Contacts of the strand formed by residues 359 - 365 (chain A) in PDB entry 3I7O
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 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.1 26.9 - - + +
358A PRO* 1.3 68.4 - - - +
360A VAL* 1.3 54.9 + - - +
361A ASP 3.6 18.4 - - - +
362A MET* 4.0 10.1 - - + -
377A THR* 3.9 17.7 - - + -
378A CYS 3.5 4.5 - - - -
379A SER* 4.5 2.9 - - - +
1005A ASN* 2.7 31.2 + - - +
1006A VAL* 4.2 1.5 - - + +
1031A GLY* 3.8 25.4 - - - +
1032A THR 3.1 14.0 + - - +
1035A GLY* 4.1 8.5 - - - -
1036A MET 4.0 7.0 - - - +
1037A ILE* 3.8 31.9 - - + -
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Residues in contact with VAL 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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358A PRO* 4.2 9.4 - - + +
359A ILE* 1.3 76.2 - - - +
361A ASP* 1.3 62.9 + - - +
378A CYS* 3.0 14.1 + - + +
380A GLY 4.8 7.9 - - - +
721A PRO 3.7 9.0 - - - +
722A ARG* 2.9 43.2 - - + +
723A LYS* 4.9 2.4 - - - +
1005A ASN* 3.8 16.8 - - - +
1006A VAL* 4.5 1.4 - - - +
18B SER* 3.9 36.0 - - - +
19B LEU* 4.7 12.3 - - + -
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Residues in contact with ASP 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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359A ILE* 3.5 5.8 - - - +
360A VAL* 1.3 79.9 - - - +
362A MET* 1.3 91.7 + - - +
378A CYS* 3.0 27.8 + - - -
722A ARG 3.5 14.6 - - - +
723A LYS* 3.0 28.5 - - + +
724A ILE* 2.9 31.2 + - - +
1006A VAL* 3.7 20.7 - - - +
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Residues in contact with MET 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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359A ILE* 4.0 5.8 - - + -
361A ASP* 1.3 95.6 + - - +
363A CYS* 1.3 67.9 + - - +
375A LEU* 3.9 22.4 - - + -
376A VAL 3.1 15.3 - - - +
377A THR* 3.8 12.6 - - + +
724A ILE* 4.2 5.5 - - - +
1006A VAL* 3.6 20.9 - - + +
1008A CYS* 4.0 17.0 - - - +
1029A LEU* 3.6 25.8 - - + +
1030A PHE* 3.6 30.7 - - - +
1031A GLY* 3.7 21.8 - - - +
1037A ILE* 5.4 0.2 - - - -
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Residues in contact with CYS 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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362A MET* 1.3 79.7 - - - +
364A VAL* 1.3 70.0 + - - +
375A LEU* 3.6 6.1 - - - -
376A VAL* 2.7 54.1 + - - +
724A ILE* 4.3 27.6 - - - +
725A CYS* 5.6 0.4 - - - -
726A TYR* 4.7 8.3 - - + +
733A PHE* 4.3 16.8 - - - -
1008A CYS* 4.5 9.0 - - - -
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Residues in contact with VAL 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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363A CYS* 1.3 76.9 - - - +
365A VAL* 1.3 91.8 + - - +
366A ASP* 3.0 18.8 - - - +
373A GLY* 3.6 24.0 - - - -
374A GLN 3.2 5.8 - - - +
375A LEU* 4.3 9.6 - - + -
726A TYR* 5.0 2.9 - - - +
733A PHE* 4.9 0.2 - - - -
1008A CYS* 4.3 11.1 - - - -
1009A HIS 3.8 8.3 - - - +
1010A GLY* 3.3 34.8 - - - -
1011A SER 4.3 4.9 - - - +
1012A LEU* 6.2 0.9 - - + -
1029A LEU* 4.5 1.8 - - + -
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Residues in contact with VAL 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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363A CYS 4.2 0.9 - - - +
364A VAL* 1.3 91.2 - - - +
366A ASP* 1.3 112.2 + - + +
367A LEU* 2.5 34.8 - - + +
372A GLN 3.1 3.4 - - - +
373A GLY* 2.7 13.9 - - - -
374A GLN* 2.4 43.3 + - + +
376A VAL* 3.4 26.5 - - + -
733A PHE* 3.5 17.7 - - + -
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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