + - - +
506A HIS 3.2 3.4 - - - -
507A MET* 3.1 33.2 + - - +
516A ARG* 2.7 47.5 + - - -
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Residues in contact with GLN 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 PRO 5.1 0.4 - - - -
502A GLN* 3.0 43.6 + - - +
503A MET* 3.3 2.3 - - - +
504A SER* 1.3 77.4 + - - +
506A HIS* 1.3 99.1 + - + +
507A MET 3.4 0.4 + - - -
508A GLU* 3.9 8.7 - - - +
516A ARG* 4.1 6.5 + - - +
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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