Contacts of the helix formed by residues 307 - 313 (chain A) in PDB entry 1FBA
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 ALA 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A GLU* 3.4 7.5 + - - +
303A ARG* 3.0 27.2 + - - +
306A GLN* 1.3 77.4 - - - +
308A SER* 1.3 57.5 + - - +
310A LEU* 3.5 9.4 + - - +
311A ARG* 3.1 26.2 + - - +
353A SER* 3.9 13.0 - - - -
356A LEU* 3.8 24.7 - - + -
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Residues in contact with SER 308 (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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276A GLU* 2.6 32.1 + - - -
307A ALA* 1.3 74.1 - - - +
309A VAL* 1.3 61.3 + - - +
311A ARG* 3.8 8.6 - - - +
312A ALA* 3.0 31.0 + - - +
326A GLU* 3.5 29.2 + - - +
330A ARG* 5.5 2.9 - - - -
352A GLY* 4.1 14.0 - - - -
353A SER* 4.1 2.4 + - - -
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Residues in contact with VAL 309 (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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58A TYR* 4.1 8.1 - - + +
61A LEU* 3.9 25.1 - - + -
62A LEU* 4.0 15.0 - - + -
276A GLU* 5.7 0.2 - - - +
305A LEU 3.6 24.5 - - - +
306A GLN* 3.2 8.9 + - + +
308A SER* 1.3 78.2 - - - +
310A LEU* 1.3 57.9 + - - +
312A ALA* 3.2 2.9 + - - +
313A TRP* 2.9 31.5 + - - +
323A GLY* 3.6 18.5 - - - +
326A GLU* 4.1 3.1 - - + -
327A LEU* 3.7 33.4 - - + +
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Residues in contact with LEU 310 (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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39A MET* 4.6 5.2 - - + -
42A ARG* 4.1 34.3 - - + +
43A LEU* 4.4 8.5 - - + -
46A ILE* 3.5 41.3 - - + +
58A TYR* 3.6 40.2 - - + +
306A GLN* 3.0 25.6 + - + +
307A ALA* 3.7 7.2 - - - +
309A VAL* 1.3 77.1 - - - +
311A ARG* 1.3 63.7 + - - +
313A TRP* 3.9 6.7 - - + +
314A ALA 3.0 20.4 + - - -
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Residues in contact with ARG 311 (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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46A ILE* 4.4 9.0 - - - +
307A ALA 3.1 18.1 + - - +
308A SER* 3.8 8.7 - - - +
309A VAL 3.3 0.2 - - - -
310A LEU* 1.3 78.6 - - - +
312A ALA* 1.3 62.5 + - - +
314A ALA* 3.7 13.7 + - - +
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Residues in contact with ALA 312 (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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308A SER 3.0 18.9 + - - +
309A VAL 3.6 3.4 - - - +
311A ARG* 1.3 75.9 - - - +
313A TRP* 1.3 64.8 + - - +
314A ALA* 4.3 0.9 - - - +
319A ASN* 3.2 22.6 - - - +
322A ALA* 3.9 30.1 - - + +
323A GLY* 3.9 3.1 - - - -
326A GLU* 3.9 11.2 - - + +
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Residues in contact with TRP 313 (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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43A LEU* 3.8 12.8 - - + -
46A ILE* 3.6 31.0 - - + -
48A VAL* 4.7 6.7 - - + -
54A ASN* 4.3 8.5 - - + -
57A ALA* 4.7 10.3 - - + -
58A TYR* 3.7 50.0 - + + -
61A LEU* 3.3 32.9 - - + +
309A VAL* 2.9 17.9 + - + +
310A LEU* 3.9 3.4 - - + +
312A ALA* 1.3 76.1 - - - +
314A ALA* 1.3 60.4 + - - +
315A GLY* 3.1 26.6 + - - -
316A LYS 3.2 32.4 + - - -
317A LYS* 4.6 1.6 - - - +
319A ASN* 3.0 39.6 + - - +
320A ILE* 4.3 7.7 - - + +
323A GLY* 4.4 1.5 - - - -
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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