Contacts of the helix formed by residues 310 - 321 (chain G) in PDB entry 1FQV
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 GLN 310 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283G GLU* 5.0 10.0 + - + +
287G GLN* 5.7 4.7 - - - +
307G LYS 2.7 30.9 + - - -
308G ASN* 4.2 3.3 - - - +
309G LEU* 1.3 81.0 - - - +
311G LYS* 1.3 66.5 + - - +
312G SER* 3.2 17.0 - - - +
313G ASP* 2.8 33.5 + - - +
314G LEU* 3.3 5.7 + - - +
334G MET* 3.8 27.1 - - - +
335G LEU* 4.3 2.4 - - - +
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Residues in contact with LYS 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310G GLN* 1.3 72.3 + - - +
312G SER* 1.3 58.1 + - - +
313G ASP 3.0 0.4 - - - -
314G LEU* 2.7 31.6 + - + +
315G SER* 2.8 19.5 + - - +
334G MET* 5.2 3.7 - - - +
335G LEU* 4.2 8.6 - - + +
338G ASP* 3.0 59.4 + - - +
339G CYS* 4.2 18.2 - - + +
341G GLN* 4.1 10.5 - - - +
342G GLU* 4.9 8.7 - - + +
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Residues in contact with SER 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G GLN* 5.8 1.0 + - - -
310G GLN* 3.6 16.0 - - - +
311G LYS* 1.3 78.6 - - - +
313G ASP* 1.3 63.2 + - - +
315G SER* 3.1 11.9 + - - -
316G THR* 3.0 32.4 + - - -
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Residues in contact with ASP 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G GLU* 6.0 0.2 - - - +
286G VAL* 4.3 6.1 - - + -
287G GLN* 3.5 36.6 + - - +
290G VAL* 3.3 29.7 - - + +
308G ASN 3.8 8.3 - - - +
309G LEU* 3.7 16.8 - - + -
310G GLN* 2.8 40.5 + - - +
311G LYS 3.0 0.6 - - - -
312G SER* 1.3 82.3 + - - +
314G LEU* 1.3 59.3 + - - +
316G THR* 4.4 2.5 + - - -
317G LEU* 3.3 15.8 + - - +
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Residues in contact with LEU 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G LEU* 5.0 4.0 - - + +
310G GLN 3.3 5.8 + - - +
311G LYS* 2.7 18.4 + - + +
313G ASP* 1.3 77.5 - - - +
315G SER* 1.3 59.6 + - - +
317G LEU* 3.8 8.2 - - + +
318G VAL* 3.0 39.0 + - + +
327G LEU* 4.8 4.5 - - + -
329G LEU* 4.1 14.4 - - + -
335G LEU* 4.5 7.4 - - + -
339G CYS* 3.5 41.1 - - + +
342G GLU* 4.0 6.5 - - + -
343G PHE* 3.6 32.5 - - + -
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Residues in contact with SER 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311G LYS* 2.8 20.3 + - - +
312G SER* 3.3 15.0 - - - -
314G LEU* 1.3 76.1 - - - +
316G THR* 1.3 56.4 + - - +
318G VAL* 3.1 3.6 + - - +
319G ARG* 2.7 40.0 + - - +
342G GLU* 3.0 30.9 + - - +
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Residues in contact with THR 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G VAL* 3.5 29.5 - - + +
291G ALA* 4.0 9.2 - - + -
312G SER* 3.0 16.4 + - - -
313G ASP* 3.9 6.9 + - - -
315G SER* 1.3 76.1 - - - +
317G LEU* 1.3 63.2 + - - +
319G ARG* 3.3 35.7 + - - +
320G ARG* 2.9 36.9 + - - +
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Residues in contact with LEU 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G VAL* 3.7 30.1 - - + -
293G VAL* 5.9 1.1 - - + -
300G LEU* 3.5 30.3 - - + -
302G LEU* 5.3 2.7 - - + -
313G ASP 3.3 15.5 + - - +
314G LEU* 3.8 11.4 - - + +
315G SER 3.2 0.4 - - - -
316G THR* 1.3 80.6 - - - +
318G VAL* 1.3 55.6 + - + +
320G ARG 3.7 0.2 - - - -
321G CYS* 2.7 49.1 + - + +
324G LEU* 3.4 26.0 - - + -
327G LEU* 4.0 21.3 - - + -
329G LEU* 5.4 5.6 - - + -
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Residues in contact with VAL 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314G LEU* 3.0 41.9 + - + +
315G SER 3.1 4.8 + - - +
317G LEU* 1.3 79.7 - - + +
319G ARG* 1.3 63.9 + - - +
321G CYS 3.8 11.5 + - - +
322G PRO* 4.1 5.4 - - - +
324G LEU* 5.9 0.4 - - + -
327G LEU* 5.5 0.7 - - + -
342G GLU* 3.3 37.0 - - + +
343G PHE 4.8 0.2 - - - +
345G GLN* 3.7 23.0 - - + +
346G LEU* 3.7 30.0 - - + +
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Residues in contact with ARG 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295G GLU* 5.3 0.2 - - - +
315G SER* 2.7 21.8 + - - +
316G THR* 3.4 40.8 + - - +
318G VAL* 1.3 76.7 - - - +
320G ARG* 1.3 75.3 + - - +
322G PRO* 4.3 7.4 - - - +
345G GLN* 6.0 1.8 - - - -
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Residues in contact with ARG 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G VAL 3.2 20.6 + - - -
291G ALA* 2.7 30.7 + - - +
292G HIS* 3.7 4.6 - - - +
293G VAL 2.7 34.3 + - - +
294G SER* 4.7 1.0 - - - +
295G GLU* 2.8 53.5 + - - +
316G THR* 2.9 26.7 + - - +
319G ARG* 1.3 93.7 - - - +
321G CYS* 1.3 73.3 + - - +
322G PRO* 3.4 3.6 - - - +
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Residues in contact with CYS 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G VAL 5.0 0.2 - - - -
293G VAL* 3.7 15.3 - - - -
294G SER 3.8 10.3 - - - -
295G GLU* 4.6 4.0 - - - +
297G ILE* 3.8 20.4 - - + -
317G LEU* 2.7 39.1 + - + +
318G VAL 3.9 3.6 - - - -
319G ARG 3.4 0.6 - - - -
320G ARG* 1.3 105.6 - - - +
322G PRO* 1.3 61.0 - - - +
323G ASN 3.2 6.9 + - - +
324G LEU* 3.7 9.1 - - + +
346G LEU* 3.6 15.8 - - - +
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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