Contacts of the helix formed by residues 252 - 261 (chain A) in PDB entry 2NTZ
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A PHE* 5.7 3.1 - - + -
200A PRO* 4.2 24.5 - - + -
204A GLU* 5.7 2.0 - - + -
241A ILE* 5.3 10.5 - - + -
247A MSE 5.5 4.9 - - + +
248A ALA 3.7 9.5 + - - +
249A GLU* 3.5 42.0 - - + +
250A ASP 3.9 1.3 - - - +
251A GLU* 1.3 77.7 - - - +
253A LYS* 1.3 73.5 + - + +
255A LYS* 3.0 4.4 + - - +
256A ILE* 2.5 60.7 + - + +
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Residues in contact with LYS 253 (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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199A PHE* 4.0 15.3 - - + -
204A GLU* 2.7 48.7 + - + +
205A LEU* 3.9 18.8 - - + -
206A THR* 4.3 9.1 + - - -
209A ASP* 3.6 31.2 + - - +
249A GLU 5.9 0.2 - - - -
250A ASP 4.9 8.3 + - - +
252A VAL* 1.3 86.7 - - + +
254A ASN* 1.3 71.0 + - - +
255A LYS 2.6 6.9 + - - -
257A LEU* 2.5 40.3 + - + +
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Residues in contact with ASN 254 (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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209A ASP* 5.6 0.2 - - - +
250A ASP 4.2 8.0 - - - +
251A GLU* 4.1 18.7 - - + +
252A VAL 3.4 0.6 - - - -
253A LYS* 1.3 98.8 - - - +
255A LYS* 1.3 61.5 + - + +
257A LEU* 4.5 6.2 - - - +
258A ARG* 3.1 30.7 + - - +
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Residues in contact with LYS 255 (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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241A ILE* 4.3 22.9 - - + -
247A MSE 5.5 8.3 - - + -
251A GLU* 3.2 36.1 - - + +
252A VAL* 3.0 2.2 + - - +
253A LYS 2.6 5.3 + - - -
254A ASN* 1.3 79.8 - - + +
256A ILE* 1.3 66.0 + - - +
257A LEU 3.1 0.9 - - - -
258A ARG* 3.7 4.2 - - + +
259A LEU* 3.1 30.7 + - + +
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Residues in contact with ILE 256 (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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198A LEU* 4.5 11.7 - - + +
199A PHE* 3.9 30.7 - - + -
200A PRO* 5.3 2.7 - - + -
234A ILE* 5.8 0.3 - - - +
238A ILE* 3.2 51.9 - - + +
241A ILE* 4.2 16.6 - - + -
252A VAL* 2.5 52.2 + - + +
253A LYS 3.7 1.8 - - - +
255A LYS* 1.3 72.0 - - - +
257A LEU* 1.3 54.1 + - - +
259A LEU* 3.3 6.3 - - + +
260A ILE* 2.7 36.2 + - + +
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Residues in contact with LEU 257 (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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199A PHE* 4.0 12.3 - - + -
205A LEU* 5.9 0.2 - - + -
209A ASP* 3.7 31.9 - - + +
212A THR* 4.4 18.8 - - + +
213A LEU* 3.7 29.4 - - + -
253A LYS* 2.5 28.0 + - + +
254A ASN* 4.5 4.5 - - - +
256A ILE* 1.3 69.6 - - - +
258A ARG* 1.3 54.0 - - + +
259A LEU 2.2 21.5 + - - -
260A ILE* 2.8 24.8 + - + +
261A THR* 3.3 20.0 + - + +
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Residues in contact with ARG 258 (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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254A ASN* 3.1 25.5 + - + +
255A LYS* 3.4 7.5 + - + +
257A LEU* 1.3 77.6 - - + +
259A LEU* 1.3 56.4 + - - +
261A THR* 3.9 9.8 + - - -
262A LYS* 3.3 24.5 - - - +
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Residues in contact with LEU 259 (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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234A ILE* 4.4 13.7 - - + -
237A GLU* 4.0 38.6 - - + +
238A ILE* 4.7 6.5 - - + +
241A ILE* 4.0 24.2 - - + -
255A LYS* 3.1 20.7 + - + +
256A ILE* 3.3 6.5 - - - +
257A LEU 2.2 16.7 + - - -
258A ARG* 1.3 69.2 - - + +
260A ILE* 1.3 60.0 + - - +
261A THR 3.2 0.7 - - - -
262A LYS* 2.9 21.6 + - - +
263A GLU* 2.6 38.7 + - + +
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Residues in contact with ILE 260 (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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195A LEU* 3.2 59.0 - - + +
198A LEU* 4.1 8.5 - - + -
199A PHE* 4.7 4.3 - - + -
213A LEU* 3.9 14.4 - - + -
216A VAL* 4.8 2.7 - - + -
230A LEU* 3.8 5.5 - - + +
234A ILE* 4.3 21.7 - - + +
256A ILE* 2.7 30.0 + - + +
257A LEU* 2.8 28.9 - - + +
259A LEU* 1.3 74.7 - - - +
261A THR* 1.3 55.8 + - + +
263A GLU 3.4 1.7 - - - -
264A ALA* 2.7 35.2 + - - +
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Residues in contact with THR 261 (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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212A THR* 4.7 7.9 - - - +
216A VAL* 4.3 24.2 - - + -
257A LEU* 3.3 37.2 + - + +
258A ARG* 3.9 9.3 + - - +
260A ILE* 1.3 76.9 - - + +
262A LYS* 1.3 72.8 + - - +
264A ALA* 2.6 29.0 + - - +
265A SER* 2.8 15.8 + - - -
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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