Contacts of the helix formed by residues 309 - 319 (chain C) in PDB entry 2V90
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 GLY 309 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B ASP 5.0 1.6 + - - -
271B GLY* 5.9 4.4 - - - -
265C GLU* 3.9 5.2 - - - -
273C PRO* 4.1 6.8 - - - +
275C GLN* 3.4 4.3 - - - -
307C GLY 4.1 1.0 + - - -
308C LEU* 1.3 74.6 - - - +
310C HIS* 1.3 60.4 + - - -
311C GLU 3.6 1.6 - - - -
312C GLU* 3.6 9.4 + - - +
313C THR* 2.6 32.9 + - - -
335E ARG* 6.3 0.2 - - - -
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Residues in contact with HIS 310 (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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263C LEU* 3.3 37.9 - - + +
265C GLU* 3.2 18.6 + - - +
275C GLN* 2.9 27.3 + - - +
309C GLY* 1.3 72.2 - - - +
311C GLU* 1.3 62.8 + - + +
313C THR* 3.1 4.9 + - - -
314C VAL* 2.9 39.2 + - + +
334E ASP 4.0 5.4 - - - -
335E ARG* 3.6 41.8 + - + +
336E GLU 3.5 1.8 - - - -
337E THR* 2.7 32.1 + - - -
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Residues in contact with GLU 311 (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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309C GLY 3.6 0.4 - - - -
310C HIS* 1.3 78.8 - - + +
312C GLU* 1.3 67.9 + - - +
314C VAL* 4.0 7.3 - - - +
315C SER* 2.9 27.0 + - - -
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Residues in contact with GLU 312 (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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269B LEU 4.3 5.2 - - - +
270B ASP* 3.3 36.9 - - - +
271B GLY* 5.6 1.1 - - - -
308C LEU* 3.7 18.2 - - + -
309C GLY* 3.6 14.6 + - - +
310C HIS 3.2 0.4 - - - -
311C GLU* 1.3 81.9 - - + +
313C THR* 1.3 62.4 + - - +
315C SER* 3.0 24.9 + - - -
316C ARG* 2.7 42.3 + - - +
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Residues in contact with THR 313 (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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263C LEU* 3.9 15.5 - - + -
275C GLN* 3.6 20.5 - - + +
297C LEU* 3.8 28.9 - - + -
300C VAL* 4.8 2.0 - - + +
305C VAL* 4.3 15.1 - - + +
308C LEU* 3.9 12.7 + - - +
309C GLY 2.6 21.9 + - - -
310C HIS 3.1 4.5 + - - -
312C GLU* 1.3 79.2 - - - +
314C VAL* 1.3 62.1 + - - +
316C ARG* 3.2 10.8 + - - +
317C ILE* 3.1 22.5 + - + +
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Residues in contact with VAL 314 (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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263C LEU* 4.5 8.1 - - + -
310C HIS* 2.9 49.3 + - + +
311C GLU* 4.0 5.6 - - - +
313C THR* 1.3 71.6 - - - +
315C SER* 1.3 58.6 + - - +
317C ILE* 3.1 10.0 + - - +
318C GLN* 2.7 54.4 + - + +
337E THR* 3.8 28.3 - - + +
339E VAL* 4.3 10.5 - - + -
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Residues in contact with SER 315 (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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311C GLU 2.9 16.3 + - - -
312C GLU* 3.0 24.0 + - - -
314C VAL* 1.3 76.4 - - - +
316C ARG* 1.3 55.7 + - - +
318C GLN* 3.6 14.5 - - - +
319C GLY* 2.7 33.3 + - - -
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Residues in contact with ARG 316 (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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270B ASP* 3.6 23.6 + - - +
300C VAL* 4.0 17.1 + - + +
303C GLU* 4.0 26.5 + - - +
304C SER 3.9 16.8 + - - -
305C VAL* 4.0 17.3 - - - +
308C LEU* 3.6 14.6 - - - +
312C GLU* 2.7 41.0 + - - +
313C THR* 3.5 7.9 - - - +
315C SER* 1.3 83.8 + - - +
317C ILE* 1.3 60.7 + - - +
319C GLY* 3.4 9.7 + - - -
320C GLN* 3.5 20.3 + - - +
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Residues in contact with ILE 317 (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 PHE* 4.1 28.5 - - + -
261C PHE* 4.2 19.5 - - + -
263C LEU* 4.3 14.1 - - + -
297C LEU* 4.0 22.0 - - + -
300C VAL* 3.9 22.0 - - + -
313C THR 3.1 16.5 + - - +
314C VAL* 3.6 8.5 - - - +
316C ARG* 1.3 73.1 - - - +
318C GLN* 1.3 67.7 + - + +
320C GLN* 3.2 16.3 + - - +
321C GLY 4.1 5.2 + - - +
324C VAL* 4.5 10.1 - - + +
326C LEU* 4.2 6.5 - - + -
339E VAL* 4.6 18.2 - - + -
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Residues in contact with GLN 318 (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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254C LYS* 5.3 7.3 + - - +
259C PHE* 6.3 0.2 - - - -
314C VAL* 2.7 43.7 + - + +
315C SER* 3.6 12.6 - - - +
317C ILE* 1.3 74.3 - - + +
319C GLY* 1.3 58.2 + - - +
320C GLN 3.0 5.5 + - - -
321C GLY* 3.1 14.4 + - - +
337E THR* 5.9 1.8 - - - +
339E VAL* 5.7 3.9 - - + +
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Residues in contact with GLY 319 (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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315C SER 2.7 20.8 + - - -
316C ARG* 3.4 5.6 + - - -
317C ILE 3.2 0.4 - - - -
318C GLN* 1.3 72.0 - - - +
320C GLN* 1.3 65.4 + - - +
321C GLY 3.4 0.8 + - - -
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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