Contacts of the helix formed by residues 498 - 503 (chain A) in PDB entry 3ZJU
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 TRP 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A TYR* 3.5 48.7 + + - -
135A TRP* 3.4 22.4 - + + -
136A GLU* 3.0 37.5 + - + +
494A MET 3.2 22.0 + - - -
495A GLU 3.8 3.1 - - - -
497A SER* 1.3 80.6 - - - +
499A TYR* 1.3 66.8 + - - +
500A TYR* 3.1 9.9 - - - -
501A ALA* 3.0 15.8 + - - +
502A ARG* 3.3 39.0 + - + -
512A MET* 3.2 32.5 - - + -
513A LEU* 5.1 3.4 - - + -
544A PHE* 3.7 28.0 - + + -
548A MET* 3.8 10.5 - - + -
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Residues in contact with TYR 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.2 9.3 - - + +
39A SER 3.9 1.2 + - - -
40A MET* 3.6 2.9 - - - +
41A LEU* 3.5 61.7 + - + +
125A LEU* 4.3 4.0 - - + +
127A THR* 4.9 2.7 - - + -
132A TYR* 3.0 28.3 + - + +
495A GLU 3.6 3.8 + - - +
496A SER* 3.3 29.4 - - - -
498A TRP* 1.3 76.8 - - - +
500A TYR* 1.3 69.2 + + + +
502A ARG* 2.9 19.0 + - - +
503A TYR* 3.1 52.0 + + - -
527A TYR* 2.7 34.3 + - - -
537A HIS* 4.2 3.6 - + - -
541A PHE* 6.1 0.2 - + - -
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Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 2.6 33.3 + - - +
38A LEU* 3.5 26.7 - - + -
497A SER 3.4 22.9 - - - -
498A TRP* 3.8 11.9 - - - -
499A TYR* 1.3 92.6 - + + +
501A ALA* 1.3 74.7 + - + +
503A TYR* 3.5 12.2 - - - +
504A THR* 4.3 1.0 - - - +
522A LEU* 3.9 19.3 - - + -
524A VAL* 4.1 9.4 - - + -
527A TYR* 5.8 0.2 - - - +
541A PHE* 3.7 23.3 - + + -
545A HIS* 2.7 40.0 + - - +
548A MET* 3.4 9.5 - - - +
559A PRO* 3.8 19.5 - - + -
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Residues in contact with ALA 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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498A TRP 3.0 9.1 + - - +
499A TYR 3.0 0.2 - - - -
500A TYR* 1.3 104.1 - - + +
502A ARG* 1.3 57.9 + - - +
503A TYR 3.3 0.2 - - - -
504A THR* 2.6 33.4 + - - -
513A LEU* 3.1 27.3 - - + +
518A ALA* 4.7 0.3 - - - +
522A LEU* 4.4 9.9 - - + -
548A MET* 4.0 13.2 - - + -
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Residues in contact with ARG 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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125A LEU* 3.8 11.3 - - + +
131A GLU 4.2 6.7 + - - -
132A TYR* 3.7 21.6 - - + -
135A TRP* 3.3 23.3 - - - +
498A TRP* 3.3 31.3 + - + +
499A TYR 2.9 8.1 + - - +
501A ALA* 1.3 72.9 - - - +
503A TYR* 1.3 57.1 + - - +
504A THR 3.0 5.4 - - - -
505A CYS* 2.9 37.7 + - - -
506A PRO* 3.2 34.2 + - + +
507A GLN 4.3 1.0 - - - -
508A TYR* 2.8 26.4 + - - +
511A GLY 3.1 17.2 + - - -
512A MET* 2.8 36.0 + - - +
513A LEU* 4.1 3.6 - - - -
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Residues in contact with TYR 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.3 22.2 - - + +
38A LEU* 3.7 7.9 - - + -
39A SER 5.5 0.6 + - - -
41A LEU* 4.0 4.2 - - + +
74A LEU* 4.4 3.4 - - + +
76A PRO* 3.4 31.4 + - + -
77A ILE* 3.0 22.8 - - - -
78A GLY* 3.0 29.3 + - - -
123A ARG* 2.9 40.8 + - + +
125A LEU* 3.7 24.2 - - + -
499A TYR* 3.1 49.6 + + - -
500A TYR* 3.5 11.7 - - - +
502A ARG* 1.3 74.8 - - - +
504A THR* 1.3 57.8 + - - +
505A CYS 3.2 0.2 - - - -
506A PRO* 3.7 6.2 - - - +
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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