Contacts of the strand formed by residues 342 - 345 (chain C) in PDB entry 1NBF
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 ARG 342 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B ASP* 3.5 13.9 + - - -
297B GLN* 2.8 29.7 + - - -
298B GLU* 3.2 35.6 - - - +
405B GLN* 3.4 11.1 - - - +
327C LYS* 5.1 1.1 - - - +
340C GLN 4.8 0.2 - - - +
341C GLN* 1.3 79.2 - - - +
343C LEU* 1.3 62.0 + - - +
344C ILE* 4.3 5.0 - - + +
349C GLN* 2.7 44.3 + - + +
368C HIS 3.6 0.9 - - - +
369C LEU* 3.5 4.2 - - - +
370C VAL* 2.9 64.3 + - + +
371C LEU 2.7 27.6 + - - +
372C ARG* 3.3 25.6 - - - +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C VAL* 4.4 1.6 - - + -
323C ILE* 4.7 7.4 - - + -
326C VAL* 4.1 10.8 - - + -
327C LYS* 4.3 25.4 - - + +
330C ILE* 3.7 33.4 - - + -
341C GLN* 4.1 0.4 - - - +
342C ARG* 1.3 74.1 - - - +
344C ILE* 1.3 61.1 + - - +
349C GLN* 3.4 7.0 - - - +
350C LEU* 2.8 50.9 + - + +
367C LEU* 4.0 28.9 - - + -
368C HIS 3.5 3.8 - - - +
369C LEU* 3.9 31.4 - - + +
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Residues in contact with ILE 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLN* 4.2 10.3 - - - +
301B ARG* 3.7 34.1 - - + -
349B ASP* 4.5 10.5 - - - +
351B GLN* 4.7 8.7 - - - +
342C ARG* 4.3 5.2 - - - +
343C LEU* 1.3 75.3 - - - +
345C PHE* 1.3 63.2 + - - +
347C GLY* 4.3 13.9 - - - +
348C LYS 3.4 7.0 - - - +
349C GLN* 3.7 32.5 - - + +
350C LEU* 5.0 0.2 - - - -
367C LEU* 3.9 1.2 - - - -
368C HIS* 2.9 52.2 + - + +
370C VAL* 4.2 16.8 - - + -
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Residues in contact with PHE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B ARG* 6.1 0.7 - - - -
345B GLU* 3.5 35.9 - - + -
343C LEU 4.2 0.4 + - - -
344C ILE* 1.3 76.1 - - - +
346C ALA* 1.3 89.4 + - + +
347C GLY 3.1 1.3 - - - -
348C LYS* 2.8 28.4 + - - +
350C LEU* 3.9 17.0 - - + +
359C TYR* 4.0 18.8 - + + -
360C ASN 4.8 2.5 - - - -
361C ILE* 3.7 24.9 - - + -
365C SER* 3.9 23.3 - - - -
366C THR 3.4 18.6 - - - -
367C LEU* 3.9 17.7 - - + -
368C HIS* 5.2 2.0 - + - -
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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