Contacts of the strand formed by residues 462 - 467 (chain E) in PDB entry 6Q2J
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 SER 462 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424E LYS* 3.5 25.1 - - - +
425E VAL 3.4 13.9 - - - -
426E CYS* 3.7 21.3 - - - -
440E TYR* 4.0 7.0 - - - -
456E THR* 3.7 4.4 - - - +
457E SER* 2.9 34.6 + - - +
460E ASP* 3.7 16.4 - - - +
461E THR* 1.3 79.5 - - - +
463E GLY* 1.3 61.0 + - - +
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Residues in contact with GLY 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E LYS* 3.4 5.9 - - - +
425E VAL* 2.9 34.8 + - - +
440E TYR* 3.2 22.9 - - - -
454E VAL* 4.3 6.3 - - - -
455E VAL 3.5 8.5 - - - -
456E THR* 4.1 3.4 - - - -
462E SER* 1.3 75.6 - - - +
464E ILE* 1.3 63.9 + - - -
465E LEU 4.1 0.2 + - - -
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Residues in contact with ILE 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421E GLN* 3.7 40.2 - - + +
423E GLY 3.9 15.0 - - - +
424E LYS* 4.8 16.6 - - + -
453E GLY 3.8 0.9 - - - +
454E VAL* 3.4 2.1 - - - -
455E VAL* 2.9 31.8 + - - +
457E SER* 4.1 26.2 - - - +
462E SER* 5.2 0.2 - - - +
463E GLY* 1.3 77.8 - - - +
465E LEU* 1.3 65.2 + - - +
466E PHE* 3.9 4.7 - - + -
571E ASP* 3.9 23.1 - - + +
573E VAL* 3.8 17.7 - - + +
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Residues in contact with LEU 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E LEU* 3.8 26.5 - - + -
421E GLN* 3.9 2.9 - - - -
422E ILE* 3.2 54.1 + - + -
423E GLY 4.1 11.7 + - - +
424E LYS 5.2 0.2 - - - +
425E VAL* 3.7 30.1 - - + +
442E LEU* 5.3 3.1 - - + -
452E LEU* 4.6 14.4 - - + -
453E GLY 3.2 7.9 - - - +
454E VAL* 3.7 20.2 - - + +
463E GLY 4.1 1.2 + - - -
464E ILE* 1.3 74.6 - - - +
466E PHE* 1.3 61.1 + - - +
485E VAL* 5.5 2.2 - - + -
500E LEU* 4.2 14.1 - - + -
502E VAL* 6.1 0.7 - - + -
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Residues in contact with PHE 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419E PHE* 3.5 39.9 - + - -
420E ALA 3.3 24.9 - - - +
421E GLN* 4.6 1.6 - - - +
422E ILE* 4.3 2.0 - - - -
452E LEU* 3.3 9.0 - - - -
453E GLY 2.9 55.2 + - - -
455E VAL* 3.5 33.7 - - + -
464E ILE 3.9 8.7 - - - -
465E LEU* 1.3 74.8 - - - +
467E VAL* 1.3 74.5 + - - +
468E ASN* 3.2 22.7 + - + -
573E VAL* 4.5 18.2 - - + -
576E GLN* 5.6 1.3 - - + -
705E NAG 4.5 14.1 - - - -
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Residues in contact with VAL 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E VAL* 4.1 7.4 - - + -
416E ALA* 4.4 12.1 - - + +
417E ARG 3.4 26.0 - - - +
418E ARG* 3.3 4.4 - - - -
419E PHE 2.8 29.6 + - - -
420E ALA* 3.5 7.9 + - + +
422E ILE* 3.8 22.6 - - + +
451E THR* 4.6 1.6 - - + +
452E LEU* 3.8 11.0 - - + -
466E PHE* 1.3 72.4 - - - +
468E ASN* 1.3 57.1 + - - +
469E ASP 3.4 25.6 - - - +
470E THR* 4.7 2.9 - - - +
473E LEU* 3.8 23.6 - - + -
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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