Contacts of the strand formed by residues 409 - 415 (chain A) in PDB entry 1NSC
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A LYS* 3.3 18.0 + - - +
349A GLY* 3.3 20.1 - - - +
350A GLY* 2.9 13.7 + - - -
365A SER* 2.8 30.0 + - - -
376A MET* 3.9 20.4 - - - +
407A TRP 4.5 0.3 + - - -
408A TYR* 1.3 76.4 - - - +
410A PHE* 1.3 67.0 + - - +
424A ILE* 4.5 2.2 - - - -
425A GLY 3.2 14.6 - - - -
426A ILE* 4.4 3.6 - - - -
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Residues in contact with PHE 410 (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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117A PRO* 3.2 30.7 - - + -
118A PHE* 3.5 14.6 - - + -
119A ILE* 3.4 26.0 - - + -
225A GLU 5.2 0.9 - - - -
226A SER* 3.9 23.6 - - - -
277A THR* 3.9 4.7 - - - -
348A LYS* 4.1 4.3 - - - -
350A GLY* 3.7 10.2 - - - -
408A TYR* 4.8 5.4 - - + -
409A SER* 1.3 81.4 - - - +
411A GLY* 1.3 63.2 + - - +
412A PHE* 3.7 20.2 - + - -
424A ILE* 3.3 5.4 - - - +
425A GLY* 2.9 58.8 + - - +
426A ILE 4.2 4.3 - - - -
427A GLU* 4.7 0.4 - - + -
442A THR* 3.9 20.9 - - + -
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Residues in contact with GLY 411 (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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119A ILE 4.8 1.6 - - - +
226A SER* 5.1 4.5 - - - -
227A ALA* 5.2 5.4 - - - +
277A THR* 3.4 15.8 - - - +
278A CYS 5.5 2.7 - - - +
351A PHE 3.3 22.8 + - - -
352A VAL* 4.1 4.5 - - - -
410A PHE* 1.3 82.9 - - - +
412A PHE* 1.3 63.4 + - - +
423A CYS 3.3 10.3 - - - -
424A ILE* 4.3 0.9 - - - -
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Residues in contact with PHE 412 (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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119A ILE* 3.4 61.0 - - + +
120A ALA* 5.0 2.9 - - - -
121A CYS* 4.0 11.7 - - - +
160A LEU* 4.9 5.4 - - + -
227A ALA* 5.5 3.8 - - + -
352A VAL* 3.6 3.3 - - - +
410A PHE* 3.7 22.2 - + - -
411A GLY* 1.3 73.8 - - - +
413A GLU* 1.3 71.4 + - - +
414A ILE* 3.9 19.3 - - + -
423A CYS* 2.8 59.8 + - + +
425A GLY* 4.0 9.9 - - - -
444A ILE* 3.8 18.6 - - + -
446A CYS* 4.9 0.2 - - - -
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Residues in contact with GLU 413 (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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85A SER* 5.2 1.0 + - - -
121A CYS* 3.4 24.9 + - - +
279A GLY* 5.2 2.9 - - - -
280A PHE* 4.6 7.9 + - - +
352A VAL* 4.0 13.2 - - + +
353A HIS* 4.1 15.3 + - - +
355A ARG* 2.7 47.1 + - - -
412A PHE* 1.3 82.7 - - - +
414A ILE* 1.3 63.5 + - - +
415A LYS* 4.1 7.0 + - - +
420A ASP* 3.5 17.6 - - + +
421A VAL 3.1 10.1 - - - +
422A PRO* 4.4 3.4 - - + -
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Residues in contact with ILE 414 (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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121A CYS* 4.1 8.3 - - - -
126A CYS* 4.3 15.0 - - - -
160A LEU* 5.4 6.3 - - + -
412A PHE* 3.9 22.9 - - + -
413A GLU* 1.3 73.4 - - - +
415A LYS* 1.3 73.9 + - - +
416A ASP 3.5 0.7 + - - +
420A ASP* 3.4 3.6 - - - -
421A VAL* 2.7 46.9 + - + +
423A CYS* 3.7 21.3 - - - -
444A ILE* 6.0 0.7 - - + -
446A CYS* 4.1 6.7 - - - -
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Residues in contact with LYS 415 (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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80A THR* 4.5 20.1 + - - +
81A TYR 3.1 25.8 + - - -
82A PRO* 4.3 1.0 - - - +
83A ARG* 3.6 20.6 - - - +
121A CYS* 4.8 7.3 - - + +
122A GLY 3.8 26.0 + - - +
123A PRO* 4.1 21.3 - - + +
413A GLU* 4.9 9.2 - - - +
414A ILE* 1.3 81.3 - - - +
416A ASP* 1.3 62.7 + - - +
417A LYS* 5.7 0.2 - - - +
420A ASP* 2.9 41.2 + - - +
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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