Contacts of the strand formed by residues 316 - 319 (chain C) in PDB entry 1FTA
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 ILE 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C MET* 4.8 3.8 - - + -
262C PHE* 4.1 12.5 - - + +
263C LEU* 3.6 0.5 - - - -
264C TYR* 2.8 39.2 + - + +
275C LEU* 4.0 27.4 - - + -
281C CYS* 3.8 39.7 - - + +
295C ALA* 4.5 4.3 - - + -
296C THR 3.2 6.1 - - - +
302C VAL* 4.0 17.5 - - + -
314C ALA 5.0 0.7 - - - +
315C PRO* 1.3 76.7 - - - +
317C ILE* 1.3 70.2 + - - +
318C LEU* 3.5 33.4 - - + -
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ILE* 3.5 31.4 - - + -
262C PHE 3.3 5.6 - - - +
263C LEU* 4.2 17.0 - - + -
265C PRO* 4.5 15.9 - - + -
295C ALA* 3.4 0.9 - - - -
296C THR* 2.8 48.0 + - + +
297C THR 4.0 16.4 - - - +
298C GLY 4.6 0.4 - - - +
316C ILE* 1.3 85.7 - - - +
318C LEU* 1.3 63.1 + - - +
324C VAL* 4.5 6.8 - - + +
327C PHE* 3.8 40.4 - - + -
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C MET* 5.4 0.9 - - + -
252C VAL* 3.8 19.1 - - + -
255C THR* 4.7 2.5 - - + -
261C ILE* 3.5 2.6 - - - +
262C PHE* 2.9 63.9 + - + +
284C MET* 3.9 25.1 - - + -
288C MET* 3.8 22.9 - - + -
294C MET 3.2 13.0 - - - +
295C ALA* 3.7 8.3 - - + -
316C ILE* 3.5 27.8 - - + -
317C ILE* 1.3 76.5 - - - +
319C GLY* 1.3 60.6 + - - +
324C VAL* 3.8 7.2 - - - -
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Residues in contact with GLY 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ILE* 3.7 10.3 - - - -
255C THR* 3.7 16.2 - - - -
260C GLY 3.6 7.2 - - - -
288C MET* 4.2 3.6 - - - +
293C GLY* 3.3 4.3 - - - -
294C MET 2.9 29.6 + - - +
318C LEU* 1.3 76.9 - - - +
320C SER* 1.3 69.0 + - - +
324C VAL* 3.6 2.9 - - - +
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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