Contacts of the strand formed by residues 392 - 398 (chain A) in PDB entry 1NNC
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 GLN 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASN* 2.7 26.5 + - - +
96A SER* 4.9 1.6 - - - -
361A TRP* 3.8 13.3 - - + -
377A LEU* 3.6 7.8 - - - +
378A LYS* 2.9 53.2 + - + +
390A PRO* 3.6 2.6 - - - +
391A THR* 1.3 81.8 + - - +
394A GLY* 1.3 67.4 + - - +
452A PHE* 3.6 28.3 - - - -
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Residues in contact with GLY 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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361A TRP* 4.1 8.0 - - - -
376A MET 3.2 11.7 - - - -
377A LEU* 4.1 9.2 - - - -
392A GLN* 1.3 87.1 - - - +
395A GLN* 1.3 63.1 + - - +
455A GLN* 4.5 2.6 - - - +
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Residues in contact with GLN 395 (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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96A SER* 3.6 16.8 - - - +
97A TRP* 3.0 60.1 + - + +
361A TRP* 4.6 2.6 - - + -
375A GLU* 3.4 2.9 - - - +
376A MET* 2.8 41.8 + - + +
392A GLN* 5.9 0.2 + - - -
394A GLY* 1.3 76.5 + - - +
396A THR* 1.3 68.6 + - - +
397A ILE* 3.6 6.7 + - + +
446A MET* 3.6 13.7 - - - +
453A LEU 4.7 4.7 + - - -
454A GLY 4.9 0.2 - - - +
455A GLN* 3.4 33.0 - - + +
456A TRP 5.4 0.9 + - - +
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Residues in contact with THR 396 (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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366A ILE* 4.4 10.3 - - + +
374A TYR 3.9 4.7 - - - +
375A GLU* 4.3 10.0 + - - +
395A GLN* 1.3 75.7 - - - +
397A ILE* 1.3 66.5 + - - +
398A VAL 3.7 23.8 - - - +
399A LEU* 4.0 20.9 - - + -
455A GLN* 2.8 25.2 + - - +
456A TRP 3.5 17.0 - - - +
457A ASP* 5.1 2.7 - - + -
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Residues in contact with ILE 397 (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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97A TRP* 5.0 0.9 - - + -
374A TYR* 2.8 29.1 + - + +
375A GLU* 4.3 0.2 - - - -
376A MET* 4.0 24.2 - - + -
395A GLN* 3.8 22.4 - - + +
396A THR* 1.3 79.3 - - - +
398A VAL* 1.3 62.2 + - + +
422A PHE* 4.1 11.9 - - + -
424A VAL* 4.5 14.4 - - + -
444A VAL* 4.7 6.5 - - + -
446A MET* 4.1 39.0 - - + -
456A TRP 4.6 2.0 - - - -
457A ASP* 3.3 5.7 - - - -
458A TRP* 2.8 36.9 + - + -
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Residues in contact with VAL 398 (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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366A ILE* 3.5 5.9 - - - +
373A GLY* 3.3 2.2 - - - -
374A TYR* 2.8 48.7 + - + +
396A THR* 3.7 3.8 - - - +
397A ILE* 1.3 89.5 - - + +
399A LEU* 1.3 65.6 + - - +
402A ASP* 3.5 33.7 - - + +
403A TRP 4.0 11.0 - - - +
404A SER* 5.0 0.4 - - - -
424A VAL* 4.7 3.8 - - + -
426A LEU* 3.8 17.0 - - + -
444A VAL* 4.8 1.8 - - + -
458A TRP 3.7 22.9 - - - +
459A PRO* 4.7 3.8 - - + -
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Residues in contact with LEU 399 (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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366A ILE* 4.5 0.7 - - + -
373A GLY* 3.4 0.7 - - - -
396A THR* 4.0 19.3 - - + -
398A VAL* 1.3 76.7 - - - +
400A ASN* 1.3 57.9 + - - +
401A THR* 3.0 18.6 - - - +
402A ASP* 2.8 38.5 + - - +
457A ASP* 3.5 34.3 + - + +
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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