Contacts of the helix formed by residues 310 - 321 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283I GLU* 4.7 11.4 + - + +
287I GLN* 5.6 5.2 - - - +
307I LYS 2.6 31.1 + - - -
308I ASN* 4.2 4.5 - - - +
309I LEU* 1.3 80.8 - - - +
311I LYS* 1.3 66.5 + - - +
312I SER* 3.2 16.4 - - - +
313I ASP* 2.7 30.7 + - - +
314I LEU* 3.4 8.7 + - - +
334I MET* 3.8 28.1 - - - +
335I LEU* 4.3 3.5 - - - +
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Residues in contact with LYS 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310I GLN* 1.3 74.2 + - - +
312I SER* 1.3 58.3 + - - +
314I LEU* 2.8 22.8 + - + +
315I SER* 2.9 18.9 + - - +
334I MET* 5.3 5.0 - - - +
335I LEU* 4.2 12.2 - - + +
338I ASP* 2.7 59.3 + - - +
339I CYS* 3.9 18.6 - - - +
341I GLN* 4.0 11.4 - - - +
342I GLU* 5.0 8.7 - - + +
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Residues in contact with SER 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I GLN* 5.7 1.7 + - - -
310I GLN* 3.7 14.9 - - - +
311I LYS* 1.3 79.2 - - - +
313I ASP* 1.3 63.9 + - - +
315I SER* 3.3 11.1 + - - -
316I THR* 3.0 31.0 + - - -
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Residues in contact with ASP 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I VAL* 4.1 10.1 - - + -
287I GLN* 3.5 33.2 + - - +
290I VAL* 3.2 36.8 - - + +
308I ASN 3.8 5.2 - - - +
309I LEU* 3.6 19.2 - - + -
310I GLN* 2.7 39.6 + - - +
311I LYS 3.0 0.6 - - - -
312I SER* 1.3 81.1 + - - +
314I LEU* 1.3 61.9 + - - +
316I THR* 4.6 0.7 - - - -
317I LEU 3.3 9.5 + - - -
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Residues in contact with LEU 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309I LEU* 4.9 4.7 - - + +
310I GLN 3.4 5.8 + - - +
311I LYS* 2.8 15.2 + - + +
313I ASP* 1.3 77.8 - - - +
315I SER* 1.3 56.9 + - - +
317I LEU* 3.4 8.6 + - + +
318I VAL* 2.9 44.6 + - + +
327I LEU* 5.0 4.0 - - + -
329I LEU* 4.1 13.9 - - + -
335I LEU* 4.2 8.7 - - + -
339I CYS* 3.5 39.9 - - + +
342I GLU* 3.8 7.9 - - + -
343I PHE* 3.6 32.3 - - + -
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Residues in contact with SER 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311I LYS* 2.9 16.7 + - - +
312I SER* 3.4 14.6 - - - -
314I LEU* 1.3 73.6 - - - +
316I THR* 1.3 54.9 + - - +
318I VAL* 3.0 3.8 + - - +
319I ARG* 2.7 40.1 + - - +
342I GLU* 2.9 34.2 + - - +
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Residues in contact with THR 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I VAL* 3.4 31.6 - - + +
291I ALA* 4.0 10.5 - - + -
312I SER 3.0 14.3 + - - -
313I ASP* 3.9 5.4 - - - -
315I SER* 1.3 76.6 - - - +
317I LEU* 1.3 64.8 + - - +
319I ARG* 3.1 36.3 + - - +
320I ARG* 2.9 35.0 + - - +
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Residues in contact with LEU 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I VAL* 3.7 28.9 - - + +
293I VAL* 5.7 1.1 - - + -
300I LEU* 3.6 29.2 - - + -
302I LEU* 5.2 3.6 - - + -
313I ASP 3.3 12.7 + - - +
314I LEU* 3.4 15.0 - - + +
316I THR* 1.3 80.0 - - - +
318I VAL* 1.3 58.1 + - + +
320I ARG* 3.7 0.4 - - - -
321I CYS* 2.8 45.3 + - + +
324I LEU* 3.6 23.8 - - + -
327I LEU* 4.0 22.9 - - + -
329I LEU* 5.5 5.8 - - + -
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Residues in contact with VAL 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314I LEU* 2.9 39.0 + - + +
315I SER 3.6 3.4 - - - +
317I LEU* 1.3 79.4 - - + +
319I ARG* 1.3 63.0 + - - +
321I CYS 3.7 12.3 + - - -
322I PRO* 4.1 4.0 - - - +
324I LEU* 5.8 0.4 - - + -
327I LEU* 5.5 1.8 - - + -
342I GLU* 3.2 37.2 - - + +
343I PHE* 5.1 0.2 - - + -
345I GLN* 3.7 23.2 - - + +
346I LEU* 3.7 30.9 - - + +
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Residues in contact with ARG 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295I GLU* 5.1 0.7 - - - +
315I SER* 2.7 22.0 + - - +
316I THR* 3.4 41.6 + - - +
318I VAL* 1.3 76.5 - - - +
320I ARG* 1.3 73.9 + - - +
322I PRO* 4.7 5.2 - - - +
345I GLN* 6.2 0.2 - - - -
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Residues in contact with ARG 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I VAL 3.1 25.5 + - - -
291I ALA* 3.2 24.7 + - - +
292I HIS* 3.6 10.1 - - - +
293I VAL* 2.5 36.3 + - - +
294I SER* 4.6 0.8 - - - +
295I GLU* 2.8 54.1 + - - +
316I THR* 2.9 22.1 + - - +
319I ARG* 1.3 95.4 - - - +
321I CYS* 1.3 71.8 + - - +
322I PRO* 3.5 3.7 - - - +
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Residues in contact with CYS 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293I VAL* 3.9 6.3 - - - -
294I SER 3.7 9.9 - - - +
295I GLU* 4.5 4.3 - - - +
297I ILE* 3.6 33.4 - - + +
317I LEU* 2.8 29.9 + - + +
318I VAL 3.9 4.4 - - - +
319I ARG 3.5 0.4 - - - -
320I ARG* 1.3 108.4 - - - +
322I PRO* 1.3 63.0 - - - +
323I ASN 3.3 3.4 + - - +
324I LEU* 3.7 10.3 - - + +
346I LEU* 3.6 15.9 - - - +
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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