Contacts of the strand formed by residues 461 - 465 (chain A) in PDB entry 3H0G
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 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ILE* 5.0 21.8 - - + -
450A PHE 3.3 6.1 - - - +
451A ASN* 3.2 30.3 - - + +
455A SER* 5.5 6.5 - - - +
458A LYS 4.0 13.6 + - - +
459A MET* 4.4 1.4 - - - -
460A SER* 1.3 75.9 - - - +
462A MET* 1.3 62.5 + - - +
496A HIS* 5.5 5.8 - - - +
511A THR* 4.0 7.0 + - - -
516A GLN* 5.6 2.3 + - - -
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Residues in contact with MET 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ILE* 4.5 3.8 - - - -
450A PHE 3.1 26.3 + - - +
459A MET* 3.6 24.2 - - + +
461A MET* 1.3 76.2 - - - +
463A GLY* 1.3 59.5 + - - +
464A HIS* 3.6 5.5 + - + -
483A PRO* 4.7 2.2 - - - -
484A TYR* 2.7 35.9 - - + +
511A THR* 3.6 9.6 - - - +
513A VAL* 3.2 43.3 - - + +
516A GLN* 3.2 28.3 - - + +
527A MET* 3.3 23.8 - - + -
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Residues in contact with GLY 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL 3.6 9.2 - - - -
449A ILE* 4.1 11.0 - - - -
462A MET* 1.3 77.4 - - - +
464A HIS* 1.3 60.6 + - - -
507A ILE 4.5 4.7 - - - -
511A THR* 3.4 17.8 + - - -
512A MET* 2.7 31.2 - - - +
513A VAL* 3.5 11.3 + - - +
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Residues in contact with HIS 464 (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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367A LEU 4.1 8.3 - - - -
368A ASP 3.9 7.0 - - - +
369A GLU 3.8 18.4 - - - -
370A LEU* 3.7 25.4 - - + -
447A VAL* 3.3 24.9 - - - +
448A VAL* 3.0 12.7 + - + +
450A PHE* 3.6 33.0 - + + +
462A MET 3.6 6.1 + - - -
463A GLY* 1.3 74.2 - - - -
465A ARG* 1.3 69.3 + - - +
466A ILE 4.1 0.9 - - - -
476A LEU* 5.2 5.9 - - + +
477A ASN 6.2 0.4 - - - -
480A VAL* 4.4 9.5 - - + +
484A TYR* 3.2 27.4 + - - -
512A MET* 4.8 0.4 - - - -
513A VAL* 3.4 28.6 - - + +
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Residues in contact with ARG 465 (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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366A SER* 4.5 0.4 + - - -
368A ASP* 3.1 40.2 + - - +
369A GLU* 3.8 23.1 + - - +
370A LEU 3.3 15.3 + - - -
444A ASP* 3.6 24.3 + - - -
445A GLY* 3.5 27.4 + - - +
446A ASP 4.2 1.1 - - - -
447A VAL* 3.9 17.7 - - + -
464A HIS* 1.3 83.3 - - - +
466A ILE* 1.3 73.5 - - - +
508A GLN* 5.8 3.4 - - - +
512A MET* 4.3 10.3 - - + -
649A LYS* 4.3 8.2 - - - +
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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