Contacts of the strand formed by residues 475 - 483 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A TRP* 3.7 16.4 - - + -
336A VAL* 4.4 9.9 - - + -
339A VAL* 4.2 18.4 - - - -
346A ILE* 5.9 3.6 - - + -
347A ALA* 5.5 2.0 - - - -
350A VAL* 4.2 26.2 - - + -
467A PHE* 4.4 16.4 - - + -
468A ILE 3.1 10.1 - - - +
469A PHE* 3.9 24.5 - - + -
473A GLY 3.8 1.0 + - - +
474A VAL* 1.3 76.4 - - - +
476A GLU* 1.3 64.9 + - - +
477A ALA* 5.4 0.9 - - + +
593A TYR* 5.7 1.8 - - + -
694A PHE* 4.1 1.4 - - + +
695A LEU* 3.4 1.6 - - - +
696A LEU* 2.7 67.5 + - + +
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Residues in contact with GLU 476 (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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467A PHE* 3.4 7.9 - - - +
468A ILE* 2.8 48.6 + - + +
470A TYR* 3.0 32.7 + - + -
475A MET* 1.3 78.3 - - - +
477A ALA* 1.3 69.6 + - - +
478A LYS* 3.1 31.8 + - - +
598A HIS* 5.3 2.6 - - - -
694A PHE 3.3 13.0 + - - +
695A LEU* 4.0 24.8 - - + +
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Residues in contact with ALA 477 (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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350A VAL* 5.2 0.2 - - + -
466A ASP 3.5 5.2 - - - -
467A PHE* 3.7 26.2 - - + -
475A MET* 5.8 0.7 - - + -
476A GLU* 1.3 78.4 - - - +
478A LYS* 1.3 62.7 + - - +
516A TYR* 4.0 8.5 - - + -
693A GLY* 3.2 3.9 - - - -
694A PHE* 2.8 63.3 + - + +
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Residues in contact with LYS 478 (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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464A ILE 3.7 1.1 - - - +
465A TRP* 3.7 2.1 - - - -
466A ASP* 3.0 36.4 + - + +
468A ILE* 3.9 25.6 - - + +
470A TYR* 5.5 1.4 + - - -
476A GLU* 3.1 31.4 + - - +
477A ALA* 1.3 75.1 - - - +
479A MET* 1.3 62.2 + - - +
480A HIS* 3.3 34.0 - - + +
516A TYR* 3.8 8.0 + - - -
691A SER* 4.2 15.0 - - - +
692A VAL 3.3 11.0 - - - +
693A GLY* 5.5 0.2 - - - -
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Residues in contact with MET 479 (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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463A TYR* 3.6 27.6 - - + -
464A ILE 3.3 7.4 - - - +
465A TRP* 3.5 40.4 - - + -
478A LYS* 1.3 75.6 - - - +
480A HIS* 1.3 80.2 + - - +
481A ALA* 3.8 2.0 - - + +
512A HIS* 5.2 6.3 - - + -
514A VAL* 3.9 22.9 - - + -
516A TYR* 4.1 4.2 + - + +
672A GLY* 6.4 0.2 - - - -
673A PHE* 4.4 16.2 - - + -
690A ASN 3.9 0.2 - - - +
691A SER* 3.1 24.8 - - - -
692A VAL* 2.9 34.6 + - + +
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Residues in contact with HIS 480 (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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462A ASP 3.7 0.9 - - - +
463A TYR* 3.4 4.0 - - - -
464A ILE* 2.8 62.1 + - + +
466A ASP* 3.2 26.6 + - - -
478A LYS* 3.3 32.3 - - + +
479A MET* 1.3 79.2 - - - +
481A ALA* 1.3 60.6 + - - +
482A THR 4.0 0.2 + - - -
687A THR* 3.9 24.6 + - + -
690A ASN 3.7 6.5 - - - +
691A SER* 3.6 13.0 - - - -
425B VAL* 4.0 29.9 - - + +
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Residues in contact with ALA 481 (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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461A TPQ 4.8 7.6 - - + +
462A ASP 3.8 3.1 - - - -
463A TYR* 4.0 22.0 - - + -
479A MET* 3.8 4.6 - - - -
480A HIS* 1.3 72.6 - - - +
482A THR* 1.3 64.1 + - - +
512A HIS* 4.8 6.7 - - + +
673A PHE* 4.2 24.7 - - + -
685A THR* 3.9 8.3 - - + +
686A ALA 3.6 19.1 - - - +
687A THR* 4.0 4.3 - - - +
690A ASN* 3.3 11.8 + - + +
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Residues in contact with THR 482 (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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461A TPQ 3.1 15.1 - - - -
462A ASP* 2.8 37.4 + - + +
464A ILE* 4.0 15.7 - - + -
481A ALA* 1.3 74.7 - - - +
483A GLY* 1.3 66.0 + - - +
685A THR* 2.6 26.5 + - - -
687A THR* 3.9 11.9 - - + -
428B ARG* 3.3 19.5 - - - +
429B ARG* 3.4 32.9 + - + +
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Residues in contact with GLY 483 (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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460A ASN 3.7 0.9 - - - -
461A TPQ 4.5 0.7 - - - -
462A ASP* 3.4 18.8 - - - -
482A THR* 1.3 85.7 + - - +
484A TYR* 1.3 59.9 + - - -
684A ASN* 3.2 23.2 + - - -
685A THR* 2.9 27.2 + - - -
429B ARG 3.5 5.1 + - - -
430B HIS* 4.2 2.5 - - - -
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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