Contacts of the strand formed by residues 512 - 516 (chain B) in PDB entry 2EZT
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 GLN 512 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510B HIS 4.4 0.4 + - - -
511B MET* 1.3 77.0 - - - +
513B ALA* 1.3 59.4 + - - +
514B PHE* 5.4 3.2 - - + -
528B GLN* 6.1 0.2 - - - +
532B ILE* 3.5 52.7 - - + +
536B GLU* 5.4 3.7 - - + +
537B PRO 4.1 4.3 + - - +
538B VAL* 3.3 8.3 - - - -
539B LEU 3.0 20.8 + - - -
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Residues in contact with ALA 513 (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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503B SER* 3.6 25.4 - - - +
506B ALA* 3.5 28.0 - - + -
511B MET 3.6 2.1 + - - +
512B GLN* 1.3 76.8 - - - +
514B PHE* 1.3 75.9 + - - +
539B LEU* 3.0 15.7 - - + +
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Residues in contact with PHE 514 (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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503B SER* 3.7 7.4 - - - -
512B GLN* 5.4 2.7 - - - -
513B ALA* 1.3 82.2 - - - +
515B ARG* 1.3 62.7 + - - +
516B VAL 4.2 0.4 - - - -
525B VAL* 3.7 42.2 - - + -
528B GLN* 3.6 50.0 - - + -
529B ALA 4.3 4.5 - - - -
532B ILE* 3.9 14.8 - - + -
538B VAL* 3.9 22.7 - - + -
539B LEU* 2.9 13.1 + - - +
540B ILE* 3.5 6.2 - - + -
541B ASP* 2.7 28.4 + - - +
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Residues in contact with ARG 515 (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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473B THR* 4.0 2.2 - - - +
499B ASP* 2.9 39.9 + - - -
500B ILE 3.4 9.7 + - - -
501B ASP* 3.4 25.5 + - - +
503B SER* 3.8 12.5 - - - +
514B PHE* 1.3 76.5 - - - +
516B VAL* 1.3 69.1 + - - +
517B ASN* 6.1 0.4 - - + -
521B GLN* 4.8 2.3 + - - +
541B ASP* 2.5 48.4 + - - +
543B VAL* 3.5 26.6 - - + +
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Residues in contact with VAL 516 (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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371B LEU* 3.8 17.3 - - + +
515B ARG* 1.3 81.0 - - - +
517B ASN* 1.3 62.7 + - - +
518B LYS 4.8 0.9 - - - +
521B GLN* 3.4 28.3 - - + +
522B LEU* 4.2 13.2 - - + -
525B VAL* 3.6 37.7 - - + -
540B ILE* 4.0 16.8 - - + -
541B ASP 3.0 14.0 + - - +
542B ALA* 3.7 3.1 - - + -
543B VAL* 2.8 29.2 + - - +
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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