Contacts of the strand formed by residues 248 - 252 (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 LEU 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A THR* 3.4 7.4 - - - +
234A VAL* 2.9 42.3 + - - +
236A LEU* 4.1 15.5 - - + +
245A LEU* 3.9 25.4 - - + +
246A PRO* 2.7 31.8 + - + +
247A ARG* 1.3 74.0 - - - +
249A ILE* 1.3 63.0 + - - +
250A ILE 4.1 0.4 - - - -
274A PHE* 3.5 33.2 - - + -
275A TYR 3.3 4.3 - - - -
276A LEU* 3.8 39.9 - - + -
284A LEU* 4.6 6.7 - - + -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLY* 3.3 26.7 - - - +
232A GLN 3.5 2.7 - - - -
233A THR* 3.6 23.1 - - + +
248A LEU* 1.3 78.9 - - - +
250A ILE* 1.3 63.5 + - - +
251A ARG* 3.5 30.7 + - + +
273A ALA 3.3 3.6 - - - +
274A PHE* 4.4 1.6 - - - -
275A TYR* 2.8 60.4 + - + +
277A LYS* 4.5 12.6 - - + -
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 5.3 5.2 - - + -
228A ILE* 3.4 32.8 - - + -
229A HIS 3.7 13.5 - - - +
230A TYR* 3.5 6.9 - - + -
231A GLY* 2.5 37.1 + - - +
232A GLN* 3.3 14.1 + - + +
234A VAL* 3.8 17.0 - - + +
248A LEU 4.1 0.8 - - - -
249A ILE* 1.3 69.9 - - - +
251A ARG* 1.3 56.2 + - - +
266A VAL* 3.9 16.4 - - + -
272A CYS* 4.7 6.7 - - + -
273A ALA 3.5 3.4 - - - +
274A PHE* 3.6 39.3 - - + -
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Residues in contact with ARG 251 (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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230A TYR* 3.6 9.6 - - - -
231A GLY* 4.5 4.0 - - - +
249A ILE* 3.7 24.8 - - + +
250A ILE* 1.3 78.3 - - - +
252A LYS* 1.3 69.3 + - - +
258A ALA* 4.8 5.8 - - + +
259A LEU 3.8 12.8 - - - +
260A LEU* 3.4 63.1 + - - +
262A ALA* 5.4 0.9 - - + -
272A CYS* 3.3 3.6 - - - -
273A ALA* 3.0 29.7 + - - +
275A TYR* 3.1 49.5 - - - +
283A TYR* 3.2 15.8 + - + +
306A GLU* 5.4 1.0 + - - -
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Residues in contact with LYS 252 (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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155A LYS* 4.4 25.6 - - - +
156A LYS 5.7 0.2 - - - +
230A TYR* 3.4 40.2 - - + +
251A ARG* 1.3 79.7 - - - +
253A VAL* 1.3 76.0 + - - +
254A ASP* 6.4 1.6 - - - -
258A ALA* 3.5 18.4 - - - +
259A LEU* 3.7 25.6 + - + -
262A ALA* 3.9 17.7 - - + +
264A ASP* 3.6 23.4 + - - +
270A HIS* 4.7 10.8 - - - -
271A LYS 4.2 4.5 - - - +
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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