Contacts of the strand formed by residues 342 - 347 (chain D) 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 VAL 342 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323D GLU 5.0 7.4 - - - +
324D TYR* 4.5 15.3 - - + -
340D VAL* 3.3 17.0 - - + +
341D PRO* 1.3 73.2 - - - +
343D VAL* 1.3 64.3 + - - +
344D GLU* 4.0 20.4 - - + +
361D GLY* 3.1 2.9 - - - -
362D GLN* 2.9 41.1 + - + +
363D ASN* 3.9 14.8 - - - +
364D PHE* 3.4 3.0 - - - -
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Residues in contact with VAL 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D PRO 5.3 0.2 - - - -
342D VAL* 1.3 76.0 - - - +
344D GLU* 1.3 60.4 + - - +
345D SER 4.1 17.5 - - - +
346D LEU* 5.2 2.0 - - + -
359D LEU* 4.7 15.0 - - + -
360D THR 4.0 2.7 - - - +
364D PHE* 3.4 28.0 - - + -
414D LEU* 4.2 25.1 - - + -
424D THR* 4.8 16.2 - - + -
426D LEU* 3.4 33.3 - - + +
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Residues in contact with GLU 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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342D VAL* 4.0 11.2 - - + +
343D VAL* 1.3 73.6 - - - +
345D SER* 1.3 63.9 + - - +
360D THR* 3.1 10.8 + - - +
361D GLY* 3.7 16.7 + - - +
362D GLN* 2.7 39.2 + - - +
426D LEU* 4.9 4.5 - - - +
2028E LEU* 5.5 9.9 - - - +
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Residues in contact with SER 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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343D VAL* 3.5 6.8 - - - +
344D GLU* 1.3 79.6 - - - +
346D LEU* 1.3 69.3 + - - +
347D GLN* 3.4 23.9 + - - -
358D GLU 3.9 0.7 - - - +
359D LEU* 3.6 2.9 - - - -
360D THR* 2.9 50.4 + - - +
426D LEU* 5.3 1.8 - - - -
1961E MET* 3.5 14.3 - - - +
1995E ASP* 5.9 6.3 - - - -
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Residues in contact with LEU 346 (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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343D VAL* 5.2 1.3 - - + -
345D SER* 1.3 78.8 + - - +
347D GLN* 1.3 65.2 + - - +
348D LEU* 4.2 1.9 + - + +
357D LEU* 3.9 27.8 - - + -
358D GLU 3.6 2.9 - - - -
359D LEU* 3.7 26.0 - - + -
412D VAL* 4.1 26.5 - - + -
426D LEU* 4.5 29.5 - - + +
427D THR 5.0 11.2 - - - +
428D PHE* 5.2 7.6 - - + +
1961E MET* 4.5 9.2 - - - +
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Residues in contact with GLN 347 (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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345D SER* 3.4 18.9 + - - -
346D LEU* 1.3 73.2 - - - +
348D LEU* 1.3 62.5 + - - +
349D ASN* 3.5 11.1 + - - +
357D LEU* 3.1 9.6 - - - +
358D GLU* 2.7 48.8 + - + +
360D THR* 4.3 16.8 + - - +
1961E MET* 2.8 45.3 - - + +
1963E ARG* 3.3 30.3 - - - +
1993E MET* 5.0 8.2 - - - +
1995E ASP* 4.8 11.5 + - - +
2005E ARG* 4.9 6.7 - - - +
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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