Contacts of the strand formed by residues 257 - 263 (chain A) in PDB entry 1FID
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLU* 5.4 10.1 - - + +
250A LEU 3.0 9.4 - - - +
251A GLU* 3.4 37.2 - - + +
255A GLY 3.8 5.8 + - - +
256A ARG* 1.3 75.3 - - - +
258A SER* 1.3 64.9 + - - +
259A THR* 6.3 0.4 - - - -
285A ASP* 4.1 7.1 - - - +
372A TRP* 4.1 5.1 + - - -
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Residues in contact with SER 258 (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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248A VAL 3.9 0.2 - - - +
249A GLU* 4.3 0.9 - - - +
250A LEU* 2.8 34.5 + - - +
257A THR* 1.3 76.8 - - - +
259A THR* 1.3 69.3 + - - +
285A ASP* 3.5 20.2 - - - -
286A ALA* 3.5 16.0 - - - +
372A TRP* 3.2 44.5 - - - -
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Residues in contact with THR 259 (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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247A ARG* 4.0 37.4 + - - +
248A VAL 3.2 10.1 - - - +
249A GLU* 4.2 17.5 - - + +
257A THR* 6.1 0.7 - - - +
258A SER* 1.3 81.9 - - - +
260A ALA* 1.3 61.1 + - - +
261A ASP* 4.9 2.1 + - - -
284A GLY* 3.1 18.3 - - - -
285A ASP* 3.2 8.7 + - - -
286A ALA* 2.9 23.0 + - - -
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Residues in contact with ALA 260 (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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246A LEU 3.7 0.9 - - - +
247A ARG* 3.5 0.5 - - - -
248A VAL* 2.9 35.5 + - + +
259A THR* 1.3 76.7 - - - +
261A ASP* 1.3 62.0 + - - +
262A TYR* 4.0 6.9 - - + -
281A PHE* 3.9 9.4 - - + -
283A GLY 3.6 5.8 - - - -
286A ALA* 4.0 4.9 - - + -
287A GLY 3.6 23.3 - - - +
369A TRP* 3.9 19.7 - - + -
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Residues in contact with ASP 261 (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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246A LEU 3.2 3.8 - - - +
247A ARG* 2.8 58.6 + - - +
259A THR* 5.3 2.2 + - - -
260A ALA* 1.3 74.3 - - - +
262A TYR* 1.3 58.9 + - - +
281A PHE* 3.4 9.8 - - - -
282A ALA* 2.7 43.4 + - + +
283A GLY 2.8 18.9 + - - +
392A LEU* 4.0 19.1 - - + +
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Residues in contact with TYR 262 (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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245A ALA* 3.3 5.0 - - - -
246A LEU* 2.9 53.2 + - + +
248A VAL* 5.1 1.8 - - + -
260A ALA* 4.0 23.3 - - + -
261A ASP* 1.3 76.3 - - - +
263A ALA* 1.3 63.2 + - - +
265A PHE* 4.1 2.9 - - + +
278A TYR* 3.6 42.2 - + + -
280A TYR 3.5 2.7 - - - +
281A PHE* 3.6 18.1 - + + -
282A ALA* 4.7 1.3 - - - -
287A GLY 4.1 0.2 + - - -
288A ASP* 2.6 40.9 + - - -
289A ALA 3.5 1.9 + - - -
290A PHE* 3.4 43.7 + + + -
369A TRP* 3.6 11.1 - + - -
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Residues in contact with ALA 263 (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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244A TYR 4.3 1.6 - - - -
245A ALA* 4.5 4.3 - - - +
261A ASP 4.3 0.2 - - - -
262A TYR* 1.3 71.9 - - - +
264A MET* 1.3 67.9 + - - +
278A TYR* 3.7 2.6 - - - +
279A ALA* 3.0 25.3 + - - +
280A TYR* 2.9 36.0 + - + +
282A ALA* 4.3 3.6 - - + +
389A PHE* 3.5 38.4 - - + -
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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