Contacts of the helix formed by residues 309 - 319 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D GLU* 3.8 5.2 - - - -
273D PRO* 4.3 7.5 - - - +
275D GLN* 3.4 4.9 - - - -
307D GLY 4.1 0.8 + - - -
308D LEU* 1.3 74.1 - - - +
310D HIS* 1.3 64.4 + - - -
311D GLU* 3.5 2.2 - - - -
312D GLU* 3.5 9.3 + - - +
313D THR* 2.9 27.5 + - - -
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Residues in contact with HIS 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D LEU* 3.2 44.7 - - + +
265D GLU* 3.1 19.1 + - - +
275D GLN* 2.8 24.3 + - - +
309D GLY* 1.3 69.2 - - - -
311D GLU* 1.3 64.6 + - - +
313D THR* 3.1 3.3 + - - -
314D VAL* 2.9 35.1 + - + +
334F ASP 4.1 5.2 - - - -
335F ARG* 3.6 39.8 + - + +
336F GLU 3.5 2.6 - - - -
337F THR* 2.7 33.4 + - - -
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D GLY 5.5 0.4 - - - -
310D HIS* 1.3 81.7 - - + +
312D GLU* 1.3 68.4 + - + +
314D VAL* 3.9 6.7 - - - +
315D SER* 3.0 25.6 + - - -
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Residues in contact with GLU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D LEU* 3.9 19.1 - - + -
309D GLY* 3.5 16.5 + - - +
310D HIS 3.2 0.4 - - - -
311D GLU* 1.3 85.8 - - + +
313D THR* 1.3 62.7 + - - +
315D SER* 2.8 25.0 + - - -
316D ARG* 2.9 49.7 + - - +
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Residues in contact with THR 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D LEU* 3.9 13.5 - - + -
275D GLN* 3.6 19.0 - - + +
297D LEU* 3.5 32.5 - - + -
300D VAL* 4.6 2.9 - - + -
305D VAL* 4.3 15.6 - - + +
308D LEU* 3.9 13.3 + - - +
309D GLY 2.9 23.1 + - - -
310D HIS 3.1 3.1 + - - -
312D GLU* 1.3 75.4 - - - +
314D VAL* 1.3 62.8 + - - +
316D ARG* 3.1 12.5 + - - +
317D ILE* 3.1 21.6 + - + +
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D LEU* 4.1 10.1 - - + -
310D HIS* 2.9 36.7 + - + +
311D GLU* 4.0 6.3 - - - +
313D THR* 1.3 71.1 - - - +
315D SER* 1.3 58.8 + - - +
317D ILE* 3.1 10.7 + - + +
318D GLN* 2.8 53.7 + - + +
337F THR* 3.7 38.1 - - + +
339F VAL* 4.7 9.9 - - + -
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Residues in contact with SER 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D GLU 3.0 16.8 + - - -
312D GLU* 2.8 30.8 + - - -
314D VAL* 1.3 76.7 - - - +
316D ARG* 1.3 55.2 + - - +
318D GLN* 3.8 13.7 - - - +
319D GLY* 2.8 28.8 + - - -
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Residues in contact with ARG 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D VAL* 4.0 18.3 + - + +
303D GLU* 4.0 25.1 + - - +
304D SER 3.8 18.0 + - - -
305D VAL* 3.8 18.7 - - - +
308D LEU* 3.6 23.2 - - - +
312D GLU* 2.9 42.3 + - - +
313D THR* 3.4 8.1 - - - +
315D SER* 1.3 74.7 - - - +
317D ILE* 1.3 66.0 + - - +
319D GLY* 3.4 8.8 + - - -
320D GLN* 3.4 19.2 + - - +
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D PHE* 3.8 32.1 - - + -
261D PHE* 4.1 19.7 - - + -
263D LEU* 4.2 15.5 - - + -
297D LEU* 4.0 22.7 - - + -
300D VAL* 3.9 21.3 - - + -
313D THR 3.1 14.9 + - - +
314D VAL* 3.5 9.4 - - - +
316D ARG* 1.3 74.1 - - - +
318D GLN* 1.3 65.4 + - + +
320D GLN* 3.0 19.2 + - - +
321D GLY 4.1 4.3 + - - +
324D VAL* 4.7 8.3 - - + +
326D LEU* 4.2 7.9 - - + -
339F VAL* 4.5 18.6 - - + -
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Residues in contact with GLN 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D LYS* 5.5 5.5 + - - +
259D PHE* 6.1 1.1 - - - -
314D VAL* 2.8 42.3 + - + +
315D SER* 3.8 10.7 - - - +
317D ILE* 1.3 76.5 - - + +
319D GLY* 1.3 58.3 + - - +
320D GLN 3.1 4.7 + - - -
321D GLY* 3.3 13.9 + - - -
337F THR* 5.5 4.8 - - - +
339F VAL* 5.5 6.4 - - + +
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Residues in contact with GLY 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D SER 2.8 21.3 + - - -
316D ARG 3.9 3.4 - - - -
317D ILE 3.2 0.2 - - - -
318D GLN* 1.3 72.1 - - - +
320D GLN* 1.3 66.2 + - - +
321D 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