Contacts of the helix formed by residues 503 - 511 (chain B) in PDB entry 2UZ1
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 503 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A ALA* 2.8 22.2 + - - +
511A PHE* 5.0 0.8 - - - -
502B GLY* 1.3 71.0 - - - -
504B TYR* 1.3 58.1 + - - +
505B HIS* 3.1 25.9 + - - -
506B GLY* 3.1 20.3 + - - -
507B VAL* 3.0 29.1 + - - +
541B ASN* 4.8 0.4 - - - -
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Residues in contact with TYR 504 (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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48A ARG* 3.0 32.5 + - - -
511A PHE* 4.1 20.2 - + - -
448B ASP* 3.4 35.4 + - + +
451B VAL* 3.9 6.7 - - + -
452B GLY* 5.3 0.9 - - - -
455B ILE* 3.7 24.1 - - + +
458B PHE* 5.0 0.7 - - - -
472B ILE* 3.4 25.8 - - + -
474B ASN* 3.6 30.1 - - - -
476B GLN* 5.7 1.1 - - - -
499B LEU* 4.8 4.8 + - - +
501B ASN 4.0 13.4 + - - -
502B GLY 4.2 9.2 - - - -
503B SER* 1.3 72.2 - - - +
505B HIS* 1.3 57.4 + - - +
507B VAL* 3.2 7.8 + - - +
508B ALA* 3.0 26.7 + - - +
539B CYS* 4.0 3.6 - - - -
541B ASN* 3.7 10.8 + - - +
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Residues in contact with HIS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B SER* 3.1 26.1 + - - -
504B TYR* 1.3 77.0 - - - +
506B GLY* 1.3 60.4 + - - +
508B ALA* 3.4 2.8 + - - +
509B ALA* 2.9 29.7 + - - +
515B GLY* 4.1 8.1 - - - -
516B TYR 3.5 34.3 - - - +
517B HIS* 3.3 42.5 - + + +
539B CYS* 4.0 12.8 - - - +
541B ASN* 3.0 23.3 + - + +
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Residues in contact with GLY 506 (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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506A GLY 4.8 0.3 - - - +
510A ALA* 3.6 12.7 - - - +
503B SER* 3.0 22.8 + - - -
505B HIS* 1.3 78.0 - - - +
507B VAL* 1.3 58.6 + - - +
509B ALA* 3.4 7.1 + - - +
510B ALA* 2.9 29.6 + - - +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A VAL* 3.9 20.6 - - + +
510A ALA* 3.7 15.3 - - + -
511A PHE* 3.6 36.1 - - + -
455B ILE* 3.7 28.5 - - + -
458B PHE* 5.2 0.2 - - + -
503B SER 3.0 19.6 + - - +
504B TYR* 3.5 8.7 - - - +
506B GLY* 1.3 77.0 - - - +
508B ALA* 1.3 62.6 + - - +
510B ALA* 3.2 15.8 + - - +
511B PHE* 3.2 25.4 + - + -
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B PHE* 3.9 28.9 - - + -
504B TYR 3.0 10.7 + - - +
505B HIS 3.7 5.4 - - - +
507B VAL* 1.3 75.1 - - - +
509B ALA* 1.3 63.5 + - - +
511B PHE* 3.0 12.3 + - - +
512B GLY 3.1 0.3 + - - -
513B ALA* 3.0 26.4 + - + +
514B ASP 5.0 1.6 - - - +
515B GLY* 5.2 0.2 - - - -
539B CYS* 3.3 34.5 - - + -
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Residues in contact with ALA 509 (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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505B HIS 2.9 18.1 + - - +
506B GLY* 3.7 7.9 - - - +
507B VAL 3.3 0.2 - - - -
508B ALA* 1.3 75.4 - - - +
510B ALA* 1.3 57.9 + - - +
512B GLY* 2.9 19.6 + - - -
513B ALA 3.3 16.1 + - - +
515B GLY* 4.9 6.5 - - - +
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Residues in contact with ALA 510 (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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502A GLY* 3.7 1.0 - - - -
503A SER* 2.9 36.9 + - - +
506A GLY* 3.6 10.1 - - - -
507A VAL* 3.5 38.8 - - + +
506B GLY 2.9 18.1 + - - +
507B VAL 3.2 0.8 + - - +
509B ALA* 1.3 77.0 - - - +
511B PHE* 1.3 59.1 + - - +
512B GLY 3.3 0.8 + - - -
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Residues in contact with PHE 511 (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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452A GLY* 6.0 1.3 - - - -
455A ILE* 4.0 17.3 - - + -
501A ASN* 3.0 23.9 + - - -
502A GLY* 4.2 11.4 - - - -
504A TYR* 4.1 22.9 - + - -
507A VAL* 3.6 27.1 - - + -
48B ARG* 5.0 1.8 - - - -
455B ILE 3.8 17.0 - - - -
456B GLY* 3.9 14.4 - - - -
458B PHE* 3.8 18.8 - - + -
459B ASP* 3.6 40.8 - - + +
462B VAL* 3.3 11.8 - - - +
507B VAL* 3.2 26.7 + - + -
508B ALA 3.0 8.5 + - - +
510B ALA* 1.3 74.8 - - - +
512B GLY* 1.3 57.9 + - - +
513B ALA 3.5 0.7 - - - -
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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