Contacts of the strand formed by residues 425 - 431 (chain A) in PDB entry 1O7F
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 CYS 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A GLU 4.0 0.3 - - - +
358A SER* 3.0 6.4 - - - -
359A HIS 2.9 30.4 + - - -
381A LYS 3.0 8.5 - - - +
382A GLY* 4.0 3.8 - - - -
383A SER 3.6 33.9 - - - -
420A LEU* 3.9 16.6 - - + -
422A GLU* 3.2 29.2 - - - -
424A ASN* 1.3 76.8 - - - +
426A HIS* 1.3 60.5 + - - +
427A PHE* 3.5 24.1 - - + -
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Residues in contact with HIS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG* 4.0 32.5 + - - -
315A ARG* 5.2 4.6 + - - -
356A PHE* 3.8 15.7 - + + -
357A GLU 3.7 3.4 - - - -
358A SER* 3.4 25.0 - - - -
379A ILE* 3.9 0.2 - - - -
380A LEU* 2.9 38.7 + - + +
381A LYS* 2.9 49.7 + - + +
424A ASN* 4.4 7.2 + - - +
425A CYS* 1.3 75.1 - - - +
427A PHE* 1.3 70.6 + - - +
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Residues in contact with PHE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 3.5 11.5 - - - -
357A GLU* 2.8 47.9 + - + +
359A HIS* 4.0 15.5 - + - -
366A LEU* 4.0 13.9 - - + -
377A TYR* 4.1 18.8 - + + -
378A ILE 3.4 5.8 - - - +
379A ILE* 4.0 28.7 - - + -
380A LEU* 4.3 5.8 - - - +
383A SER 5.7 0.2 - - - -
384A VAL* 3.8 17.9 - - + -
403A PHE* 4.1 11.9 - + - -
420A LEU* 3.5 30.1 - - + -
425A CYS* 3.5 30.3 - - + -
426A HIS* 1.3 79.7 - - - +
428A LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 428 (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 MET* 4.7 2.9 - - + -
314A LEU* 3.7 28.5 - - + -
333A LEU* 4.1 1.6 - - + -
336A ILE* 3.4 33.4 - - + -
339A LEU* 4.7 2.0 - - + -
354A LEU* 3.8 29.4 - - + -
355A ILE 3.5 4.5 - - - +
356A PHE* 4.6 0.7 - - + -
376A TRP 3.8 0.2 - - - +
377A TYR* 3.4 5.7 - - - +
378A ILE* 2.8 58.3 + - + +
380A LEU* 3.4 30.7 - - + +
427A PHE* 1.3 76.0 - - - +
429A ARG* 1.3 59.3 + - - +
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Residues in contact with ARG 429 (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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353A VAL 4.8 0.2 - - - +
354A LEU* 3.7 6.5 - - - +
355A ILE* 2.8 72.9 + - + +
357A GLU* 2.6 42.0 + - + +
375A SER* 3.5 17.3 + - - -
376A TRP 3.4 5.8 - - - +
377A TYR* 3.6 27.3 + - + -
428A LEU* 1.3 76.0 - - - +
430A VAL* 1.3 65.7 + - - +
431A ASP* 2.8 38.1 + - - +
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Residues in contact with VAL 430 (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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339A LEU* 5.3 0.7 - - + -
350A LEU* 4.0 19.5 - - + -
353A VAL* 5.4 3.6 - - + -
354A LEU* 3.7 22.2 - - + +
374A THR 3.7 0.2 - - - +
375A SER* 3.3 1.9 - - - -
376A TRP* 2.8 63.9 + - + +
378A ILE* 5.1 7.0 - - + -
408A LEU* 3.7 10.2 - - + +
429A ARG* 1.3 76.3 - - - +
431A ASP* 1.3 64.4 + - - +
435A PHE* 4.0 38.4 - - + +
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Residues in contact with ASP 431 (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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353A VAL* 5.7 1.0 - - - +
355A ILE* 3.4 14.1 - - - +
374A THR* 3.2 10.1 - - - +
375A SER* 2.9 12.9 + - - -
408A LEU* 4.1 2.2 - - - -
429A ARG* 2.8 47.3 + - - +
430A VAL* 1.3 75.9 - - - +
432A LYS* 1.3 60.9 + - - +
433A GLU* 4.4 6.5 - - + +
434A ASP* 3.3 20.6 + - - +
435A PHE* 2.9 27.0 + - - +
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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