Contacts of the helix formed by residues 307 - 320 (chain F) in PDB entry 6G2T
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 307 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218F VAL* 3.7 16.3 - - - +
219F ALA 5.6 0.2 - - - -
220F LEU* 5.7 5.9 - - - -
305F TYR 3.6 0.2 + - - -
306F PRO* 1.3 72.5 - - - +
308F ILE* 1.3 58.5 + - - +
309F ALA 3.3 2.6 - - - +
310F ASP* 3.3 19.2 + - - +
311F ARG* 2.9 32.6 + - - +
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Residues in contact with ILE 308 (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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218F VAL* 3.4 24.2 - - + -
260F LEU* 5.7 5.4 - - + -
261F PHE* 4.7 9.0 - - + -
273F ILE* 5.1 6.1 - - + -
298F LEU* 4.0 20.2 - - + -
302F THR 3.5 24.9 - - - +
303F THR* 3.6 22.2 - - + +
305F TYR* 3.2 32.9 + - + +
306F PRO 3.3 1.2 + - - -
307F GLY* 1.3 76.6 - - - +
309F ALA* 1.3 58.9 + - - +
311F ARG* 3.4 1.2 + - - +
312F MET* 2.9 45.5 + - + +
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Residues in contact with ALA 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F LEU* 4.0 11.6 - - + +
307F GLY 4.8 0.6 - - - +
308F ILE* 1.3 79.6 - - - +
310F ASP* 1.3 63.5 + - - +
312F MET* 3.9 3.4 - - - +
313F GLN* 3.0 31.2 + - - +
328F ILE* 4.2 13.3 - - + +
330F ALA* 4.0 26.7 - - + +
334F ARG* 5.8 1.3 - - - +
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Residues in contact with ASP 310 (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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220F LEU* 5.0 22.0 - - + +
307F GLY* 3.3 19.1 + - - +
308F ILE 3.3 0.8 - - - -
309F ALA* 1.3 79.6 - - - +
311F ARG* 1.3 62.5 + - - +
313F GLN* 3.5 13.8 + - - +
314F LYS* 3.4 22.4 + - - +
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Residues in contact with ARG 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F VAL* 3.4 26.7 - - + -
219F ALA 3.2 22.8 + - - +
220F LEU* 3.5 12.0 + - - +
221F ASP* 3.8 2.0 + - - +
222F PHE* 3.4 25.5 - - - +
223F GLU* 5.6 1.2 + - - -
258F GLU* 2.9 33.8 + - - -
261F PHE* 3.3 22.1 - - + +
262F GLN* 5.2 4.9 - - - +
307F GLY 2.9 20.9 + - - +
308F ILE 4.0 2.0 - - - +
310F ASP* 1.3 70.4 - - - +
312F MET* 1.3 66.3 + - - +
314F LYS* 3.1 36.9 - - - +
315F GLU* 2.9 38.9 + - - +
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Residues in contact with MET 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F MET* 5.4 4.7 - - + -
261F PHE* 3.4 24.2 - - + -
273F ILE* 3.5 24.0 - - + +
274F HIS* 3.7 30.5 - - + +
277F THR* 4.4 7.4 - - - +
296F THR* 6.0 2.5 - - + -
298F LEU* 5.0 16.2 - - + -
308F ILE* 2.9 38.1 + - + +
309F ALA* 3.9 5.8 - - - +
311F ARG* 1.3 76.2 - - - +
313F GLN* 1.3 58.5 + - - +
315F GLU* 3.8 3.2 - - - +
316F ILE* 2.9 49.1 + - + +
328F ILE* 3.7 12.6 - - + -
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Residues in contact with GLN 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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309F ALA 3.0 19.6 + - - +
310F ASP* 3.8 14.8 - - - +
311F ARG 3.3 0.2 - - - -
312F MET* 1.3 78.2 - - - +
314F LYS* 1.3 58.6 + - - +
316F ILE* 4.1 1.7 - - - +
317F THR* 2.7 39.0 + - - +
326F ILE* 3.9 24.2 + - + +
327F LYS* 5.8 0.2 - - - -
328F ILE* 3.4 22.4 + - + +
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Residues in contact with LYS 314 (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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220F LEU* 2.8 31.4 - - + +
221F ASP* 4.5 10.1 + - - +
310F ASP 3.4 7.5 + - - +
311F ARG* 3.1 34.6 - - - +
313F GLN* 1.3 80.2 - - - +
315F GLU* 1.3 79.8 + - - +
317F THR* 3.4 5.3 + - - -
318F ALA* 2.9 30.7 + - - +
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Residues in contact with GLU 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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261F PHE* 3.1 19.2 - - - -
274F HIS* 2.9 48.2 + - + +
278F PHE* 4.7 1.1 - - - -
311F ARG* 2.9 53.0 + - - +
312F MET* 3.8 3.8 - - - +
314F LYS* 1.3 95.2 + - - +
316F ILE* 1.3 63.7 + - - +
318F ALA* 3.6 5.7 + - - +
319F LEU* 3.3 28.8 + - - +
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Residues in contact with ILE 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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274F HIS* 4.6 10.8 - - + +
277F THR* 4.8 15.0 - - + -
278F PHE* 3.1 27.5 - - + -
281F ILE* 5.8 2.7 - - + -
293F TYR* 4.1 18.8 - - + +
296F THR* 4.8 10.3 - - + +
312F MET* 2.9 37.7 + - + +
313F GLN 4.1 1.8 - - - +
315F GLU* 1.3 74.9 - - - +
317F THR* 1.3 59.7 + - - +
320F ALA* 2.9 34.5 + - - +
326F ILE* 3.8 20.2 - - + -
328F ILE* 3.8 22.7 - - + -
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Residues in contact with THR 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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313F GLN* 2.7 28.7 + - - +
314F LYS* 3.7 5.6 - - - -
316F ILE* 1.3 77.2 - - - +
318F ALA* 1.3 58.4 + - - +
320F ALA* 2.8 23.0 - - - +
321F PRO 4.7 3.8 - - - +
322F SER* 5.2 6.1 + - - -
324F MET 6.0 1.1 - - - +
326F ILE* 3.5 29.7 + - + +
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Residues in contact with ALA 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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314F LYS 2.9 18.5 + - - +
315F GLU* 3.9 6.7 - - - +
316F ILE 3.3 0.2 - - - -
317F THR* 1.3 79.9 - - - +
319F LEU* 1.3 64.7 + - + +
320F ALA 3.7 2.8 - - - +
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Residues in contact with LEU 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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274F HIS* 4.3 16.6 - - + -
275F GLU* 4.8 12.6 - - + +
278F PHE* 3.3 41.1 - - + -
315F GLU 3.3 10.2 + - - +
318F ALA* 1.3 80.7 - - + +
320F ALA* 1.3 62.9 + - - +
321F PRO* 4.0 1.0 - - - +
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Residues in contact with ALA 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F PHE* 3.5 6.0 - - + -
293F TYR* 3.5 30.7 - - + -
316F ILE 2.9 22.0 + - - +
317F THR 2.8 18.2 - - - +
318F ALA 3.7 3.5 - - - +
319F LEU* 1.3 79.2 - - - +
321F PRO* 1.3 78.4 - - + +
322F SER 3.6 0.5 + - - -
324F MET* 6.3 0.2 - - + -
326F ILE* 4.3 7.6 - - + -
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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