Contacts of the strand formed by residues 357 - 365 (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 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A PHE* 3.3 12.1 - - - -
318A ASN* 4.0 7.9 - - - -
355A ASN 3.5 1.8 + - - -
356A ASN* 1.3 76.1 - - - +
358A ASN* 1.3 59.7 + - - -
359A TYR* 3.4 7.8 - - - -
375A MET* 3.7 15.5 - - - +
376A ALA 2.9 32.3 + - - -
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Residues in contact with ASN 358 (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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316A LEU 3.6 1.2 - - - +
317A PHE* 3.5 3.9 - - - -
318A ASN* 2.8 46.2 + - - +
319A GLY 4.6 1.5 + - - +
357A GLY* 1.3 70.8 - - - -
359A TYR* 1.3 61.5 + - - +
360A THR* 3.9 10.2 + - - -
373A SER* 3.4 4.1 + - - -
374A ILE 3.1 27.6 + - - +
375A MET* 3.6 9.7 - - - -
1H NAG 1.5 75.4 + - - +
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Residues in contact with TYR 359 (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* 3.5 5.5 - - - +
301A ILE* 3.7 13.9 - - + -
315A TRP* 3.9 16.6 - + + -
316A LEU 3.4 4.9 - - - -
317A PHE* 3.6 25.7 - + - -
322A LEU* 3.9 20.0 - - + -
328A ILE* 5.2 1.4 - - + +
346A LEU* 3.5 28.9 - - + -
348A LEU* 4.8 6.1 - - + +
355A ASN* 2.5 48.3 + - - +
357A GLY 3.4 14.1 - - - -
358A ASN* 1.3 73.0 - - - +
360A THR* 1.3 61.9 + - - +
373A SER* 3.1 2.6 - - - -
374A ILE* 2.7 42.3 + - + +
376A ALA* 4.1 6.5 - - + -
378A PHE* 3.7 16.8 - + - -
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Residues in contact with THR 360 (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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314A ARG 3.6 1.0 - - - +
315A TRP* 3.1 11.0 - - - -
316A LEU* 2.9 53.0 + - + +
319A GLY 5.3 2.9 + - - -
358A ASN* 3.9 10.2 + - - -
359A TYR* 1.3 72.7 - - - +
361A LEU* 1.3 61.6 + - - +
362A LEU* 3.8 17.7 - - + +
371A SER* 3.4 23.3 - - - +
372A ALA 3.2 4.3 - - - +
373A SER* 2.4 23.6 + - - +
1H NAG 4.5 8.8 + - - +
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Residues in contact with LEU 361 (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* 3.6 19.7 - - + +
290A LEU* 3.5 33.6 - - + +
303A PHE* 3.5 31.2 - - + -
305A VAL* 5.4 0.2 - - + -
313A LEU* 3.7 35.9 - - + -
314A ARG 3.5 8.5 - - - +
315A TRP* 4.0 24.4 - - + +
359A TYR 4.2 0.4 + - - -
360A THR* 1.3 73.9 - - - +
362A LEU* 1.3 68.6 + - - +
363A ALA 4.1 0.3 + - - -
370A ALA 3.9 0.3 - - - +
371A SER* 3.5 6.1 + - - -
372A ALA* 2.7 27.8 + - - +
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Residues in contact with LEU 362 (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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312A SER 3.2 6.1 - - - +
313A LEU* 3.3 3.1 - - - -
314A ARG* 2.7 75.1 + - + +
316A LEU* 3.3 37.7 - - + -
360A THR* 3.8 12.3 - - + +
361A LEU* 1.3 74.0 - - - +
363A ALA* 1.3 59.5 + - - +
364A ALA* 4.1 1.1 - - + -
369A GLN* 3.2 30.5 - - - +
370A ALA 3.7 1.8 - - - -
371A SER* 3.6 26.7 - - - +
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Residues in contact with ALA 363 (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 5.5 - - + +
288A VAL* 3.0 33.4 - - + -
305A VAL* 3.5 18.8 - - + -
311A PRO* 3.7 9.0 - - + -
312A SER 3.4 4.5 - - - -
313A LEU* 3.8 6.5 - - + -
361A LEU 4.1 0.6 - - - -
362A LEU* 1.3 71.7 - - - +
364A ALA* 1.3 61.1 + - - +
369A GLN* 3.3 3.2 - - - +
370A ALA* 2.8 38.1 + - + -
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Residues in contact with ALA 364 (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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310A ALA 4.4 0.2 - - - +
311A PRO* 3.0 5.7 - - - +
312A SER* 2.8 45.1 + - - +
362A LEU* 4.1 1.1 - - + -
363A ALA* 1.3 75.4 - - - +
365A ASN* 1.3 62.0 + - - +
368A GLY 3.6 10.8 - - - +
369A GLN* 4.2 14.6 - - + +
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Residues in contact with ASN 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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284A PHE 3.5 13.1 + - - -
286A ALA* 3.5 24.4 + - - +
308A GLN 4.1 2.2 + - - -
309A PRO* 3.5 25.8 + - + +
310A ALA 4.6 1.1 - - - +
311A PRO* 4.2 5.4 - - + -
364A ALA* 1.3 74.9 - - - +
366A PRO* 1.3 70.4 - - + +
367A PHE* 2.8 45.8 + - - +
368A GLY* 3.0 20.2 + - - +
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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