Contacts of the strand formed by residues 430 - 437 (chain C) in PDB entry 6VSB
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 430 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380C TYR* 2.7 38.3 + - - +
382C VAL* 5.2 0.2 - - - -
412C PRO* 5.3 3.5 - - - +
425C LEU* 4.3 21.9 - - + +
426C PRO* 4.6 11.4 + - - +
428C ASP 3.6 7.5 + - - -
429C PHE* 1.3 81.6 + - - +
431C GLY* 1.3 70.3 + - - +
432C CYS* 3.6 2.9 - - - +
433C VAL* 6.0 2.2 - - + -
464C PHE* 4.8 4.8 - - + -
512C VAL* 4.0 20.2 - - + -
513C LEU 4.1 1.8 - - - +
514C SER* 3.8 23.3 - - - +
515C PHE 5.3 1.6 - - - +
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Residues in contact with GLY 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C CYS* 3.0 13.5 - - - +
380C TYR 3.2 1.6 + - - -
382C VAL* 4.2 7.6 - - - +
430C THR* 1.3 74.8 - - - +
432C CYS* 1.3 73.2 + - - +
513C LEU 3.0 21.7 + - - -
515C PHE* 3.4 35.9 - - - +
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Residues in contact with CYS 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C PHE* 4.4 3.8 - - + -
378C LYS 3.3 6.7 - - - +
379C CYS* 2.0 43.5 - - - +
380C TYR 4.6 0.7 - - - +
382C VAL* 5.4 0.4 - - - -
387C LEU* 4.1 19.3 - - - -
430C THR* 3.6 2.6 + - - +
431C GLY* 1.3 83.4 - - - +
433C VAL* 1.3 65.4 + - - +
434C ILE* 3.8 18.8 - - + +
511C VAL 4.0 1.0 - - - +
512C VAL* 3.8 6.7 - - - +
513C LEU* 3.3 35.7 + - + +
515C PHE* 4.8 7.4 - - - -
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C THR* 3.8 6.8 - - + +
378C LYS* 2.6 45.3 + - + +
380C TYR* 3.5 30.3 - - + -
407C VAL 5.3 2.5 - - - +
410C ILE* 3.4 45.5 - - + +
411C ALA* 5.0 1.8 - - - -
425C LEU* 5.2 7.4 - - + -
430C THR* 6.0 2.7 - - + -
432C CYS* 1.3 75.2 - - - +
434C ILE* 1.3 71.3 + - - +
435C ALA* 6.1 0.7 - - + -
510C VAL* 4.7 2.0 - - + -
511C VAL 4.4 0.9 - - - -
512C VAL* 4.6 7.9 - - + -
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Residues in contact with ILE 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C PHE* 4.5 12.3 - - + -
368C LEU* 5.7 1.3 - - + -
374C PHE* 3.5 27.6 - - + -
376C THR* 3.5 4.0 - - - +
377C PHE* 3.4 33.7 - - + -
432C CYS* 3.8 20.9 - - + +
433C VAL* 1.3 87.1 - - - +
435C ALA* 1.3 68.0 + - - +
436C TRP* 4.6 4.5 - - + -
510C VAL* 3.2 25.6 - - - +
511C VAL* 3.3 38.4 + - + +
513C LEU* 5.2 10.5 - - + -
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Residues in contact with ALA 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C PHE* 3.7 1.2 - - - -
375C SER* 2.7 31.0 + - - -
376C THR* 3.1 24.3 + - + +
407C VAL* 5.1 10.3 - - + -
433C VAL* 6.1 0.7 - - + -
434C ILE* 1.3 81.9 - - - +
436C TRP* 1.3 57.6 + - - +
508C TYR* 4.4 13.7 - - + -
509C ARG 3.3 8.3 - - - +
510C VAL* 3.6 18.6 - - + -
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Residues in contact with TRP 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C VAL 4.3 0.4 - - - -
342C PHE* 3.3 65.3 + + + -
344C ALA 5.5 0.2 - - - -
347C PHE* 3.6 19.3 - + - -
373C SER* 3.2 29.8 - - - +
374C PHE* 5.0 1.1 - - + -
375C SER* 3.8 10.1 - - - +
434C ILE* 4.6 6.3 - - + -
435C ALA* 1.3 78.9 - - - +
437C ASN* 1.3 85.7 + - - +
438C SER* 4.9 3.2 - - - -
508C TYR* 3.2 9.6 - - - -
509C ARG* 3.0 61.7 + - + +
511C VAL* 3.8 17.9 - - + -
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Residues in contact with ASN 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C SER* 3.8 7.7 + - - +
436C TRP* 1.3 91.8 - - - +
438C SER* 1.3 71.0 + - - +
439C ASN* 3.0 28.7 + - - +
440C ASN* 4.6 3.6 + - - +
503C VAL* 3.5 10.3 - - - +
506C GLN* 3.3 23.1 - - - +
507C PRO 3.9 1.1 - - - -
508C TYR* 3.2 45.5 + - + +
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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