Contacts of the helix formed by residues 462 - 470 (chain B) in PDB entry 4IYM
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 HIS 462 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B VAL* 4.3 24.2 - - + -
109B PHE* 5.1 1.3 - - + -
156B TRP* 3.8 41.7 + + - +
160B PRO* 5.1 0.2 - - - -
441B VAL* 5.7 0.8 - - - +
442B PRO 3.9 11.5 + - - -
443B LEU 3.2 22.7 - - - -
444B ALA* 3.1 13.7 + - - +
446B HIS 2.7 23.0 + - - -
447B SER* 3.7 3.3 - - - -
448B PHE* 3.4 30.4 - - + +
461B GLN* 1.3 89.7 + - + +
463B GLY* 1.3 69.8 + - - +
465B ASP* 3.7 6.4 + - - +
466B SER* 3.0 31.4 + - - -
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Residues in contact with GLY 463 (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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109B PHE* 3.3 22.4 - - - -
444B ALA 3.0 13.1 + - - -
445B TYR 3.9 4.7 - - - -
446B HIS 3.1 23.0 + - - -
447B SER* 4.5 1.6 - - - -
462B HIS* 1.3 79.5 - - - +
464B THR* 1.3 58.4 + - - -
466B SER* 2.7 25.8 + - - -
467B ILE* 3.8 2.1 - - - +
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Residues in contact with THR 464 (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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120A GLU* 4.2 23.7 + - - +
468A LYS* 5.1 3.8 + - - -
109B PHE* 4.0 3.1 - - + -
116B LEU* 4.6 17.5 - - + -
135B ARG* 4.6 3.8 + - - -
445B TYR 4.7 3.9 + - - +
447B SER* 5.3 0.8 - - - -
463B GLY* 1.3 70.1 - - - -
465B ASP* 1.3 71.5 + - - +
467B ILE* 3.1 20.4 + - - +
468B LYS* 3.2 12.8 + - - +
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Residues in contact with ASP 465 (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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468A LYS* 2.8 40.7 + - - -
473A THR* 4.8 3.7 + - - -
447B SER* 4.4 8.5 - - - -
458B ASP 4.4 1.0 - - - +
459B LEU* 3.6 14.7 - - + +
460B ASN* 2.7 52.4 + - + +
462B HIS 3.8 6.3 - - - +
463B GLY* 3.2 0.4 - - - -
464B THR* 1.3 82.7 + - - +
466B SER* 1.3 62.9 + - - +
468B LYS* 3.0 8.9 + - - +
469B PHE* 3.0 20.7 + - - +
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Residues in contact with SER 466 (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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109B PHE* 4.4 2.3 - - - -
160B PRO* 3.6 26.9 - - - +
243B GLN* 5.7 1.8 - - - +
460B ASN 4.0 6.5 + - - -
461B GLN* 4.5 0.4 - - - -
462B HIS* 3.0 34.3 + - - -
463B GLY 2.7 21.0 + - - -
465B ASP* 1.3 76.2 - - - +
467B ILE* 1.3 58.2 + - - +
469B PHE* 3.1 6.3 + - - +
470B TRP* 3.0 39.0 + - - +
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Residues in contact with ILE 467 (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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109B PHE* 4.6 6.5 - - + -
110B VAL* 4.8 2.9 - - + -
113B ILE* 4.1 14.1 - - + -
116B LEU* 3.8 39.5 - - + +
117B GLN* 4.6 5.4 - - - -
135B ARG* 3.5 18.6 - - - +
160B PRO* 4.1 12.8 - - + -
164B CYS* 3.9 24.2 - - - -
463B GLY 3.8 14.1 - - - +
464B THR* 3.1 13.2 + - - +
466B SER* 1.3 81.4 - - - +
468B LYS* 1.3 56.5 + - - +
470B TRP 3.5 0.5 + - - -
471B THR* 2.7 38.3 + - + +
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Residues in contact with LYS 468 (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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458A ASP 4.6 5.0 - - - +
459A LEU* 4.0 19.7 - - + -
464A THR* 5.4 3.0 + - - -
465A ASP* 2.8 35.2 + - - -
468A LYS* 5.7 2.9 - - + -
135B ARG* 3.7 27.9 - - - +
241B ARG* 3.4 4.2 + - - -
459B LEU* 4.0 14.8 - - + +
464B THR 3.2 10.6 + - - +
465B ASP* 3.0 10.5 + - - +
467B ILE* 1.3 77.5 - - - +
469B PHE* 1.3 60.2 - - - +
471B THR* 3.1 24.2 + - - +
473B THR* 3.8 19.3 + - - +
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Residues in contact with PHE 469 (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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458A ASP* 3.2 29.4 - - - -
138B VAL* 4.1 1.4 - - - +
218B ALA* 4.1 7.2 - - + -
219B VAL 3.5 25.6 - - - -
220B SER* 4.5 0.2 - - - -
241B ARG* 2.9 41.0 + - + +
242B ALA* 3.6 26.7 - - - -
243B GLN* 3.7 35.9 - - + +
459B LEU* 3.7 10.8 - - + -
465B ASP 3.0 11.8 + - - +
466B SER* 3.1 11.8 + - - +
468B LYS* 1.3 78.5 - - - +
470B TRP* 1.3 93.3 + + + +
471B THR 3.3 0.4 - - - -
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Residues in contact with TRP 470 (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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137B PRO* 4.1 0.3 - - - +
138B VAL* 3.7 21.5 + - + -
141B GLY* 3.6 24.2 - - - -
142B ALA 4.0 11.7 - - - -
157B MSE 3.7 13.9 + - + +
160B PRO* 3.9 11.5 - - + +
161B ALA* 3.4 38.6 - - + -
164B CYS* 4.0 10.5 - - - -
166B ASN* 2.7 37.9 + - + +
168B PHE* 3.9 24.2 - + - -
218B ALA* 3.8 16.6 - - + -
220B SER* 4.1 13.2 - - - -
243B GLN* 4.6 4.8 + - - -
466B SER* 3.0 29.4 + - - +
467B ILE 3.5 0.4 + - - -
468B LYS 3.3 0.2 - - - -
469B PHE* 1.3 102.4 - + - +
471B THR* 1.3 65.1 + - - +
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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