Contacts of the strand formed by residues 389 - 394 (chain A) in PDB entry 3NKO
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 LEU 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 3.4 22.4 - - + +
206A PRO* 3.6 22.9 - - + -
208A LYS* 3.7 31.0 - - - +
385A VAL* 3.3 3.9 - - + +
386A PRO 3.2 33.6 - - - +
387A GLY 3.1 2.5 + - - -
388A THR* 1.3 81.7 - - - +
390A GLY* 1.3 61.2 + - - +
391A ARG* 4.1 11.9 - - + +
444A HIS* 4.3 10.8 - - + +
445A LEU 3.8 2.7 - - - -
447A VAL* 3.6 11.7 - - - +
453A VAL* 3.6 3.1 - - - +
475A GLY 4.5 3.6 - - - +
1008A SCN 3.4 29.2 - - - -
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Residues in contact with GLY 390 (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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384A LEU* 4.0 10.1 - - - -
385A VAL 3.1 7.0 - - - -
389A LEU* 1.3 74.9 - - - +
391A ARG* 1.3 63.8 + - - -
444A HIS* 3.3 11.3 + - - -
445A LEU* 2.7 52.1 + - - +
453A VAL* 4.3 1.6 - - - -
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Residues in contact with ARG 391 (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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228A VAL* 4.1 5.0 + - - +
231A SER 2.8 25.3 + - - -
232A MET* 3.6 19.4 - - - +
383A THR 3.7 1.0 - - - +
384A LEU* 3.5 4.9 - - - +
385A VAL* 2.9 57.6 + - + +
389A LEU* 4.1 4.9 - - + +
390A GLY* 1.3 79.6 - - - +
392A ILE* 1.3 62.5 + - - +
393A ARG* 5.5 0.3 + - - -
434A TYR* 3.7 27.2 + - - -
439A ARG 4.2 5.9 + - - -
440A ILE* 4.7 1.6 - - - -
441A GLU* 2.6 44.8 + - + +
443A LEU 3.6 5.6 - - - +
444A HIS* 3.7 17.9 - - + +
1008A SCN 3.6 29.7 - - - -
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Residues in contact with ILE 392 (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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372A LEU* 4.1 21.1 - - + -
382A ILE* 4.0 33.0 - - + -
383A THR 3.5 3.4 - - - +
384A LEU* 3.6 17.3 - - + -
391A ARG* 1.3 77.3 - - - +
393A ARG* 1.3 63.7 + - - +
402A TYR* 3.5 22.4 + - + +
407A ILE* 4.7 4.7 - - + -
411A LEU* 4.2 8.1 - - + -
441A GLU* 3.4 17.1 - - - +
442A ASP 5.0 0.3 + - - -
443A LEU* 3.1 44.6 + - + +
445A LEU* 4.2 20.2 - - + -
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 3.4 41.1 - - - +
240A THR* 4.7 4.8 + - - +
382A ILE* 3.5 3.8 - - - +
383A THR* 2.8 53.8 + - - +
385A VAL* 3.9 11.1 - - - +
391A ARG 5.5 0.4 + - - +
392A ILE* 1.3 75.6 - - - +
394A PRO* 1.3 83.0 + - + +
397A PRO* 6.4 0.4 - - - +
402A TYR* 4.1 9.2 - - - -
441A GLU* 3.0 34.2 + - + -
1009A SCN 3.4 35.0 - - - -
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Residues in contact with PRO 394 (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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381A ASP 3.7 8.7 - - - +
382A ILE* 4.3 0.2 - - - -
383A THR* 4.3 0.7 + - - -
393A ARG* 1.3 101.8 + - + +
395A LYS* 1.3 67.0 + - - +
396A ILE 3.3 21.6 + - - +
397A PRO* 4.2 4.5 - - + +
398A ASN* 4.1 8.7 - - - +
399A ASN* 3.8 23.6 - - + +
402A TYR* 3.7 42.8 - - + -
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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