Contacts of the helix formed by residues 309 - 319 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B GLU* 3.7 8.5 - - - -
273B PRO* 4.0 8.1 - - - +
275B GLN* 3.3 4.0 - - - -
307B GLY 4.1 0.4 + - - -
308B LEU* 1.3 72.1 - - - +
310B HIS* 1.3 60.3 + - - -
311B GLU 3.6 1.3 - - - -
312B GLU* 3.7 10.8 + - - +
313B THR* 2.9 31.5 + - - -
270C ASP 5.0 2.4 + - - -
271C GLY* 5.9 2.6 + - - -
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Residues in contact with HIS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU* 3.3 35.7 - - + +
264B ARG* 4.5 2.0 - - - -
265B GLU* 3.1 27.3 + - + +
275B GLN* 3.0 25.0 + - - +
309B GLY* 1.3 69.6 - - - -
311B GLU* 1.3 85.3 + - + +
313B THR* 3.1 3.5 + - - -
314B VAL* 2.8 54.7 + - + +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 1.3 94.1 + - + +
312B GLU* 1.3 65.6 + - - +
314B VAL* 4.0 12.8 - - - +
315B SER* 3.0 25.8 + - - -
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.6 19.3 - - + -
309B GLY* 3.7 14.0 + - - +
310B HIS 3.3 0.2 - - - -
311B GLU* 1.3 79.0 - - - +
313B THR* 1.3 61.7 + - - +
315B SER* 3.3 7.7 + - - -
316B ARG* 2.8 52.7 + - - +
269C LEU 4.1 10.1 - - - +
270C ASP* 3.4 33.9 - - - +
271C GLY* 5.6 1.3 - - - -
272E ARG* 5.9 0.2 + - - -
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU* 3.9 13.2 - - + -
275B GLN* 3.5 21.0 - - + +
297B LEU* 3.7 30.3 - - + -
300B VAL* 4.6 0.7 - - + -
305B VAL* 3.8 18.4 - - + +
308B LEU* 3.8 14.2 - - - +
309B GLY 2.9 22.0 + - - -
310B HIS 3.1 4.2 + - - -
312B GLU* 1.3 71.7 - - - +
314B VAL* 1.3 66.5 + - - +
316B ARG* 3.1 20.2 + - - +
317B ILE* 3.2 13.1 + - + +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 4.0 11.0 - - + -
310B HIS* 2.8 49.5 + - + +
311B GLU* 4.0 14.8 - - - +
313B THR* 1.3 75.0 - - - +
315B SER* 1.3 58.6 + - - +
317B ILE* 3.0 13.4 + - + +
318B GLN* 2.8 53.9 + - + +
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B GLU 3.0 19.8 + - - -
312B GLU* 3.5 10.3 - - - -
313B THR 3.1 0.2 - - - -
314B VAL* 1.3 76.5 - - - +
316B ARG* 1.3 57.7 + - - +
318B GLN* 3.3 13.7 + - - +
319B GLY* 2.9 27.4 + - - -
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B VAL* 3.7 19.1 + - + +
303B GLU* 3.7 31.6 + - - +
304B SER 3.6 18.6 + - - -
305B VAL* 3.8 18.8 - - - +
308B LEU* 3.6 16.8 - - - +
312B GLU* 2.8 37.9 + - - +
313B THR 3.1 7.5 + - - +
315B SER* 1.3 79.4 - - - +
317B ILE* 1.3 61.3 + - - +
319B GLY* 3.4 8.6 + - - -
320B GLN* 3.6 18.4 + - - +
270C ASP* 4.0 14.5 - - - +
272E ARG* 5.1 6.5 - - - +
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B PHE* 4.3 26.6 - - + -
261B PHE* 4.3 20.0 - - + -
263B LEU* 4.0 19.3 - - + -
297B LEU* 3.9 22.0 - - + -
300B VAL* 3.8 22.0 - - + -
313B THR* 3.2 14.9 + - + +
314B VAL* 3.0 11.3 + - + +
316B ARG* 1.3 74.5 - - - +
318B GLN* 1.3 66.5 + - + +
320B GLN* 3.3 17.5 + - - +
321B GLY 4.2 4.3 + - - +
324B VAL* 4.3 12.1 - - + +
326B LEU* 4.1 6.5 - - + -
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LYS* 5.6 5.3 + - - +
259B PHE* 6.2 0.9 - - - -
314B VAL* 2.8 39.4 + - + +
315B SER* 3.7 11.0 - - - +
317B ILE* 1.3 80.8 - - + +
319B GLY* 1.3 60.2 + - - +
320B GLN 3.1 1.8 + - - -
321B GLY* 3.2 13.7 + - - +
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B SER 2.9 15.4 + - - -
316B ARG* 3.4 3.5 + - - -
317B ILE 3.3 0.8 - - - -
318B GLN* 1.3 75.7 - - - +
320B GLN* 1.3 70.2 + - - +
321B GLY 3.4 0.4 - - - -
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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