Contacts of the strand formed by residues 347 - 352 (chain A) in PDB entry 2IB8
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 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A LEU* 3.8 27.1 - - + -
342A LEU* 4.6 6.7 - - + -
343A LYS 4.3 0.9 - - - +
344A LYS 3.2 16.0 + - - +
345A GLU 4.4 0.2 - - - -
346A ASP* 1.3 78.7 - - - +
348A ALA* 1.3 59.3 + - - +
349A MET 3.4 24.9 - - - +
350A TRP* 3.5 32.9 + - + +
373A LYS* 2.9 26.4 + - - -
407A TYR* 3.9 12.3 - - + +
409A LEU* 3.8 14.1 - - + +
423A LEU* 3.5 31.4 - - + -
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Residues in contact with ALA 348 (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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346A ASP 3.6 3.8 + - - +
347A ILE* 1.3 72.6 - - - +
349A MET* 1.3 63.7 + - + +
373A LYS* 3.5 27.5 - - - +
402A LEU* 4.4 2.2 - - + -
406A GLU* 3.7 41.5 - - + +
407A TYR 2.9 14.9 + - - +
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Residues in contact with MET 349 (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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347A ILE* 3.4 6.1 - - - +
348A ALA* 1.3 82.8 - - + +
350A TRP* 1.3 60.2 + - - +
351A GLU* 4.2 7.0 - - + +
373A LYS 3.7 4.7 - - - -
376A ILE* 3.7 42.4 - - + +
397A HIS* 4.0 15.5 - - + -
398A LEU* 3.7 26.1 - - + +
401A ALA* 3.6 37.7 - - + +
402A LEU* 3.9 19.7 - - + -
406A GLU* 5.7 1.3 - - - +
407A TYR 3.5 1.8 + - - -
408A GLY* 3.3 2.9 - - - -
409A LEU 3.0 24.1 + - - -
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Residues in contact with TRP 350 (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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333A ALA* 4.1 6.3 - - + -
337A LEU* 4.2 15.5 - - + -
344A LYS* 3.9 15.1 + - + -
347A ILE* 3.5 40.2 + - + +
349A MET* 1.3 75.7 - - - +
351A GLU* 1.3 64.0 + - - +
352A VAL* 3.9 16.2 - - + -
367A LEU* 4.1 24.7 - - + -
369A ILE* 3.8 42.2 - - + +
373A LYS* 2.9 33.2 + - + +
374A VAL* 3.6 13.4 - - + -
375A ASN* 2.9 27.4 + - - -
376A ILE* 4.8 0.5 + - - +
409A LEU* 3.4 46.0 - - + -
411A SER* 5.7 0.9 - - - -
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Residues in contact with GLU 351 (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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349A MET* 4.2 7.2 + - - +
350A TRP* 1.3 72.8 - - - +
352A VAL* 1.3 61.6 + - - +
353A ASN 3.8 0.4 + - - -
375A ASN* 3.3 25.5 - - - +
376A ILE 4.4 1.9 + - - -
377A ASN 5.1 0.7 + - - -
378A GLY 4.6 7.4 - - - +
379A GLY* 5.6 0.5 - - - -
393A ARG* 4.5 7.4 + - - -
394A ILE* 3.4 41.9 - - + +
397A HIS* 3.6 25.6 - - + -
398A LEU* 3.8 26.9 - - + +
409A LEU 2.9 9.4 + - - +
410A ALA* 3.2 9.7 - - + -
411A SER 2.8 28.2 + - - +
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Residues in contact with VAL 352 (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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329A PRO* 4.8 3.6 - - + -
350A TRP* 3.9 21.5 - - + -
351A GLU* 1.3 73.5 - - - +
353A ASN* 1.3 73.5 + - - +
354A GLU 3.1 0.5 + - - -
359A VAL* 4.7 3.8 - - + -
360A VAL* 3.9 14.3 - - + +
363A ASN* 3.8 38.4 - - + +
364A ILE* 6.3 0.4 - - + -
367A LEU* 5.8 1.6 - - + -
369A ILE* 5.3 4.9 - - + -
374A VAL* 4.4 15.0 - - + -
375A ASN* 3.0 31.5 + - - +
411A SER* 3.6 20.6 - - - +
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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