Contacts of the helix formed by residues 474 - 481 (chain B) in PDB entry 2W93
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 TYR 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.1 19.5 - - + +
26A PRO* 3.6 15.1 - - + +
48A ASN 4.4 7.1 + - - -
49A ALA* 5.8 0.3 - - - -
415B ILE* 4.9 0.9 - - + -
445B GLY* 3.4 29.8 + - - -
448B GLN* 4.9 3.5 + - - -
449B LEU* 4.8 4.9 - - - +
473B GLY* 1.3 71.1 - - - -
475B THR* 1.3 63.9 + - - +
476B ILE 3.3 2.5 - - - -
477B GLN* 3.1 28.1 + - + -
478B LYS* 3.1 24.5 + - - +
487B TYR 3.6 23.1 - - - -
488B ASN* 2.9 19.5 + - - +
489B GLU 4.8 0.9 - - - -
490B ILE* 3.5 20.2 - - + +
600B TPP 3.2 44.4 - - + -
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Residues in contact with THR 475 (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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390B THR* 3.9 5.7 - - - +
471B ASN* 3.2 41.3 - - + +
473B GLY 4.1 1.8 - - - +
474B TYR* 1.3 71.3 - - - +
476B ILE* 1.3 64.4 + - - +
478B LYS* 3.0 22.3 + - + +
479B LEU* 3.1 19.5 + - - +
541B PRO 4.5 0.4 - - - +
542B VAL 2.6 30.3 + - - +
543B PHE* 4.4 4.9 - - - -
544B ASP 3.7 14.4 + - - -
600B TPP 2.9 16.2 + - - -
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Residues in contact with ILE 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 4.8 4.3 - - + -
389B GLY* 3.8 24.0 - - - +
390B THR* 4.5 0.2 - - - +
393B PHE* 3.9 13.5 - - + -
475B THR* 1.3 77.1 + - - +
477B GLN* 1.3 65.4 + - - +
479B LEU* 3.3 7.3 + - - +
480B ILE* 3.2 29.3 + - + +
549B LEU* 3.7 41.5 - - + -
553B ALA* 4.5 0.5 - - - +
600B TPP 2.9 56.7 + - + +
602B PY0 3.8 26.5 - - + +
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Residues in contact with GLN 477 (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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26A PRO* 3.4 24.4 - - - +
27A GLY* 3.4 13.8 - - - -
31A LEU* 4.1 11.2 - - + +
474B TYR* 3.1 13.8 + - + +
475B THR 3.1 0.4 - - - -
476B ILE* 1.3 77.0 - - - +
478B LYS* 1.3 61.5 + - - +
480B ILE* 2.9 7.7 + - + +
481B HIS 2.9 32.4 + - - +
488B ASN* 2.7 27.9 + - - +
600B TPP 2.9 45.3 + - + +
602B PY0 3.2 21.0 + - - +
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Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASN 4.7 0.2 + - - -
472B ASP 3.1 18.2 + - - -
473B GLY* 4.1 1.8 - - - -
474B TYR 3.1 16.9 + - - +
475B THR* 3.0 15.8 + - - +
477B GLN* 1.3 76.8 - - - +
479B LEU* 1.3 62.4 + - - +
481B HIS 3.9 2.9 + - - -
482B GLY 4.1 0.2 - - - -
483B PRO* 3.5 49.4 - - + +
488B ASN* 3.3 38.4 - - + +
489B GLU* 2.8 35.3 + - - -
542B VAL* 3.5 21.9 - - + +
543B PHE* 4.1 18.6 - - + -
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Residues in contact with LEU 479 (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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475B THR* 3.1 16.1 + - - +
476B ILE* 3.6 6.7 - - - +
477B GLN 3.1 0.6 - - - -
478B LYS* 1.3 79.0 - - - +
480B ILE* 1.3 63.8 + - - +
543B PHE* 4.2 28.9 - - + +
545B ALA* 3.4 32.3 - - + -
549B LEU* 4.3 16.6 - - + -
550B VAL* 4.1 25.6 - - + +
553B ALA* 3.5 20.7 - - + +
554B LYS* 4.7 1.7 + - - -
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Residues in contact with ILE 480 (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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28A ASP* 4.1 18.4 - - + +
31A LEU* 4.1 14.8 - - + -
292B PHE* 5.4 2.7 - - + -
476B ILE* 3.2 19.1 - - + +
477B GLN* 2.9 9.1 + - + +
479B LEU* 1.3 80.3 - - - +
481B HIS* 1.3 63.8 + - + +
553B ALA* 3.7 25.3 - - + +
554B LYS* 5.8 0.2 - - - -
556B THR* 4.3 8.7 - - + -
557B ALA* 3.5 35.7 - - + +
560B ASN* 5.4 0.2 - - - +
602B PY0 3.5 37.9 - - - +
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Residues in contact with HIS 481 (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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31A LEU* 3.7 32.3 - - + +
32A SER* 4.4 8.3 - - - -
35A ASP* 2.5 28.1 + - - -
477B GLN 2.9 15.3 + - - +
478B LYS 3.9 1.5 + - - -
479B LEU 3.5 1.2 - - - -
480B ILE* 1.3 85.0 + - + +
482B GLY* 1.3 63.2 + - - +
483B PRO* 3.9 2.0 - - - -
487B TYR* 3.2 26.2 + - - -
488B ASN* 3.0 13.0 + - - -
557B ALA* 5.5 3.0 - - + +
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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