Contacts of the strand formed by residues 379 - 383 (chain A) in PDB entry 3NBN
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 THR 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A PRO 5.7 0.2 - - - +
368A LEU 4.0 7.0 - - - +
369A ARG* 3.7 32.1 - - - +
370A VAL* 2.9 30.1 + - + +
377A ALA 3.1 8.7 + - - -
378A GLU* 1.3 80.3 + - - +
380A MET* 1.3 61.7 + - - +
381A TYR* 4.7 1.1 - - + +
387A MET* 4.0 26.7 - - + -
388A LEU 3.6 7.0 - - - +
389A CYS* 3.7 0.2 - - - +
34C HIS* 2.5 34.9 + - - +
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Residues in contact with MET 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A MET* 3.7 35.4 - - + -
378A GLU* 4.2 25.6 - - - +
379A THR* 1.3 77.3 - - - +
381A TYR* 1.3 61.9 + - - +
382A ARG* 3.7 0.8 + - - -
387A MET* 3.6 1.7 - - - +
388A LEU* 2.6 53.3 + - + +
390A VAL* 4.2 11.7 - - + -
27C ILE* 5.0 10.1 - - + +
30C CYS* 3.3 47.3 - - + +
31C ARG* 3.8 13.2 - - - +
34C HIS* 3.3 4.0 - - + -
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Residues in contact with TYR 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PHE* 4.0 4.2 + - + -
365A THR* 3.8 30.4 - - - +
366A PRO* 3.8 24.1 - - + +
379A THR* 5.5 1.6 - - + -
380A MET* 1.3 72.4 - - - +
382A ARG* 1.3 63.3 + - - +
383A CYS* 3.3 28.3 - - - -
384A GLY* 3.1 9.8 + - - -
387A MET* 3.7 19.3 - - + -
2072B GLU* 2.9 23.6 + - - -
30C CYS 4.9 0.3 - - - +
33C HIS* 3.5 14.4 - - - -
34C HIS* 3.0 29.2 + - + +
37C CYS* 3.6 39.7 - - + -
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Residues in contact with ARG 382 (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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358A GLU* 5.8 1.6 - - - +
380A MET* 3.7 2.2 + - - -
381A TYR* 1.3 81.2 - - - +
383A CYS* 1.3 66.2 + - - +
386A SER* 3.2 25.6 + - - +
387A MET* 4.1 0.2 - - - +
388A LEU* 3.5 35.3 - - + +
2005B ARG* 2.9 31.6 + - + +
2006B LEU* 4.8 1.7 - - + -
2007B ALA* 3.1 25.4 - - - +
2038B ALA 4.4 0.2 - - - +
2039B VAL* 3.8 40.6 + - + +
2041B ASN* 4.7 4.6 - - - +
2072B GLU* 5.1 0.2 - - - +
29C LEU* 5.0 5.3 + - - +
30C CYS* 4.6 19.3 - - - +
33C HIS* 3.1 62.3 + - - +
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Residues in contact with CYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PHE* 4.1 1.0 - - - +
381A TYR* 3.3 18.4 - - - -
382A ARG* 1.3 79.4 - - - +
384A GLY* 1.3 56.8 + - - +
385A GLU* 2.6 29.8 + - - -
386A SER* 2.8 42.6 + - - +
2035B TRP* 4.3 10.5 - - - -
2038B ALA* 3.6 32.5 - - - +
2039B VAL* 3.8 8.3 - - + -
2072B GLU* 3.1 18.4 - - - +
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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