Contacts of the strand formed by residues 362 - 366 (chain A) in PDB entry 3SN5
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 ASN 362 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.0 7.4 - - - +
360A SER* 4.0 3.6 - - - -
361A LEU* 1.3 68.9 - - - +
363A ILE* 1.3 59.3 + - - +
364A ARG* 2.7 42.0 + - - +
388A ALA* 3.1 4.2 - - - -
389A LEU* 2.9 53.2 + - + +
391A PRO* 4.8 4.6 - - + +
435A MET* 3.6 23.2 - - + +
438A GLY* 3.7 15.0 - - - -
442A THR* 3.1 16.1 + - - -
601A HEM 3.7 16.3 + - - -
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Residues in contact with ILE 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 6.0 1.1 - - + -
97A TRP* 4.6 4.2 - - - +
100A PHE* 3.8 53.8 - - + -
101A HIS* 5.1 13.0 - - + +
361A LEU* 3.4 36.8 + - + +
362A ASN* 1.3 78.3 + - - +
364A ARG* 1.3 72.5 - - - +
365A THR* 4.7 0.2 - - - +
386A ILE* 3.9 30.3 - - + -
387A ILE 3.7 2.5 - - - -
388A ALA* 4.0 9.0 - - + -
442A THR* 3.8 19.8 - - - +
601A HEM 4.7 2.8 + - - -
1429A K2B 6.4 0.4 - - + -
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Residues in contact with ARG 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.4 39.0 + - - +
89A LEU* 3.5 23.8 - - - +
95A PHE* 3.5 36.0 - - + -
96A ASP 3.4 13.9 - - - +
97A TRP* 4.5 7.2 - - + -
362A ASN* 2.7 55.3 + - - +
363A ILE* 1.3 77.5 - - - +
365A THR* 1.3 62.5 + - - +
386A ILE* 3.5 4.5 - - - +
387A ILE* 2.8 54.3 + - + +
389A LEU* 4.4 3.0 - - - +
442A THR* 3.5 14.3 + - - +
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 6.0 1.1 - - - +
95A PHE* 3.4 7.1 - - - -
96A ASP* 2.8 44.5 + - - -
99A LYS* 5.4 5.6 - - + +
100A PHE* 4.3 19.1 + - - +
363A ILE* 4.7 0.2 - - - +
364A ARG* 1.3 77.7 + - - +
366A ALA* 1.3 66.9 + - - +
367A LYS 3.5 0.2 + - - -
384A ASP* 3.5 29.2 - - + +
385A ASP 3.3 12.6 - - - +
386A ILE* 4.1 13.5 - - + +
387A ILE* 5.3 0.7 - - - -
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Residues in contact with ALA 366 (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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94A TYR 3.5 5.8 - - - -
95A PHE* 5.1 0.2 - - - +
96A ASP* 5.6 0.2 - - - -
365A THR* 1.3 71.4 - - - +
367A LYS* 1.3 60.9 + - - +
368A GLU 3.7 11.7 - - - +
370A PHE* 3.8 18.4 - - + -
381A ILE* 3.8 7.6 - - + -
382A ARG 3.3 26.0 - - - +
383A LYS* 4.2 0.5 - - - +
384A ASP* 2.8 31.1 + - - +
385A ASP 2.9 13.8 + - - +
387A ILE* 4.6 3.5 - - + +
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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