Contacts of the helix formed by residues 309 - 319 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265F GLU* 3.7 7.2 - - - -
273F PRO* 4.3 7.3 - - - +
275F GLN* 3.3 0.4 - - - -
307F GLY 4.3 0.4 + - - -
308F LEU* 1.3 79.0 - - - +
310F HIS* 1.3 61.7 + - - -
311F GLU 3.5 2.2 - - - -
312F GLU* 3.6 7.0 + - - +
313F THR* 2.7 32.1 + - - -
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Residues in contact with HIS 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D ASP 4.2 0.4 - - - -
335D ARG* 3.6 48.1 + - - +
337D THR* 2.7 25.8 + - - -
263F LEU* 3.2 35.8 - - + +
265F GLU* 2.9 19.8 + - + +
275F GLN* 2.9 25.3 + - - +
309F GLY* 1.3 72.2 - - - -
311F GLU* 1.3 77.4 + - + +
313F THR* 3.3 2.8 + - - -
314F VAL* 2.9 45.8 + - + +
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Residues in contact with GLU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 4.9 5.2 + - - -
334D ASP 3.7 13.7 - - - +
335D ARG* 5.8 3.7 - - - +
337D THR* 4.9 1.1 + - - -
309F GLY 3.5 0.2 - - - -
310F HIS* 1.3 99.4 - - + +
312F GLU* 1.3 59.2 + - - +
314F VAL* 3.2 14.3 + - - +
315F SER* 2.9 30.1 + - - -
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Residues in contact with GLU 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F LEU* 3.3 34.0 - - + +
309F GLY* 3.6 10.0 + - - +
310F HIS 3.3 0.4 - - - -
311F GLU* 1.3 79.5 - - - +
313F THR* 1.3 56.6 + - - +
315F SER* 2.9 23.9 + - - -
316F ARG* 3.1 40.9 + - - +
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Residues in contact with THR 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F LEU* 4.0 12.6 - - + -
275F GLN* 3.6 20.0 - - + +
297F LEU* 3.7 30.1 - - + -
300F VAL* 4.6 1.1 - - + -
305F VAL* 4.1 15.3 - - + +
308F LEU* 3.7 20.8 + - - +
309F GLY 2.7 23.1 + - - -
310F HIS 3.7 3.8 - - - -
312F GLU* 1.3 73.8 - - - +
314F VAL* 1.3 66.2 + - - +
316F ARG* 3.5 4.7 + - - +
317F ILE* 3.1 28.9 + - + +
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Residues in contact with VAL 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D THR* 4.0 22.4 - - + +
339D VAL* 4.9 9.4 - - + -
263F LEU* 4.4 8.7 - - + -
310F HIS* 2.9 49.7 + - + +
311F GLU* 3.2 14.1 + - - +
313F THR* 1.3 77.2 - - - +
315F SER* 1.3 56.7 + - - +
317F ILE* 3.3 9.3 + - + +
318F GLN* 2.9 55.1 + - + +
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Residues in contact with SER 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F GLU 2.9 16.0 + - - -
312F GLU* 2.9 31.2 + - - -
314F VAL* 1.3 75.9 - - - +
316F ARG* 1.3 52.0 + - - +
318F GLN* 3.0 12.3 + - - +
319F GLY* 2.5 36.2 + - - -
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Residues in contact with ARG 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300F VAL* 3.8 17.5 + - + +
303F GLU* 3.7 40.4 + - - +
304F SER 3.9 14.1 + - - -
305F VAL* 4.0 10.4 - - - +
308F LEU* 3.6 22.9 - - - +
312F GLU* 3.1 44.0 + - - +
313F THR* 3.6 5.2 - - - +
315F SER* 1.3 78.7 - - - +
317F ILE* 1.3 63.0 + - - +
319F GLY* 3.6 5.2 + - - +
320F GLN* 3.4 22.0 + - - +
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Residues in contact with ILE 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D VAL* 5.0 17.9 - - + -
259F PHE* 4.1 29.0 - - + -
261F PHE* 4.3 14.8 - - + -
263F LEU* 4.2 15.5 - - + -
297F LEU* 3.9 22.9 - - + -
300F VAL* 4.0 24.0 - - + -
313F THR 3.1 18.2 + - - +
314F VAL* 3.6 8.7 - - - +
316F ARG* 1.3 74.2 - - - +
318F GLN* 1.3 66.8 + - + +
320F GLN* 3.2 20.0 + - - +
321F GLY 4.0 5.2 + - - +
324F VAL* 4.7 4.3 - - + +
326F LEU* 4.3 10.5 - - + -
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Residues in contact with GLN 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D THR* 5.7 2.2 - - - +
339D VAL* 5.6 6.1 - - + +
254F LYS* 5.5 4.8 + - - +
314F VAL* 2.9 42.4 + - + +
315F SER* 3.6 10.5 - - - +
317F ILE* 1.3 76.1 - - + +
319F GLY* 1.3 56.7 + - - +
320F GLN 3.0 10.8 + - - -
321F GLY* 3.2 13.8 + - - +
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Residues in contact with GLY 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F SER 2.5 20.2 + - - -
316F ARG* 3.6 4.2 + - - -
317F ILE 3.3 0.6 - - - -
318F GLN* 1.3 70.9 - - - +
320F GLN* 1.3 65.3 + - - +
321F GLY 3.5 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