Contacts of the helix formed by residues 294 - 304 (chain C) in PDB entry 6ZGI
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 ASP 294 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C CYS 4.5 2.3 - - - +
292C ALA 3.6 1.5 - - - -
293C LEU* 1.3 106.4 - - - +
295C PRO* 1.3 71.4 - - + +
296C LEU* 3.9 14.4 - - + +
297C SER* 3.3 14.9 + - - +
298C GLU* 3.0 26.7 + - - +
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Residues in contact with PRO 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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293C LEU 4.9 0.2 - - - +
294C ASP* 1.3 84.2 - - + +
296C LEU* 1.3 60.2 + - - +
298C GLU* 3.1 13.8 + - + +
299C THR* 2.9 32.7 + - - +
315C THR* 4.0 18.0 - - + +
595C VAL* 5.5 2.0 - - + -
597C VAL* 4.3 15.9 - - + -
608C VAL* 6.2 2.5 - - + -
610C VAL* 4.6 20.0 - - + -
636C TYR* 4.5 26.7 - - + -
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Residues in contact with LEU 296 (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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294C ASP* 3.2 8.4 - - + +
295C PRO* 1.3 79.1 - - - +
297C SER* 1.3 59.4 + - - +
299C THR* 2.6 27.0 + - - +
300C LYS* 2.9 34.8 + - - +
308C VAL* 4.5 11.2 - - + -
597C VAL* 4.6 6.5 - - + +
599C THR* 4.5 13.7 - - + +
602C THR* 4.5 15.7 - - - +
605C SER 5.9 0.2 - - - +
606C ASN* 4.0 33.7 - - + +
608C VAL* 4.2 28.1 - - + +
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Residues in contact with SER 297 (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 VAL* 4.0 12.1 - - - +
290C ASP 3.3 25.3 + - - -
291C CYS* 4.3 2.6 - - - -
293C LEU* 4.3 10.9 - - - +
294C ASP* 3.3 24.9 + - - +
295C PRO 3.3 0.2 - - - -
296C LEU* 1.3 78.7 - - - +
298C GLU* 1.3 57.6 + - - +
300C LYS* 3.3 14.2 + - - +
301C CYS* 2.9 28.6 + - - +
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Residues in contact with GLU 298 (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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291C CYS 3.7 17.7 + - - +
292C ALA* 6.2 0.2 - - - -
294C ASP 3.0 13.8 + - - +
295C PRO* 3.1 15.2 + - - +
297C SER* 1.3 78.1 - - - +
299C THR* 1.3 57.2 + - - +
301C CYS* 3.2 4.8 + - + +
302C THR* 2.9 36.5 + - - +
315C THR* 3.3 24.2 - - + +
316C SER* 3.2 30.0 - - - -
636C TYR* 5.7 0.7 + - - -
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Residues in contact with THR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C PRO 2.9 15.5 + - - +
296C LEU* 2.6 32.4 + - - +
298C GLU* 1.3 71.8 - - - +
300C LYS* 1.3 58.7 + - - +
302C THR* 3.8 5.6 - - - +
303C LEU* 2.9 42.3 + - - +
308C VAL* 4.5 5.4 - - - +
313C TYR* 3.8 24.6 - - + -
314C GLN 5.0 2.7 - - - +
315C THR* 3.6 12.8 - - + -
597C VAL* 3.6 25.0 - - + +
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Residues in contact with LYS 300 (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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276C LEU* 4.2 3.0 - - - +
289C VAL* 4.4 20.4 - - + +
296C LEU* 2.9 36.0 + - + +
297C SER* 3.4 17.4 + - - +
299C THR* 1.3 77.6 + - - +
301C CYS* 1.3 61.0 + - - +
303C LEU* 3.6 1.5 + - - -
304C LYS* 3.0 18.2 + - - -
305C SER 3.2 24.8 + - - +
306C PHE* 3.3 28.5 + - - +
308C VAL* 3.7 17.5 - - + +
602C THR* 4.2 21.7 - - - +
606C ASN* 5.1 3.2 + - - -
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Residues in contact with CYS 301 (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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50C SER* 4.8 8.7 - - - -
274C THR* 4.9 4.7 - - - -
276C LEU* 4.4 13.9 - - - +
289C VAL* 5.0 1.1 - - + +
291C CYS* 2.0 51.6 - - + -
297C SER 2.9 14.7 + - - +
298C GLU* 3.5 8.1 - - + +
299C THR 3.2 0.2 - - - -
300C LYS* 1.3 76.3 - - - +
302C THR* 1.3 63.5 + - - +
304C LYS* 3.4 21.7 + - - +
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Residues in contact with THR 302 (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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761A THR* 4.4 30.0 + - + +
298C GLU* 2.9 24.1 + - - +
299C THR* 3.8 7.0 - - - -
301C CYS* 1.3 74.0 - - - +
303C LEU* 1.3 66.5 + - + +
304C LYS* 3.1 12.6 + - - +
315C THR 5.6 1.6 + - - -
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Residues in contact with LEU 303 (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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299C THR* 2.9 23.4 + - - +
300C LYS* 4.2 1.8 - - - +
302C THR* 1.3 78.9 - - + +
304C LYS* 1.3 67.8 + - - +
305C SER* 3.4 17.3 + - - +
307C THR 4.8 0.4 - - - +
308C VAL* 4.2 34.1 - - + -
309C GLU 5.5 0.4 - - - +
313C TYR* 4.3 26.0 - - + +
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Residues in contact with LYS 304 (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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48C LEU* 3.3 28.8 + - + +
50C SER* 3.0 33.5 + - - +
276C LEU* 4.3 15.6 - - + +
300C LYS 3.0 8.3 + - - -
301C CYS 3.4 13.5 + - - +
302C THR 3.1 8.1 - - - +
303C LEU* 1.3 81.4 - - - +
305C SER* 1.3 59.3 + - - +
964C LYS* 6.3 4.5 - - + -
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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