Contacts of the helix formed by residues 287 - 295 (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 SER 287 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C GLN* 3.4 15.3 + - - -
286C LEU* 1.3 79.0 - - - +
288C VAL* 1.3 64.4 + - - +
289C ALA* 3.8 9.0 + - - +
290C GLU* 2.6 37.0 + - - +
291C ILE* 3.0 21.8 + - - +
373C ARG* 4.1 8.7 - - - +
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C SER* 1.3 71.6 - - - +
289C ALA* 1.3 55.3 + - - +
291C ILE* 3.5 8.7 - - - +
292C THR* 2.6 40.5 + - - +
319C TYR* 3.9 20.4 - - + -
322C ASP 4.8 0.2 - - - +
323C VAL* 3.7 34.3 - - + -
327C ASP* 3.9 48.5 - - + +
328C VAL* 4.0 8.7 - - + -
331C ALA* 4.4 0.9 - - + -
373C ARG* 3.8 11.6 - - - +
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Residues in contact with ALA 289 (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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287C SER* 3.2 8.6 + - - +
288C VAL* 1.3 78.9 - - - +
290C GLU* 1.3 57.4 + - + +
292C THR* 3.8 0.5 - - - -
293C ASN* 2.9 39.8 + - - +
327C ASP 5.3 1.3 + - - +
330C ALA 6.1 0.2 - - - -
331C ALA* 4.0 21.3 - - + +
334C THR* 5.8 2.0 - - + +
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Residues in contact with GLU 290 (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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284C GLU* 4.6 6.6 - - - +
285C GLN* 2.9 34.5 + - - +
286C LEU* 3.1 23.9 + - + +
287C SER* 2.6 32.0 + - - +
289C ALA* 1.3 76.7 - - + +
291C ILE* 1.3 59.3 + - + +
293C ASN* 3.3 6.7 + - - +
294C ALA* 2.9 27.3 + - - +
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Residues in contact with ILE 291 (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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273C ALA* 3.5 14.7 - - + +
274C PRO* 4.0 27.4 - - + -
286C LEU* 4.1 20.0 - - + +
287C SER 3.0 14.8 + - - +
288C VAL* 3.5 17.0 - - - +
290C GLU* 1.3 75.6 - - - +
292C THR* 1.3 63.1 + - - +
294C ALA* 3.6 9.4 + - - -
295C CYS* 3.3 21.1 - - - -
319C TYR* 4.6 6.7 - - + -
373C ARG* 3.9 27.8 - - + +
374C ALA* 4.0 24.5 - - - +
375C VAL* 3.5 9.1 - - + +
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Residues in contact with THR 292 (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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288C VAL 2.6 24.1 + - - -
289C ALA 3.8 4.0 - - - -
291C ILE* 1.3 75.6 - - - +
293C ASN* 1.3 64.4 + - - +
295C CYS* 3.3 15.4 + - - +
296C PHE* 3.3 18.2 - - + -
317C LEU* 4.3 19.3 - - + -
319C TYR* 2.7 32.4 + - - +
331C ALA* 3.8 15.0 - - + +
332C ILE* 4.3 3.6 - - + -
335C ILE* 3.7 22.2 - - + -
375C VAL* 4.7 2.9 - - - -
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Residues in contact with ASN 293 (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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289C ALA* 2.9 33.2 + - - +
290C GLU* 3.7 5.2 - - - +
292C THR* 1.3 74.9 - - - +
294C ALA* 1.3 61.5 + - - +
296C PHE* 3.2 18.5 + - - +
297C GLU* 3.8 13.1 + - - +
331C ALA 5.1 0.2 + - - -
334C THR* 3.7 10.7 + - - -
335C ILE* 3.7 25.3 - - - +
338C LYS* 2.8 35.0 + - - +
341C ILE* 5.8 0.9 - - - +
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Residues in contact with ALA 294 (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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273C ALA* 4.1 15.0 - - + -
274C PRO* 6.0 0.7 - - + -
290C GLU 2.9 16.5 + - - +
291C ILE* 3.7 9.9 - - - +
292C THR 3.3 0.4 - - - -
293C ASN* 1.3 76.5 - - - +
295C CYS* 1.3 59.5 + - - +
296C PHE 3.3 0.5 + - - -
297C GLU* 3.4 22.0 + - - +
300C ASN* 2.8 34.6 + - - +
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Residues in contact with CYS 295 (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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271C THR* 3.8 16.2 - - + +
272C TYR 5.0 0.2 - - - -
273C ALA* 3.9 11.2 - - - -
291C ILE 3.3 17.0 - - - -
292C THR* 3.5 11.7 - - - +
293C ASN 3.2 1.2 + - - -
294C ALA* 1.3 76.2 - - - +
296C PHE* 1.3 57.9 + - + +
297C GLU 3.5 0.4 - - - -
301C GLN* 2.9 21.6 + - - -
317C LEU* 4.7 2.2 - - + -
375C VAL* 3.6 22.4 - - - -
377C MET* 3.3 49.1 - - + +
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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