Contacts of the strand formed by residues 461 - 465 (chain A) in PDB entry 6T8G
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 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A LEU* 5.0 0.4 - - - -
459A MET* 3.6 3.2 - - - +
460A PRO* 1.3 108.6 + - + +
462A LEU* 1.3 65.7 - - - +
615A ILE* 5.4 1.3 - - + -
616A ALA* 4.2 13.5 + - + -
619A ALA* 3.4 34.6 - - + +
620A ARG* 4.9 0.8 + - - +
624A ILE 3.7 11.7 - - - -
625A HIS* 5.0 0.9 - + - -
626A LEU* 3.0 35.5 + - + +
645A ASN 3.7 20.2 - - - -
646A ILE* 3.7 25.6 - - + -
647A PRO* 4.8 1.1 - - + +
648A THR* 3.1 29.4 + - - +
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A LEU* 3.8 13.9 - - + -
443A LEU* 5.9 0.9 - - + -
456A LEU* 3.7 20.9 - - + -
459A MET* 3.6 24.0 - - + -
461A HIS* 1.3 79.5 - - - +
463A LEU* 1.3 71.5 + - - +
464A VAL* 5.1 1.6 - - + -
479A MET* 3.7 26.9 - - + -
626A LEU 3.0 10.1 + - - +
627A ILE* 3.7 14.8 - - + -
628A LEU* 3.0 24.0 + - - +
646A ILE* 4.0 3.8 - - - +
648A THR* 3.4 11.4 - - + +
650A ILE* 3.7 31.0 - - + -
680A TYR* 5.6 0.9 - - + -
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 1.3 75.7 - - - +
464A VAL* 1.3 63.7 + - - +
597A PHE* 4.9 7.4 - - + -
628A LEU* 3.4 38.1 - - + -
638A ILE* 4.5 19.7 - - + -
642A ILE* 5.4 3.1 - - + -
646A ILE* 3.8 23.1 - - + -
648A THR 3.4 5.9 + - - -
649A ARG* 3.5 40.6 - - + +
650A ILE* 2.8 30.4 + - - +
663A ILE* 3.9 23.6 - - + -
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Residues in contact with VAL 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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462A LEU* 5.1 2.2 - - + -
463A LEU* 1.3 80.2 - - - +
465A ALA* 1.3 66.6 + - - +
472A LYS* 3.7 34.1 - - + +
475A GLY* 6.3 0.7 - - - -
476A VAL* 4.9 8.5 - - + -
479A MET* 4.5 26.0 - - + -
597A PHE* 5.7 0.2 - - - -
627A ILE* 5.0 6.3 - - + -
628A LEU 2.6 19.1 + - - +
629A ALA* 3.3 11.9 - - + -
630A THR* 3.2 25.9 + - - +
650A ILE* 3.2 9.0 - - + +
652A PHE* 4.6 16.2 - - + -
663A ILE* 4.8 2.0 - - - +
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Residues in contact with ALA 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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464A VAL* 1.3 77.0 - - - +
466A GLY* 1.3 53.9 + - - +
472A LYS* 3.7 8.7 - - - -
630A THR* 4.0 8.7 - - + -
633A PRO* 3.8 22.2 - - + -
650A ILE 3.1 6.5 + - - -
651A ALA* 3.3 1.7 - - + -
652A PHE* 2.4 38.8 + - - +
654A VAL* 4.7 2.5 - - + -
663A ILE* 3.7 33.2 - - + -
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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