Contacts of the helix formed by residues 364 - 373 (chain A) in PDB entry 1FBV
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 THR 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A LYS* 5.8 2.5 - - + -
363A VAL* 1.3 78.7 - - - +
365A GLN* 1.3 59.8 + - - +
366A GLU* 3.0 13.6 + - - +
367A GLN* 2.8 61.7 + - - +
368A TYR* 3.1 14.5 + - - -
1029C GLU* 4.2 5.8 - - - -
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Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 3.3 26.6 + - - -
218A GLY* 4.6 0.6 - - - +
219A LEU* 3.1 58.0 - - + +
220A GLU 4.4 1.0 - - - +
363A VAL 4.8 2.8 - - - +
364A THR* 1.3 74.9 - - - +
366A GLU* 1.3 57.4 + - - +
368A TYR* 3.6 6.5 + - - +
369A GLU 3.0 20.6 + - - -
1008C MET* 3.4 8.3 - - + +
1029C GLU* 3.0 39.9 + - + +
1032C LEU* 5.9 1.6 - - + -
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Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A THR* 3.0 10.3 + - - +
365A GLN* 1.3 77.8 - - - +
367A GLN* 1.3 66.1 + - + +
369A GLU* 3.1 1.3 + - - +
370A LEU* 2.9 35.6 + - + +
1008C MET* 4.0 7.2 - - - -
1012C GLU* 2.8 27.2 - - - +
1015C ARG* 3.2 29.7 + - - +
1029C GLU* 3.2 21.2 + - - +
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A VAL* 4.6 10.8 - - + +
264A THR* 3.4 29.6 - - - +
361A ILE* 5.6 0.2 - - - +
362A LYS 3.8 6.3 + - - +
363A VAL* 3.4 18.1 - - + +
364A THR* 2.8 57.2 + - - +
366A GLU* 1.3 79.3 - - + +
368A TYR* 1.3 63.6 + - - +
370A LEU* 3.3 10.7 + - + +
371A TYR* 3.0 21.5 + - - +
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Residues in contact with TYR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A SER* 5.8 1.8 - - - -
217A SER* 5.3 2.9 - - - -
219A LEU* 3.7 22.4 - - + +
220A GLU* 3.2 51.4 + - + -
223A ALA* 3.4 20.1 - - + +
258A TRP* 3.8 10.3 - + - -
259A ASN* 2.5 33.6 + - - -
263A VAL* 3.8 12.1 - - + -
363A VAL* 3.5 28.6 - - + +
364A THR 3.1 23.8 + - - -
365A GLN* 3.9 9.4 - - - +
366A GLU 3.3 0.2 - - - -
367A GLN* 1.3 77.7 - - - +
369A GLU* 1.3 55.9 + - - +
371A TYR* 3.3 4.1 + - - +
372A CYS* 3.0 33.5 + - - -
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 4.0 9.1 - - + +
365A GLN 3.0 7.0 + - - +
366A GLU* 3.1 4.2 + - - +
368A TYR* 1.3 72.7 - - - +
370A LEU* 1.3 68.4 + - - +
372A CYS* 3.2 4.2 + - - +
373A GLU* 2.9 62.7 + - - +
1005C ARG* 3.2 35.3 + - - +
1008C MET* 3.2 64.7 - - + +
1009C LYS* 3.9 5.0 - - - +
1012C GLU* 4.4 6.3 - - + -
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A GLU* 2.9 33.5 + - + +
367A GLN* 3.7 8.1 - - + +
369A GLU* 1.3 77.0 - - - +
371A TYR* 1.3 63.0 + - - +
373A GLU* 3.3 14.9 + - - +
374A MET* 3.5 16.3 + - - +
1012C GLU* 3.6 17.3 - - + +
1016C LYS* 3.2 38.1 + - + +
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Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA* 3.6 30.1 - - + -
226A SER* 3.8 9.7 + - - -
227A THR* 2.3 35.0 + - - +
258A TRP* 3.7 10.6 + + - -
262A ALA* 3.2 35.0 - - + +
263A VAL* 3.4 28.0 - - + +
268A TYR* 3.7 23.5 + + - -
270A ALA* 5.9 1.3 - - + -
367A GLN 3.0 14.0 + - - +
368A TYR* 3.4 12.8 - - - +
369A GLU 3.1 0.2 - - - -
370A LEU* 1.3 74.7 - - - +
372A CYS* 1.3 59.5 + - - +
374A MET* 2.8 37.8 - - + +
375A GLY 4.3 0.7 + - - -
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Residues in contact with CYS 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 4.5 6.3 - - - -
222A MET* 3.8 19.5 - - + -
223A ALA* 3.4 36.6 - - - -
226A SER* 4.3 9.6 + - - -
368A TYR 3.0 23.0 + - - +
369A GLU* 3.2 8.7 + - - +
371A TYR* 1.3 74.5 - - - +
373A GLU* 1.3 60.0 + - + +
374A MET 3.0 9.7 + - - -
375A GLY* 3.5 11.1 + - - +
376A SER* 5.3 0.9 + - - -
377A THR* 4.0 9.1 - - - +
1005C ARG* 3.7 21.5 + - - +
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS* 4.6 1.4 + - - -
369A GLU* 2.9 46.3 + - - +
370A LEU* 3.7 8.0 - - - +
371A TYR 3.2 0.6 - - - -
372A CYS* 1.3 76.6 - - + +
374A MET* 1.3 62.8 + - - +
375A GLY 3.5 6.1 - - - +
377A THR* 3.9 14.3 + - + +
2004A SO4 4.4 8.5 + - - -
1005C ARG* 6.3 0.2 - - - +
1009C LYS* 4.2 19.7 - - + +
1012C GLU* 3.5 26.8 - - - +
1013C GLU* 5.9 0.2 - - - +
1016C LYS* 3.6 20.3 + - - +
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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