Contacts of the strand formed by residues 507 - 516 (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 PRO 507 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C VAL* 3.9 13.0 - - + -
402C ILE 3.8 4.7 - - - +
437C ASN* 3.8 0.2 - - - +
438C SER* 2.8 32.3 + - - +
442C ASP* 3.5 27.8 - - + -
443C SER* 4.0 11.9 - - - +
451C TYR* 4.4 0.9 - - + -
495C TYR* 3.0 22.6 - - + +
497C PHE* 4.1 14.1 - - + -
498C GLN 5.6 0.7 - - - +
505C TYR 4.2 0.2 - - - +
506C GLN* 1.3 105.4 - - + +
508C TYR* 1.3 64.8 + - - +
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Residues in contact with TYR 508 (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* 4.5 13.5 - - - -
376C THR* 6.1 0.9 - - - -
401C VAL* 3.2 5.6 - - - +
402C ILE* 3.1 39.9 + - + +
404C GLY* 3.6 20.4 - - - -
407C VAL* 5.6 5.4 - - + -
435C ALA* 4.4 16.2 - - + -
436C TRP 3.2 26.5 - - - +
437C ASN* 3.2 37.3 + - + +
438C SER* 3.6 3.4 - - - -
503C VAL* 3.8 20.6 - - - +
506C GLN* 3.4 12.8 - - + -
507C PRO* 1.3 78.2 - - - +
509C ARG* 1.3 61.1 + - - +
510C VAL* 3.8 4.7 + - + -
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Residues in contact with ARG 509 (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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347C PHE* 3.6 20.2 - - + -
400C PHE 3.6 4.7 - - - -
401C VAL* 4.5 5.4 - - + +
435C ALA* 3.3 2.6 - - - -
436C TRP* 3.0 69.5 + - + +
438C SER* 3.8 10.0 + - - -
508C TYR* 1.3 70.6 - - - +
510C VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 510 (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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347C PHE* 4.2 3.2 - - - -
398C ASP 3.3 2.6 - - - +
399C SER* 3.5 2.1 - - - -
400C PHE* 2.8 65.4 + - + +
402C ILE* 3.9 26.0 - - + -
407C VAL* 5.2 4.7 - - + -
410C ILE* 4.3 11.9 - - + -
433C VAL* 4.7 2.9 - - + -
434C ILE 3.2 14.4 - - - +
435C ALA* 3.6 23.3 - - + -
508C TYR* 4.4 3.4 - - + +
509C ARG* 1.3 73.9 - - - +
511C VAL* 1.3 62.0 + - - +
512C VAL* 4.0 15.0 - - + -
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Residues in contact with VAL 511 (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* 3.6 29.8 - - + +
342C PHE* 3.3 32.1 - - + -
347C PHE* 5.5 0.7 - - + -
397C ALA* 4.1 6.3 - - + -
398C ASP 3.2 7.4 - - - +
399C SER* 5.1 2.5 - - - -
434C ILE* 3.3 41.0 + - + +
436C TRP* 3.8 13.0 - - + -
510C VAL* 1.3 74.9 - - - +
512C VAL* 1.3 62.9 + - - +
513C LEU* 3.9 21.3 + - + -
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Residues in contact with VAL 512 (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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396C TYR 3.1 6.6 - - - +
397C ALA* 3.3 0.9 - - - -
398C ASP* 2.8 36.1 + - + +
400C PHE* 4.2 3.8 - - + -
410C ILE* 3.7 31.2 - - + -
423C TYR* 3.6 28.3 - - + +
425C LEU* 4.7 8.1 - - + -
430C THR* 4.0 24.7 - - + -
432C CYS 3.8 7.9 - - - +
433C VAL* 4.6 7.6 - - + -
510C VAL* 4.0 9.2 - - + -
511C VAL* 1.3 75.6 - - - +
513C LEU* 1.3 63.2 + - - +
514C SER* 3.7 6.6 + - - +
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Residues in contact with LEU 513 (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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338C PHE* 4.8 12.1 - - + -
341C VAL* 5.5 0.2 - - + -
342C PHE* 5.1 5.4 - - + -
358C ILE* 5.0 6.1 - - + -
365C TYR* 5.1 8.1 - - + -
368C LEU* 4.6 20.6 - - + -
377C PHE* 6.6 0.2 - - + -
395C VAL* 4.2 17.7 - - + -
396C TYR 3.3 1.8 - - - +
397C ALA* 3.6 29.8 - - + -
430C THR* 4.1 1.0 - - - +
431C GLY* 3.0 27.7 + - - -
432C CYS* 3.3 22.6 + - + +
434C ILE* 5.2 8.5 - - + -
511C VAL* 3.9 15.9 - - + +
512C VAL* 1.3 71.8 - - - +
514C SER* 1.3 60.3 + - - +
515C PHE* 3.8 15.2 - - + -
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Residues in contact with SER 514 (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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355C ARG* 5.2 1.4 + - - -
395C VAL* 3.5 4.7 - - - -
396C TYR* 2.7 51.0 + - - +
430C THR* 3.8 11.1 - - - +
431C GLY 4.4 3.1 - - - +
464C PHE* 3.0 37.6 - - - -
512C VAL* 3.7 5.2 + - - +
513C LEU* 1.3 69.8 - - - +
515C PHE* 1.3 64.6 + - - +
516C GLU 3.6 0.9 + - - -
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Residues in contact with PHE 515 (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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365C TYR* 3.7 36.3 - + - -
382C VAL* 4.2 13.2 - - + -
387C LEU* 3.6 23.8 - - + -
392C PHE* 3.8 33.7 - + + -
394C ASN 4.3 0.2 - - - -
395C VAL* 3.6 31.9 - - + -
429C PHE* 3.3 31.2 - - + -
430C THR* 5.3 1.0 - - - +
431C GLY* 3.4 35.5 - - - +
432C CYS* 4.8 2.9 - - - -
513C LEU* 3.6 14.1 + - + -
514C SER* 1.3 71.6 - - - +
516C GLU* 1.3 60.4 + - - +
517C LEU* 3.7 1.6 - - + -
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Residues in contact with GLU 516 (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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200A TYR* 4.3 14.1 - - + +
392C PHE* 3.8 1.8 - - - +
393C THR* 2.5 46.4 + - - +
394C ASN* 3.1 22.5 + - + +
396C TYR* 4.7 10.3 - - + -
514C SER 4.8 1.3 - - - +
515C PHE* 1.3 70.4 - - - +
517C LEU* 1.3 59.4 + - - +
519C HIS* 4.9 7.2 - - + -
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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