Contacts of the strand formed by residues 495 - 501 (chain A) in PDB entry 2HAZ
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 SER 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A SER* 4.9 1.9 + - - -
494A PRO* 1.3 74.5 + - - +
496A ILE* 1.3 63.2 + - - +
497A ASP* 3.7 3.5 + - - -
510A PHE* 3.0 5.8 - - - +
511A ASP* 2.6 61.0 + - - +
512A GLU 5.0 0.6 + - - -
579A SER* 4.7 0.7 - - - -
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Residues in contact with ILE 496 (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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495A SER* 1.3 72.7 - - - +
497A ASP* 1.3 65.4 + - - +
498A GLN 4.1 5.6 - - - +
499A VAL* 4.0 10.1 - - + -
508A VAL* 4.0 23.1 - - + -
509A GLN 3.5 10.5 - - - +
510A PHE* 4.2 0.2 - - - +
565A VAL* 3.5 36.8 - - + +
566A ARG* 3.9 9.9 - - - -
567A LEU* 4.3 11.2 - - + +
579A SER* 3.7 22.4 - - - +
580A ALA 4.3 5.1 + - - +
582A SER* 3.8 26.0 - - - +
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Residues in contact with ASP 497 (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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101A NA 2.4 31.2 - - - -
495A SER* 3.7 2.3 + - - +
496A ILE* 1.3 79.4 - - - +
498A GLN* 1.3 63.1 + - + +
509A GLN* 2.7 31.0 + - + +
510A PHE 4.9 1.4 - - - -
511A ASP* 3.1 17.4 - - - +
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Residues in contact with GLN 498 (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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496A ILE* 3.8 2.7 - - - -
497A ASP* 1.3 84.0 - - + +
499A VAL* 1.3 65.4 + - - +
500A GLU* 3.4 27.8 - - + +
507A GLN 3.8 0.3 - - - +
509A GLN* 2.8 61.9 + - + +
582A SER* 5.4 2.7 - - - -
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Residues in contact with VAL 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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496A ILE* 4.0 8.1 - - + -
498A GLN* 1.3 81.2 + - - +
500A GLU* 1.3 65.3 + - - +
501A PRO* 3.1 11.4 - - - +
506A ALA* 3.7 20.2 - - + -
507A GLN 3.3 9.0 - - - +
508A VAL* 4.2 10.5 - - + -
565A VAL* 4.0 20.4 - - + -
582A SER* 3.9 19.9 + - - +
584A PHE* 3.6 40.0 - - + +
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Residues in contact with GLU 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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498A GLN* 3.4 21.3 - - - +
499A VAL* 1.3 72.1 - - - +
501A PRO* 1.3 66.3 - - - +
502A TYR* 3.8 21.6 + - + +
506A ALA* 3.4 2.0 - - - -
507A GLN* 2.9 54.9 + - + +
509A GLN* 2.8 37.4 + - - +
551A ILE* 4.9 1.6 - - - +
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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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499A VAL* 3.1 13.4 - - + +
500A GLU* 1.3 86.2 - - - +
502A TYR* 1.3 71.1 + - - +
505A THR 3.8 4.9 - - - +
506A ALA* 3.9 3.6 - - + -
584A PHE* 3.8 26.0 - - + -
585A LYS 3.1 30.1 - - - +
586A THR* 4.1 1.8 - - + -
587A GLN* 3.0 23.6 + - + -
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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