Contacts of the strand formed by residues 475 - 483 (chain B) in PDB entry 3HIG
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 MET 475 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B TRP* 3.9 16.4 - - + -
336B VAL* 4.3 9.2 - - + -
339B VAL* 4.7 10.3 - - - -
346B ILE* 6.4 2.0 - - + -
350B VAL* 4.6 17.3 - - + -
467B PHE* 3.6 34.5 - - + -
468B ILE 3.1 11.9 - - - +
469B PHE* 3.8 26.5 - - + -
470B TYR* 4.8 0.2 - - - -
473B GLY 3.8 2.2 + - - -
474B VAL* 1.3 76.4 - - - +
476B GLU* 1.3 74.5 + - - +
477B ALA* 4.8 0.9 - - + +
593B TYR* 6.1 1.1 - - + -
694B PHE* 5.7 1.2 - - + -
695B LEU* 3.5 2.8 - - - +
696B LEU* 2.8 61.3 + - + +
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Residues in contact with GLU 476 (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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466B ASP 4.0 0.2 - - - +
467B PHE* 3.4 4.3 - - - -
468B ILE* 2.9 46.8 + - + +
470B TYR* 3.1 28.9 + - + -
475B MET* 1.3 82.6 - - - +
477B ALA* 1.3 70.6 + - - +
478B LYS* 3.2 31.2 + - - +
598B HIS* 4.3 14.7 + - - -
694B PHE 3.3 13.2 - - - +
695B LEU* 3.6 20.1 - - + +
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Residues in contact with ALA 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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350B VAL* 5.2 0.2 - - + -
466B ASP 3.5 4.9 - - - -
467B PHE* 3.7 24.0 - - + -
475B MET* 4.8 1.1 - - + +
476B GLU* 1.3 77.4 - - - +
478B LYS* 1.3 63.3 + - - +
516B TYR* 3.9 9.9 - - + -
693B GLY* 3.2 4.8 - - - -
694B PHE* 2.9 64.9 + - + +
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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
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464B ILE 4.3 0.7 - - - -
465B TRP* 3.6 2.8 - - - -
466B ASP* 2.8 37.4 + - + +
468B ILE* 3.8 23.0 - - + +
470B TYR* 5.7 0.6 + - - -
476B GLU* 3.2 30.5 + - - +
477B ALA* 1.3 75.7 - - - +
479B MET* 1.3 62.2 + - - +
480B HIS* 3.2 36.0 - - + +
516B TYR* 3.9 7.8 + - - -
691B SER* 4.2 14.4 - - - +
692B VAL 3.4 12.1 - - - +
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Residues in contact with MET 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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463B TYR* 3.7 24.0 - - + -
464B ILE 3.2 7.0 - - - +
465B TRP* 3.6 42.6 - - + -
478B LYS* 1.3 73.7 - - - +
480B HIS* 1.3 82.1 + - - +
481B ALA* 3.6 7.0 - - + +
512B HIS* 5.4 4.0 - - + -
514B VAL* 4.3 15.5 - - + -
516B TYR* 4.1 4.7 + - + +
673B PHE* 4.2 19.5 - - + -
690B ASN 5.1 0.4 - - - +
691B SER* 3.2 6.2 - - - -
692B VAL* 2.9 51.6 + - + +
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Residues in contact with HIS 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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425A VAL* 4.0 34.7 - - + +
462B ASP 3.7 0.9 - - - +
463B TYR* 3.4 2.3 - - - -
464B ILE* 2.9 49.2 + - + +
466B ASP* 3.2 26.8 + - - -
478B LYS* 3.2 33.2 - - + +
479B MET* 1.3 80.9 - - - +
481B ALA* 1.3 58.9 + - - +
482B THR 4.0 0.2 + - - -
687B THR* 3.9 25.9 + - + -
690B ASN 3.5 6.3 - - - +
691B SER* 3.5 13.3 - - - -
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Residues in contact with ALA 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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461B TPQ 4.9 7.0 - - - +
462B ASP 3.8 3.1 - - - -
463B TYR* 4.0 22.0 - - + -
479B MET* 3.6 3.7 - - + -
480B HIS* 1.3 71.9 - - - +
482B THR* 1.3 64.5 + - - +
512B HIS* 4.9 6.7 - - + +
673B PHE* 4.3 20.4 - - + -
685B THR* 3.9 7.7 - - + +
686B ALA 3.6 18.5 - - - +
687B THR* 3.8 6.2 - - - +
690B ASN* 3.1 17.1 + - + +
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Residues in contact with THR 482 (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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428A ARG* 3.3 18.6 - - - +
429A ARG* 3.3 34.3 + - + +
461B TPQ 3.1 16.1 - - - -
462B ASP* 2.8 37.5 + - + +
464B ILE* 4.0 16.2 - - + -
481B ALA* 1.3 75.6 - - - +
483B GLY* 1.3 66.0 + - - +
685B THR* 2.7 25.8 + - - -
687B THR* 3.9 12.8 - - + -
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Residues in contact with GLY 483 (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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429A ARG 3.5 3.5 + - - -
430A HIS* 4.4 2.0 - - - -
460B ASN 3.7 0.9 - - - -
461B TPQ 4.5 0.4 - - - -
462B ASP* 3.4 19.1 - - - -
482B THR* 1.3 87.1 + - - +
484B TYR* 1.3 60.5 + - - -
684B ASN* 3.1 22.4 + - - -
685B THR* 2.9 27.8 + - - -
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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