Contacts of the helix formed by residues 295 - 310 (chain U) in PDB entry 6FF7
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 295 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288U LEU* 3.2 26.0 + - - +
289U VAL* 4.5 3.5 - - - -
291U ARG 2.9 12.4 + - - -
294U ASP* 1.3 76.9 - - - +
296U HIS* 1.3 57.7 + - - +
297U LEU 3.4 1.8 - - - -
298U PHE* 3.3 14.0 + - - +
299U SER* 2.8 31.1 + - - -
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Residues in contact with HIS 296 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291U ARG 3.9 2.6 + - - -
292U GLU 3.5 20.2 - - - +
293U GLU* 3.5 9.4 + - - +
294U ASP 3.4 2.8 - - - -
295U GLY* 1.3 76.1 - - - +
297U LEU* 1.3 63.4 + - - +
299U SER* 3.2 8.7 + - - -
300U GLN* 3.1 21.7 + - - +
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Residues in contact with LEU 297 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251U GLU* 5.7 8.7 - - + -
293U GLU 5.0 0.4 + - - -
294U ASP 4.8 3.4 + - - +
295U GLY 3.4 0.2 - - - -
296U HIS* 1.3 78.5 - - - +
298U PHE* 1.3 58.0 + - - +
300U GLN* 3.2 7.4 + - - +
301U LEU* 2.9 30.4 + - - +
437U ASN* 4.8 19.2 - - + +
449U CYS 5.6 5.4 - - - +
451U ALA* 5.2 2.2 - - + +
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Residues in contact with PHE 298 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247U VAL 5.7 1.6 - - - +
250U CYS* 5.6 7.2 - - + -
251U GLU* 5.3 19.1 - - + +
254U ILE* 5.4 3.1 - - - +
288U LEU* 5.4 10.8 - - + +
289U VAL* 5.7 2.2 - - - +
294U ASP 5.2 1.9 + - - +
295U GLY* 3.3 18.3 + - - +
297U LEU* 1.3 78.3 - - - +
299U SER* 1.3 57.2 + - - +
301U LEU* 3.7 6.3 - - - +
302U LEU* 2.9 28.7 + - - +
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Residues in contact with SER 299 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289U VAL* 4.9 20.2 - - - +
295U GLY 2.8 17.6 + - - -
296U HIS* 3.4 9.0 - - - -
297U LEU 3.2 0.2 - - - -
298U PHE* 1.3 77.9 - - - +
300U GLN* 1.3 57.2 + - - +
302U LEU* 3.1 9.4 + - - +
303U ASP* 3.0 27.0 + - - +
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Residues in contact with GLN 300 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296U HIS 3.1 12.8 + - - +
297U LEU* 3.2 9.2 + - - +
299U SER* 1.3 73.3 - - - +
301U LEU* 1.3 66.5 + - - +
303U ASP* 3.4 9.4 + - - +
304U MET* 3.3 19.1 + - - +
437U ASN* 5.6 5.2 - - + -
451U ALA* 3.7 24.0 - - + +
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Residues in contact with LEU 301 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251U GLU* 5.0 7.2 - - + +
254U ILE* 4.1 25.0 - - + +
255U GLU* 5.2 2.2 - - + +
258U ILE* 5.6 1.4 - - - +
297U LEU 2.9 16.8 + - - +
298U PHE* 3.7 7.2 - - - +
300U GLN* 1.3 75.6 - - - +
302U LEU* 1.3 62.8 + - - +
304U MET* 3.2 10.4 + - - +
305U LEU* 3.0 22.1 + - - +
450U LEU 6.4 0.2 - - - -
451U ALA* 4.4 10.4 - - + +
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Residues in contact with LEU 302 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254U ILE* 5.1 4.0 - - + +
283U CYS* 5.4 13.5 - - + +
289U VAL* 6.3 1.6 - - + -
298U PHE 2.9 16.1 + - - +
299U SER* 3.1 14.1 + - - +
301U LEU* 1.3 77.6 - - - +
303U ASP* 1.3 56.1 + - - +
305U LEU* 3.2 9.1 + - - +
306U LYS* 2.9 29.0 + - - +
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Residues in contact with ASP 303 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299U SER 3.0 12.4 + - - +
300U GLN* 3.6 11.2 - - - +
301U LEU 3.3 0.2 - - - -
302U LEU* 1.3 74.6 - - - +
304U MET* 1.3 61.9 + - - +
306U LYS* 3.4 9.1 + - - +
307U PHE* 3.1 21.1 + - - +
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Residues in contact with MET 304 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258U ILE* 5.3 11.4 - - + +
300U GLN 3.3 9.5 + - - +
301U LEU* 3.2 13.3 + - - +
303U ASP* 1.3 79.6 - - - +
305U LEU* 1.3 62.0 + - - +
307U PHE* 3.2 21.1 + - - +
308U TYR* 3.3 8.1 + - - +
451U ALA* 6.1 5.2 - - + -
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Residues in contact with LEU 305 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254U ILE* 5.1 13.5 - - + +
257U MET* 5.2 7.6 - - + -
258U ILE* 5.0 13.6 - - + +
261U GLU* 5.7 1.3 - - - +
301U LEU 3.0 13.5 + - - +
302U LEU* 3.5 11.7 - - - +
304U MET* 1.3 73.8 - - - +
306U LYS* 1.3 61.4 + - - +
308U TYR* 3.0 7.8 + - - +
309U THR* 2.8 30.3 + - - -
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Residues in contact with LYS 306 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280U LEU* 6.1 6.1 - - + -
302U LEU 2.9 13.4 + - - +
303U ASP* 3.6 13.0 - - - +
305U LEU* 1.3 74.7 - - - +
307U PHE* 1.3 63.1 + - - +
308U TYR 3.1 0.7 + - - -
309U THR* 3.3 6.4 + - - +
310U GLY* 3.2 19.9 + - - -
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Residues in contact with PHE 307 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303U ASP 3.1 13.5 + - - +
304U MET* 3.2 13.4 + - - +
306U LYS* 1.3 77.4 - - - +
308U TYR* 1.3 55.9 + - - +
310U GLY 3.6 2.4 - - - +
311U PHE* 3.3 23.0 + - - +
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Residues in contact with TYR 308 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258U ILE* 5.0 4.9 - - + +
261U GLU* 3.9 35.9 - - + +
262U ALA* 4.9 6.5 - - + +
304U MET 3.3 7.3 + - - +
305U LEU* 3.0 10.0 + - - +
307U PHE* 1.3 77.7 - - - +
309U THR* 1.3 63.9 - - - +
310U GLY 3.1 1.8 - - - -
311U PHE* 3.1 22.0 + - + +
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Residues in contact with THR 309 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261U GLU* 5.1 3.9 - - - +
271U ASN* 6.5 0.9 - - - -
274U LEU* 6.4 2.0 - - - -
280U LEU* 5.6 9.6 - - - -
305U LEU 2.8 19.8 + - - -
306U LYS* 3.3 6.7 + - - -
308U TYR* 1.3 72.9 - - - +
310U GLY* 1.3 56.4 + - - +
311U PHE 3.4 0.7 + - - +
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Residues in contact with GLY 310 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306U LYS 3.2 12.4 + - - -
307U PHE 3.6 5.3 - - - +
308U TYR 3.1 0.4 - - - -
309U THR* 1.3 78.9 - - - +
311U PHE* 1.3 63.2 + - - +
312U GLU* 3.7 1.9 + - - +
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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