Contacts of the strand formed by residues 383 - 388 (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 SER 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ILE* 4.5 3.7 - - - +
382A GLY* 1.3 75.5 - - - -
384A VAL* 1.3 68.9 + - - +
397A LEU 2.9 20.6 - - - -
398A HIS* 3.8 19.8 + - - +
421A ARG* 3.0 40.7 + - - +
422A GLU* 2.9 21.2 + - - -
425A CYS* 3.6 12.7 - - - +
427A PHE* 5.9 0.2 - - - -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 4.3 1.6 - - + -
383A SER* 1.3 82.3 - - - +
385A ASN* 1.3 65.9 + - - +
396A THR* 3.3 7.3 - - - -
397A LEU* 2.9 60.2 + - + -
403A PHE* 4.3 5.6 - - + -
418A ILE* 3.7 27.4 - - + -
419A VAL 3.2 10.1 - - - +
420A LEU* 3.7 24.7 - - + -
421A ARG* 3.8 4.4 - - - +
427A PHE* 3.8 21.1 - - + -
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Residues in contact with ASN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 2.8 43.7 + - - +
384A VAL* 1.3 74.5 - - - +
386A VAL* 1.3 61.4 + - - +
387A VAL* 3.8 7.2 + - + +
393A VAL* 4.0 19.3 - - + +
395A CYS 3.8 3.8 - - - -
396A THR* 3.4 12.5 - - - +
417A SER 3.5 4.7 - - - +
418A ILE* 3.6 3.6 - - - +
419A VAL* 2.7 35.4 + - + +
420A LEU 4.5 2.2 + - - -
421A ARG* 2.6 38.7 + - - +
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 3.8 28.0 - - + -
105A CYS* 4.2 4.3 - - - -
385A ASN* 1.3 74.1 - - - +
387A VAL* 1.3 60.0 + - - +
393A VAL* 3.3 4.5 - - - +
394A VAL* 3.0 45.9 + - + +
395A CYS* 2.9 25.3 + - - +
397A LEU* 3.8 33.7 - - + -
416A ALA* 3.9 13.9 - - + -
417A SER 3.5 2.9 - - - -
418A ILE* 4.0 12.8 - - + -
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 4.8 11.0 - - + -
369A GLN* 4.2 0.5 - - - +
385A ASN* 4.3 6.5 - - + +
386A VAL* 1.3 77.5 - - - +
388A ILE* 1.3 70.2 - - - +
389A TYR* 4.2 2.0 - - - +
392A GLY* 3.2 17.0 - - - +
393A VAL* 3.9 19.7 - - + -
416A ALA* 3.5 3.5 - - - +
417A SER* 2.7 51.7 + - - +
419A VAL* 4.2 21.3 - - + -
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Residues in contact with ILE 388 (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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92A VAL* 3.7 39.0 - - + -
94A GLU* 6.4 2.7 - - + -
104A ILE* 4.7 5.4 - - + -
369A GLN* 3.5 16.4 - - - +
386A VAL* 5.3 0.2 - - + -
387A VAL* 1.3 81.1 - - - +
389A TYR* 1.3 75.8 - - - +
391A LYS* 3.0 31.8 + - + +
392A GLY* 3.0 16.0 + - - -
394A VAL* 4.0 28.3 - - + -
415A ALA 3.9 8.7 - - - +
416A ALA* 3.6 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