Contacts of the strand formed by residues 368 - 376 (chain A) in PDB entry 2IFG
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 GLY 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ALA* 5.6 1.1 - - - -
364A ALA* 3.6 2.6 - - - +
365A ASN* 3.0 33.1 + - - +
366A PRO 3.4 0.8 - - - -
367A PHE* 1.3 82.1 - - - +
369A GLN* 1.3 63.3 + - - +
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Residues in contact with GLN 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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286A ALA* 5.1 2.2 - - - -
314A ARG* 3.8 13.1 + - - +
362A LEU* 3.2 43.3 - - + +
363A ALA 3.3 10.1 - - - +
364A ALA* 4.2 11.1 - - + +
368A GLY* 1.3 76.6 - - - +
370A ALA* 1.3 72.8 + - - +
371A SER* 4.4 2.8 + - - -
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Residues in contact with ALA 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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286A ALA* 3.8 27.3 - - - +
287A SER* 3.9 1.8 - - - +
288A VAL* 3.3 31.6 - - + +
361A LEU 3.9 0.2 - - - +
362A LEU* 3.7 0.7 - - - -
363A ALA 2.8 32.9 + - - +
369A GLN* 1.3 76.1 - - - +
371A SER* 1.3 63.6 + - - +
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Residues in contact with SER 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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288A VAL* 4.6 7.4 - - - +
360A THR* 3.4 22.0 - - - +
361A LEU 3.5 4.5 - - - -
362A LEU* 3.6 13.3 - - - +
369A GLN* 5.1 3.6 - - - -
370A ALA* 1.3 78.1 - - - +
372A ALA* 1.3 64.0 + - - +
373A SER* 4.8 0.9 + - - -
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Residues in contact with ALA 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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288A VAL* 4.0 8.9 - - + +
289A GLN* 4.0 11.4 - - - -
290A LEU* 3.5 39.8 - - + +
360A THR* 3.2 2.7 - - - +
361A LEU 2.7 35.2 + - - -
371A SER* 1.3 77.4 + - - +
373A SER* 1.3 62.2 + - - +
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Residues in contact with SER 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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290A LEU* 3.9 5.1 - - - +
358A ASN* 3.4 19.8 + - - -
359A TYR 3.1 4.3 - - - -
360A THR* 2.4 32.7 + - - +
371A SER* 4.8 0.9 + - - -
372A ALA* 1.3 72.8 - - - +
374A ILE* 1.3 66.6 + - - +
1H NAG 4.2 24.3 + - - +
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A LEU* 3.4 29.2 - - + -
291A HIS 4.4 11.9 - - - +
292A THR* 4.2 25.8 - - + +
293A ALA* 4.9 2.2 - - + +
301A ILE* 3.8 22.0 - - + -
357A GLY 3.7 0.3 - - - +
358A ASN* 3.1 6.2 + - - +
359A TYR* 2.7 44.1 + - + +
373A SER* 1.3 78.6 - - - +
375A MET* 1.3 84.7 + - + +
376A ALA* 3.8 1.7 + - + -
1H NAG 4.6 4.9 - - + -
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Residues in contact with MET 375 (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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292A THR* 5.8 0.2 - - - -
293A ALA* 5.4 2.1 + - - +
357A GLY* 3.5 22.7 - - - +
358A ASN* 3.6 25.6 - - - +
374A ILE* 1.3 95.2 - - + +
376A ALA* 1.3 62.9 + - - +
1H NAG 3.9 25.3 - - + +
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Residues in contact with ALA 376 (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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293A ALA* 4.1 17.0 - - + -
301A ILE* 4.7 4.7 - - + -
356A ASN* 3.3 5.4 - - - +
357A GLY 2.9 32.1 + - - -
359A TYR* 4.1 14.1 - - + -
374A ILE* 3.8 2.9 + - + +
375A MET* 1.3 79.9 - - - +
377A ALA* 1.3 60.9 + - - +
378A PHE* 3.5 30.1 - - + -
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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