Contacts of the strand formed by residues 357 - 365 (chain A) in PDB entry 3SAJ
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 GLY 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A LYS* 4.3 3.8 - - - +
352A GLU 3.8 0.7 - - - +
353A MET* 3.3 1.1 - - - +
354A LYS* 2.5 46.3 + - - +
355A HIS 3.0 1.9 - - - -
356A ASP* 1.3 81.2 - - - +
358A ILE* 1.3 63.8 + - - -
359A ARG* 4.2 1.3 - - - -
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Residues in contact with ILE 358 (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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217A PHE* 4.7 2.9 - - + -
218A MET* 4.0 19.5 - - + -
222A LEU* 4.0 26.7 - - + -
226A LYS* 4.0 25.3 - - + +
351A ILE* 4.5 10.8 - - + -
352A GLU 3.5 3.6 - - - +
353A MET* 3.2 46.0 - - + -
357A GLY* 1.3 73.4 - - - -
359A ARG* 1.3 61.9 + - - +
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Residues in contact with ARG 359 (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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351A ILE* 4.0 6.1 - - - +
352A GLU 2.8 35.0 + - - +
357A GLY 5.5 1.3 - - - -
358A ILE* 1.3 75.1 + - - +
360A LYS* 1.3 97.5 + - - +
361A ILE* 3.4 8.8 + - + +
375A LEU 4.0 20.7 + - - +
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Residues in contact with LYS 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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239A ASN* 5.9 3.0 - - - +
349A HIS* 3.4 35.7 + - + -
350A VAL 3.4 16.6 - - - +
351A ILE* 4.1 17.8 - - + +
359A ARG* 1.3 106.1 + - - +
361A ILE* 1.3 59.9 + - - +
362A GLY* 3.2 24.6 + - - +
363A TYR* 4.1 18.5 - - - +
373A ALA* 4.5 12.4 - - + +
375A LEU* 4.9 4.2 - - - +
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Residues in contact with ILE 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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118A ILE* 6.1 0.7 - - + -
121A HIS* 5.6 5.2 - - + +
122A TYR* 3.5 20.0 - - + +
233A THR* 4.0 14.6 - - + -
350A VAL* 2.9 29.2 + - + +
352A GLU* 2.7 57.7 - - + +
359A ARG* 3.7 11.4 - - + +
360A LYS* 1.3 73.7 - - - +
362A GLY* 1.3 56.5 + - - +
370A PHE* 3.7 18.3 - - + -
372A PRO* 3.7 3.1 - - - +
373A ALA* 3.4 18.3 + - - +
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Residues in contact with GLY 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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350A VAL* 2.9 26.4 + - - +
360A LYS* 3.2 20.5 - - - +
361A ILE* 1.3 82.1 - - - +
363A TYR* 1.3 62.8 + - - -
370A PHE* 3.9 3.1 - - - -
371A VAL 3.3 13.9 - - - -
373A ALA* 3.7 13.2 - - - +
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Residues in contact with TYR 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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347A THR* 3.9 23.8 - - + -
348A LEU 3.1 15.3 - - - +
349A HIS* 4.3 0.7 - - - +
350A VAL* 3.7 3.1 - - - -
360A LYS* 4.1 20.2 - - - +
362A GLY* 1.3 78.6 - - - +
364A TRP* 1.3 67.9 + - - +
365A ASN* 3.7 23.4 + - - -
368A ASP* 4.7 5.2 + - - -
369A LYS 4.9 1.1 - - - -
370A PHE* 3.2 9.5 - - - -
371A VAL* 2.8 64.7 + - + +
373A ALA* 6.4 0.7 - - - -
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Residues in contact with TRP 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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110A GLU 5.2 0.7 - - - -
113A GLU* 3.6 28.7 - - + -
114A ALA* 3.5 40.8 - - + +
117A SER* 3.1 28.8 + - - -
118A ILE* 4.5 1.6 - - + -
235A PHE* 5.1 0.4 - - + -
346A TYR* 3.7 27.3 - + - +
347A THR* 3.5 1.7 - - - -
348A LEU* 2.7 50.2 + - + +
350A VAL* 4.4 10.8 - - + -
363A TYR* 1.3 79.4 - - - +
365A ASN* 1.3 84.7 + - - +
366A GLU* 3.5 21.8 - - + -
369A LYS* 3.1 31.5 - - + +
370A PHE* 3.6 13.7 - - + -
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Residues in contact with ASN 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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345A ASN* 6.0 2.0 - - - +
346A TYR 3.3 20.2 - - - +
347A THR* 4.1 10.1 + - - +
363A TYR* 3.7 21.0 + - - -
364A TRP* 1.3 85.9 - - - +
366A GLU* 1.3 64.7 + - - +
367A ASP* 3.2 5.9 + - - +
368A ASP* 2.6 53.1 + - - +
369A LYS* 2.9 27.8 + - - -
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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