Contacts of the strand formed by residues 394 - 403 (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 ASN 394 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A TYR* 3.6 32.7 + - - +
230A PRO* 4.7 2.0 - - - +
357C ARG* 4.1 21.1 + - - +
358C ILE 3.7 6.7 - - - +
359C SER* 3.1 29.1 + - - -
392C PHE* 4.0 3.3 - - - +
393C THR* 1.3 98.3 + - - +
395C VAL* 1.3 70.0 + - - +
396C TYR* 4.4 11.1 + - + -
516C GLU* 3.1 28.1 + - + +
523C THR* 5.1 0.2 - - - -
524C VAL* 4.3 1.8 - - - -
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Residues in contact with VAL 395 (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* 6.3 0.7 - - + -
357C ARG* 3.9 3.3 - - - +
358C ILE* 3.0 46.2 + - + +
365C TYR* 4.0 9.2 - - - +
392C PHE* 4.6 4.5 - - + -
394C ASN* 1.3 81.3 - - - +
396C TYR* 1.3 74.8 + - - +
513C LEU* 4.2 18.4 - - + -
514C SER 3.5 6.5 - - - +
515C PHE* 3.6 35.4 - - + -
524C VAL* 3.9 27.8 - - + -
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Residues in contact with TYR 396 (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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198A ASP 4.8 4.2 + - - -
199A GLY* 5.0 3.8 + - - -
200A TYR* 3.6 35.6 + + - -
230A PRO* 4.3 10.7 - - - +
355C ARG* 3.5 42.2 - - + +
356C LYS 3.8 7.6 - - - -
357C ARG* 4.8 12.8 - - + -
394C ASN* 4.4 12.0 + - + -
395C VAL* 1.3 79.3 - - - +
397C ALA* 1.3 59.2 + - - +
398C ASP 4.0 0.4 - - - -
512C VAL 3.1 4.7 - - - +
513C LEU* 3.3 2.5 - - - -
514C SER* 2.7 55.3 + - - -
516C GLU* 4.7 9.2 - - + -
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Residues in contact with ALA 397 (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* 4.0 24.0 - - + +
355C ARG* 3.4 4.5 - - - -
356C LYS* 3.4 40.1 + - + +
358C ILE* 4.4 11.9 - - + -
395C VAL 4.1 1.4 + - - -
396C TYR* 1.3 72.0 - - - +
398C ASP* 1.3 62.1 + - - +
399C SER* 3.7 3.2 + - - -
511C VAL* 4.1 1.1 - - + -
512C VAL 3.3 4.9 - - - -
513C LEU* 3.6 19.5 - - + -
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Residues in contact with ASP 398 (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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353C TRP* 4.2 11.2 - - + -
354C ASN 3.5 11.0 - - - +
355C ARG* 4.3 11.0 - - - +
396C TYR 3.9 0.8 + - - +
397C ALA* 1.3 71.3 - - - +
399C SER* 1.3 58.7 + - - +
400C PHE* 3.8 6.7 - - + -
423C TYR* 3.5 30.1 - - + +
510C VAL 3.3 2.8 - - - +
511C VAL* 3.2 6.5 - - - -
512C VAL* 2.8 37.2 + - + +
514C SER* 6.2 0.4 - - - +
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Residues in contact with SER 399 (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* 5.0 12.8 - - - -
347C PHE* 4.0 25.7 - - - -
348C ALA* 4.2 4.5 + - - +
353C TRP* 3.7 0.2 - - - -
354C ASN* 3.0 53.7 + - - +
355C ARG* 4.5 0.5 + - - -
397C ALA 3.7 4.0 + - - -
398C ASP* 1.3 72.6 - - - +
400C PHE* 1.3 63.4 + - - +
510C VAL 3.5 4.9 - - - -
511C VAL* 4.7 1.6 - - - +
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Residues in contact with PHE 400 (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* 3.8 7.0 - - - -
348C ALA 3.3 13.7 - - - +
350C VAL* 3.9 22.2 - - + -
353C TRP* 3.6 26.7 - - + -
398C ASP* 3.8 15.3 - - + -
399C SER* 1.3 80.1 - - - +
401C VAL* 1.3 71.1 + - - +
402C ILE* 4.4 4.0 - - + -
410C ILE* 4.0 21.1 - - + -
423C TYR* 3.8 41.7 - + - -
509C ARG* 3.6 1.9 - - - -
510C VAL* 2.8 63.2 + - + +
512C VAL* 4.2 3.4 - - + -
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Residues in contact with VAL 401 (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* 3.5 30.5 - - + -
348C ALA 3.2 7.1 + - - +
349C SER* 4.8 0.3 - - - -
350C VAL* 3.3 28.8 + - - +
400C PHE* 1.3 74.7 - - - +
402C ILE* 1.3 61.2 + - - +
438C SER* 4.4 4.0 - - - +
442C ASP* 5.7 0.4 - - + -
451C TYR* 3.6 54.9 - - + +
495C TYR* 5.3 0.4 - - + -
507C PRO* 3.9 19.1 - - + -
508C TYR 3.2 18.8 - - - +
509C ARG* 4.5 3.8 - - + +
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Residues in contact with ILE 402 (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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350C VAL* 4.5 9.4 - - + -
400C PHE* 4.4 6.1 - - + -
401C VAL* 1.3 78.1 - - - +
403C ARG* 1.3 82.6 + - - +
404C GLY 3.6 0.2 + - - -
406C GLU* 4.0 19.7 - - + +
407C VAL* 4.5 10.1 - - + -
410C ILE* 3.8 19.1 - - + -
418C ILE* 3.6 41.5 - - + -
453C TYR* 6.4 1.1 - - + -
495C TYR* 4.9 4.9 - - - -
507C PRO* 3.8 3.9 - - - +
508C TYR* 3.1 29.9 + - + +
510C VAL* 3.9 26.5 - - + -
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Residues in contact with ARG 403 (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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402C ILE* 1.3 91.6 - - - +
404C GLY* 1.3 68.3 + - - +
405C ASP* 3.5 2.0 - - + +
406C GLU* 3.3 24.4 + - + +
407C VAL* 3.5 1.7 + - - +
418C ILE* 5.9 1.1 - - + -
453C TYR* 5.6 7.6 - - + -
495C TYR* 3.9 31.2 - - + -
505C TYR* 4.7 15.7 - - + -
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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