Contacts of the strand formed by residues 454 - 461 (chain A) in PDB entry 2H5G
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 VAL 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A GLY 4.2 5.6 - - - +
453A ARG* 1.3 81.4 + - - +
455A LEU* 1.3 61.4 + - - +
456A ARG 3.6 20.2 - - - +
457A ARG* 4.4 10.8 - - + -
467A GLU* 3.9 22.7 - - - +
468A GLN 3.7 4.3 - - - +
469A VAL* 3.9 9.4 - - + -
789A ILE* 3.4 44.5 - - + +
790A PRO* 5.6 6.5 - - + -
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Residues in contact with LEU 455 (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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453A ARG* 3.3 49.6 - - - +
454A VAL* 1.3 76.1 - - - +
456A ARG* 1.3 63.2 + - + +
468A GLN* 2.7 34.5 + - + +
469A VAL 4.7 0.9 - - - -
470A THR* 4.1 13.9 - - + +
760A THR* 3.6 31.2 - - + -
789A ILE* 3.4 11.4 - - - +
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Residues in contact with ARG 456 (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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454A VAL* 3.6 4.0 - - - +
455A LEU* 1.3 85.4 - - + +
457A ARG* 1.3 62.1 + - - +
458A THR* 4.3 9.5 + - - +
466A LEU* 6.0 2.3 - - + +
467A GLU* 3.1 7.8 - - - +
468A GLN* 2.9 53.3 + - + +
762A TRP* 3.6 25.5 - - + -
786A ASN* 4.0 24.8 + - - +
789A ILE* 3.7 6.1 - - - -
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Residues in contact with ARG 457 (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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454A VAL* 4.4 7.2 - - + -
456A ARG* 1.3 76.0 - - - +
458A THR* 1.3 63.2 + - - +
459A ARG* 5.9 1.4 - - - +
465A GLU* 6.3 0.2 - - - -
466A LEU 3.4 9.0 - - - +
467A GLU* 4.6 10.7 + - + +
786A ASN* 3.5 5.2 - - - +
787A LEU* 2.8 62.7 + - + +
788A PRO* 3.4 26.4 + - - +
789A ILE* 3.8 20.6 - - + +
790A PRO* 6.4 0.4 - - - -
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Residues in contact with THR 458 (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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456A ARG* 4.3 13.4 + - - +
457A ARG* 1.3 75.8 + - - +
459A ARG* 1.3 66.9 + - - +
460A ILE* 3.2 19.7 + - + -
465A GLU* 3.7 3.6 - - - +
466A LEU* 2.7 51.2 + - - +
784A HIS* 4.0 12.3 - - + +
785A GLU 3.5 20.4 - - - +
786A ASN* 2.8 26.0 + - - +
787A LEU* 4.5 1.6 - - - -
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Residues in contact with ARG 459 (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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457A ARG* 5.9 1.0 - - - +
458A THR* 1.3 72.2 - - - +
460A ILE* 1.3 64.0 + - - +
461A ALA 3.4 22.4 - - - +
462A LYS* 4.8 4.9 - - - +
463A ASN 5.3 1.3 - - - +
465A GLU* 2.7 35.7 + - - +
783A LEU* 3.8 20.7 - - + +
784A HIS 3.1 2.6 + - - -
785A GLU* 2.8 57.1 + - + +
787A LEU* 4.1 28.9 - - + +
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Residues in contact with ILE 460 (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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458A THR* 4.0 14.6 - - + -
459A ARG* 1.3 72.3 - - - +
461A ALA* 1.3 54.7 + - - +
464A LEU* 2.8 34.3 + - + +
466A LEU* 3.7 43.1 - - + -
764A LEU* 4.0 11.9 - - + -
782A TYR* 3.5 31.0 - - + -
783A LEU 2.7 27.4 + - - -
784A HIS* 3.2 21.6 + - + +
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Residues in contact with ALA 461 (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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459A ARG* 3.3 13.0 - - - +
460A ILE* 1.3 79.9 - - - +
462A LYS* 1.3 71.1 + - - +
463A ASN 3.1 0.9 + - - -
464A LEU* 2.8 25.9 + - + +
769A HIS* 5.0 0.9 - - - +
774A PHE* 3.7 25.6 - - + -
781A LYS 3.7 18.8 - - - +
783A LEU* 3.9 10.8 - - - -
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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