Contacts of the strand formed by residues 434 - 440 (chain F) in PDB entry 6S7T
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 THR 434 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F PHE* 5.3 6.3 - - + -
420F LEU* 4.7 4.7 - - + -
431F PRO* 3.7 27.4 - - + +
432F HIS 4.1 1.2 + - - -
433F GLN* 1.3 79.8 - - - +
435F PHE* 1.3 66.0 + - - +
436F VAL* 5.6 0.7 - - - -
449F PHE 4.1 0.2 - - - +
450F VAL* 4.2 3.6 - - - +
451F ALA* 3.3 42.3 + - - +
459F TYR* 4.3 9.9 - - + -
483F LEU* 5.8 2.5 - - - -
484F ILE 3.2 7.9 - - - -
485F ILE* 3.6 23.1 - - + -
230G ILE* 5.8 1.8 - - - +
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Residues in contact with PHE 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433F GLN* 3.2 58.1 - - + -
434F THR* 1.3 77.9 - - - +
436F VAL* 1.3 62.3 + - - +
437F ARG 3.7 1.6 + - - -
448F VAL* 3.4 29.8 - - + -
449F PHE 3.3 10.1 - - - -
450F VAL* 4.7 7.9 - - + -
483F LEU* 4.0 1.1 - - - -
484F ILE* 2.9 44.3 + - + +
222G TYR* 3.8 19.7 - + + -
230G ILE* 3.6 32.8 - - + -
233G TYR* 6.1 0.9 - + - -
234G PRO* 3.8 7.9 - - + -
237G VAL* 3.6 22.9 - - + -
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Residues in contact with VAL 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416F LEU* 5.4 2.7 - - + -
418F PHE* 4.9 9.0 - - + -
435F PHE* 1.3 71.6 - - - +
437F ARG* 1.3 60.2 + - - +
438F LEU* 4.2 5.3 + - + +
447F VAL 3.7 2.1 - - - +
448F VAL* 3.5 0.7 - - - -
449F PHE* 2.9 47.6 + - + +
450F VAL 5.3 2.0 - - - +
451F ALA* 5.1 11.0 - - + -
461F PHE* 4.6 27.8 - - + -
481F LEU* 3.5 37.5 - - + -
482F TYR 3.7 3.4 - - - +
483F LEU* 3.4 24.2 - - + -
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Residues in contact with ARG 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435F PHE 3.7 1.2 + - - -
436F VAL* 1.3 73.3 - - - +
438F LEU* 1.3 61.3 + - - +
439F HIS* 3.9 25.9 + - - +
446F GLU* 2.2 41.3 + - - +
447F VAL 3.2 4.3 - - - +
448F VAL* 3.7 22.9 - - + -
480F THR 3.3 0.9 - - - +
481F LEU 3.8 0.7 - - - -
482F TYR* 2.9 76.2 + - + +
484F ILE* 3.6 29.5 - - + +
495F LEU* 5.4 6.9 - - - +
219G SER* 4.3 26.6 + - - -
220G THR* 5.3 1.4 - - - +
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Residues in contact with LEU 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436F VAL* 4.8 7.2 - - + +
437F ARG* 1.3 73.0 - - - +
439F HIS* 1.3 60.6 + - - +
440F ASN 4.0 0.3 + - - -
445F GLN 4.0 0.5 - - - +
446F GLU* 3.1 6.6 - - - +
447F VAL* 2.9 37.9 + - + +
449F PHE* 4.2 13.2 - - + -
461F PHE* 5.5 3.8 - - + -
463F LEU* 4.9 8.7 - - + -
472F PHE* 3.5 36.3 - - + -
479F TYR* 3.9 21.7 - - + -
480F THR 3.1 6.7 - - - +
481F LEU* 3.6 43.7 - - + +
501F VAL* 5.4 6.1 - - + -
503F ILE* 4.5 10.5 - - + -
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Residues in contact with HIS 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437F ARG* 3.9 28.5 + - - +
438F LEU* 1.3 71.8 - - - +
440F ASN* 1.3 73.4 + - - +
441F GLN* 3.5 13.9 + - + -
444F GLY* 3.7 27.6 + - - -
445F GLN 3.9 1.3 - - - -
446F GLU* 4.1 6.2 - - - +
478F THR 4.2 0.2 - - - +
479F TYR* 3.5 2.7 - - - -
480F THR* 2.9 36.2 + - - +
482F TYR* 4.4 20.2 - + + -
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Residues in contact with ASN 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439F HIS* 1.3 73.6 + - - +
441F GLN* 1.3 60.2 + - - +
442F LYS* 3.1 21.2 + - - +
443F THR* 3.4 28.0 + - + +
444F GLY* 2.8 31.9 + - - -
445F GLN* 2.8 21.2 + - - +
475F ALA* 6.2 1.0 - - - +
476F SER 5.4 0.4 + - - -
477F GLY* 4.3 12.7 - - - -
478F THR 3.2 14.2 + - - +
479F TYR* 3.3 36.8 + - + -
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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