Contacts of the strand formed by residues 302 - 306 (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 GLN 302 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B LYS 2.9 26.1 + - - -
379B TYR* 3.4 17.7 - - - -
380B ASP* 2.9 43.2 + - + +
386B LEU* 4.5 4.6 - - - +
301C MET* 1.3 73.7 - - - +
303C ILE* 1.3 69.9 + - - +
304C PHE* 3.9 8.4 - - + -
314C THR* 3.4 24.8 + - + +
315C LEU 3.2 10.3 - - - +
316C GLU* 3.9 10.8 + - - +
363C LYS* 3.5 6.3 - - - +
364C GLU* 2.8 26.6 + - + +
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Residues in contact with ILE 303 (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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301C MET* 4.7 3.1 - - + +
302C GLN* 1.3 81.0 - - - +
304C PHE* 1.3 69.8 + - - +
314C THR* 3.5 5.0 - - - -
315C LEU* 2.9 53.2 + - + +
317C VAL* 3.5 34.5 - - + -
326C VAL* 4.7 2.2 - - + -
356C LEU* 4.7 4.7 - - + -
361C ILE* 4.3 16.2 - - + -
362C GLN 3.8 20.0 - - - +
363C LYS* 4.5 2.5 - - - -
364C GLU* 4.1 2.7 - - - +
365C SER* 3.6 11.2 - - - +
367C LEU* 3.8 31.9 - - + -
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Residues in contact with PHE 304 (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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332B ILE* 3.5 32.3 - - + -
373B LEU* 4.1 14.8 - - + -
379B TYR* 4.1 7.0 - + - -
391B LYS* 3.6 16.4 - - + -
302C GLN* 3.9 17.7 - - + -
303C ILE* 1.3 78.0 - - - +
305C VAL* 1.3 66.1 + - - +
312C THR* 3.8 24.2 - - + -
313C ILE 3.3 2.5 - - - -
314C THR* 3.8 25.8 - - + -
364C GLU* 3.4 40.6 - - + -
365C SER 2.8 9.4 + - - +
366C THR* 3.4 14.3 - - + +
367C LEU* 2.8 32.2 + - - +
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Residues in contact with VAL 305 (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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303C ILE* 4.9 0.9 - - + -
304C PHE* 1.3 81.5 - - - +
306C LYS* 1.3 65.8 + - - +
307C THR 3.4 2.3 + - - +
312C THR* 3.5 2.0 - - - -
313C ILE* 2.9 47.2 + - + +
315C LEU* 3.8 34.1 - - + -
330C ILE* 4.0 24.7 - - + -
343C LEU* 4.4 3.8 - - + -
366C THR* 4.8 0.9 - - - -
367C LEU* 3.2 20.9 - - + +
369C LEU* 4.0 23.3 - - + -
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Residues in contact with LYS 306 (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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351B GLN* 4.7 4.8 + - + +
353B SER* 5.2 4.5 + - - +
366B ASP* 4.8 6.6 + - - -
367B TYR* 3.4 50.0 + - + +
371B GLU* 5.3 2.9 - - - +
304C PHE 4.3 0.4 - - - -
305C VAL* 1.3 72.1 - - - +
307C THR* 1.3 68.1 + - - +
310C GLY* 3.2 40.8 - - - +
311C LYS 3.4 7.2 - - - +
312C THR* 4.3 9.4 - - - +
366C THR* 4.3 9.2 - - + +
367C LEU 2.8 13.6 + - - +
368C HIS* 4.1 24.8 - - + +
369C LEU* 3.1 23.4 + - - +
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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