Contacts of the strand formed by residues 342 - 345 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A ASP* 3.5 15.6 + - - -
297A GLN* 2.7 30.3 + - - -
298A GLU* 3.4 19.7 + - - +
301A ARG* 5.0 1.0 - - - +
405A GLN* 3.5 9.3 + - - -
327D LYS* 5.3 1.1 - - - +
340D GLN 4.5 1.1 - - - +
341D GLN* 1.3 77.4 - - - +
343D LEU* 1.3 62.2 + - - +
344D ILE* 4.0 5.2 - - + +
349D GLN* 2.7 45.2 + - - +
368D HIS 3.4 3.5 - - - +
369D LEU* 3.6 2.8 - - - +
370D VAL* 3.0 64.1 + - + +
371D LEU 3.0 23.9 + - - +
372D ARG* 3.4 40.1 - - + +
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305D VAL* 4.9 0.9 - - + -
323D ILE* 4.2 12.3 - - + -
326D VAL* 3.7 28.0 - - + -
327D LYS* 3.9 30.9 - - + +
330D ILE* 3.7 24.2 - - + -
341D GLN* 4.6 1.3 - - - +
342D ARG* 1.3 77.0 - - - +
344D ILE* 1.3 60.5 - - - +
349D GLN* 3.3 6.1 - - - +
350D LEU* 2.8 52.1 + - + +
367D LEU* 4.5 16.8 - - + -
368D HIS 4.5 2.9 - - - +
369D LEU* 4.1 19.5 - - + +
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Residues in contact with ILE 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A GLN* 3.2 31.6 - - - +
301A ARG* 4.0 17.3 - - - -
349A ASP* 4.6 4.7 - - - +
351A GLN* 3.9 21.3 - - - +
342D ARG* 4.2 7.2 - - - +
343D LEU* 1.3 76.3 - - - +
345D PHE* 1.3 65.2 + - - +
347D GLY 4.6 5.6 - - - +
348D LYS 3.4 12.6 - - - +
349D GLN* 4.6 7.2 - - + -
367D LEU* 4.8 0.7 - - - -
368D HIS* 2.8 54.1 + - + +
370D VAL* 3.7 28.7 - - + -
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Residues in contact with PHE 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A GLU* 3.5 34.3 - - + -
343D LEU 4.1 0.6 + - - -
344D ILE* 1.3 75.3 - - - +
346D ALA* 1.3 89.3 + - + +
347D GLY 3.1 1.6 - - - -
348D LYS* 2.9 27.5 + - - +
350D LEU* 4.1 13.4 - - + +
359D TYR* 3.7 20.8 - + + -
360D ASN 4.7 2.9 - - - -
361D ILE* 3.6 26.9 - - + -
365D SER* 3.9 21.3 - - - -
366D THR 3.3 18.8 - - - -
367D LEU* 3.7 19.3 - - + -
368D HIS* 5.2 2.2 - + - -
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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