Contacts of the strand formed by residues 373 - 381 (chain C) in PDB entry 6WVM
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 ARG 373 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C PRO* 3.4 8.5 - - - +
285C GLN 3.7 12.9 + - - -
286C LEU* 3.1 31.0 + - - +
287C SER* 4.1 6.8 - - - +
288C VAL* 3.8 17.7 - - - +
291C ILE* 3.9 14.1 - - + -
320C ARG 3.4 6.1 - - - -
322C ASP* 3.2 43.2 + - - +
323C VAL* 3.6 18.6 - - + -
360C PRO* 4.4 2.5 - - - -
371C VAL* 3.2 24.1 - - - +
372C GLN* 1.3 111.4 + - - +
374C ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 374 (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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272C TYR* 3.8 31.4 - - + +
273C ALA 3.2 13.2 - - - +
274C PRO* 4.0 3.1 - - + -
291C ILE* 4.0 5.7 - - - +
319C TYR* 3.4 6.4 - - - +
320C ARG* 2.8 40.9 + - + +
323C VAL* 4.8 0.5 - - - +
360C PRO* 4.0 12.1 - - + +
371C VAL* 4.8 0.2 - - + -
373C ARG* 1.3 75.4 - - - +
375C VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 375 (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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272C TYR* 3.5 7.2 - - - -
273C ALA* 2.8 39.0 + - + +
291C ILE* 3.5 35.7 - - + +
292C THR* 4.5 1.1 - - - +
295C CYS* 3.6 12.9 - - - -
317C LEU* 4.0 14.6 - - + -
318C LEU 3.6 12.1 - - - +
319C TYR* 3.6 34.3 - - + -
320C ARG* 6.0 0.4 - - - -
374C ALA* 1.3 75.0 - - - +
376C CYS* 1.3 73.6 + - - +
377C MET 4.1 0.6 + - - +
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Residues in contact with CYS 376 (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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234C ILE* 3.8 33.9 - - - -
237C SER* 3.8 25.1 - - - +
238C ILE* 4.9 0.4 - - - -
271C THR 3.4 15.3 - - - -
272C TYR* 4.4 5.6 - - + +
316C CYS 3.5 1.9 - - - +
318C LEU* 2.8 39.5 + - + +
375C VAL* 1.3 74.6 - - - +
377C MET* 1.3 57.8 + - - +
378C LEU* 3.6 28.0 + - + -
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Residues in contact with MET 377 (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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269C LEU 4.1 0.5 - - - +
270C ALA* 3.4 3.1 - - - -
271C THR* 3.0 49.2 + - + +
295C CYS* 3.3 34.0 - - + +
296C PHE* 3.2 45.8 - - + -
301C GLN* 4.8 5.8 - - - +
312C TYR* 4.5 4.5 - - + +
315C CYS* 4.2 8.3 - - + -
316C CYS 3.4 9.0 - - - +
317C LEU* 3.6 24.9 - - + -
375C VAL 4.0 1.4 - - - -
376C CYS* 1.3 71.4 - - - +
378C LEU* 1.3 68.4 + - - +
379C SER* 3.9 21.6 + - - +
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Residues in contact with LEU 378 (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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202C PHE* 3.3 36.1 - - + -
234C ILE* 4.5 1.3 - - + -
238C ILE* 3.7 21.5 - - + -
255C PHE* 3.9 18.6 - - + -
259C LEU* 3.7 11.2 - - + +
268C PRO* 5.0 0.2 - - + -
269C LEU 3.4 5.2 - - - +
270C ALA* 3.9 13.2 - - + -
315C CYS* 3.6 0.9 - - - -
316C CYS* 2.8 33.9 + - + +
318C LEU* 3.6 32.1 - - + -
376C CYS* 3.6 25.4 - - - +
377C MET* 1.3 74.5 - - - +
379C SER* 1.3 60.2 + - - +
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Residues in contact with SER 379 (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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268C PRO* 3.7 6.2 - - - +
269C LEU* 2.8 47.1 + - - +
301C GLN* 5.9 0.9 - - - -
312C TYR* 3.2 34.5 - - - -
314C ALA 3.5 4.0 - - - -
315C CYS* 3.4 7.7 - - - -
377C MET* 3.9 22.2 - - - -
378C LEU* 1.3 73.8 - - - +
380C ASN* 1.3 61.0 + - - +
381C THR* 3.5 5.0 + - - +
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Residues in contact with ASN 380 (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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259C LEU* 2.8 34.0 + - + +
260C VAL* 4.9 0.4 - - - +
261C PRO* 3.8 2.9 - - - +
265C ILE* 2.8 27.5 + - - -
266C HIS* 4.2 6.3 - - - +
267C PHE 3.8 3.4 - - - +
268C PRO* 3.9 12.2 - - - +
312C TYR* 3.8 1.6 - - - -
313C MET* 2.8 48.4 + - + +
314C ALA 2.9 21.7 + - - +
379C SER* 1.3 71.4 + - - +
381C THR* 1.3 55.2 + - - +
432C TYR* 2.9 23.2 + - - -
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Residues in contact with THR 381 (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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267C PHE 5.1 1.4 + - - -
269C LEU* 3.6 36.3 - - + +
307C PRO* 4.4 7.0 + - + +
310C GLY* 4.4 0.7 - - - -
311C LYS 3.3 19.5 + - - -
312C TYR* 4.0 19.1 + - + -
313C MET* 3.7 6.7 - - - -
379C SER* 3.5 8.7 + - - +
380C ASN* 1.3 77.0 + - - +
382C THR* 1.3 64.5 + - - +
383C ALA* 3.2 20.9 + - + +
384C ILE* 3.6 9.2 - - - +
432C TYR* 3.6 14.4 - - - -
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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