Contacts of the helix formed by residues 246 - 262 (chain A) in PDB entry 2NZ2
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 THR 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 4.8 11.1 + - - -
245A GLN* 1.3 88.3 - - + +
247A SER* 1.3 60.1 + - - +
248A LEU 3.6 0.2 - - - -
249A GLU* 3.4 26.9 + - - +
250A LEU* 3.0 32.7 + - - +
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 3.7 9.4 + - - +
69A VAL* 4.1 6.6 - - - +
70A GLU* 2.7 44.5 + - - +
74A TRP* 3.9 21.9 - - - -
232A PRO 5.3 1.1 - - - -
246A THR* 1.3 72.5 - - - +
248A LEU* 1.3 69.9 + - - +
250A LEU* 3.4 12.4 - - - +
251A PHE* 3.2 23.9 + - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 5.8 1.6 - - - +
65A SER* 4.0 20.4 - - - +
66A ARG* 3.4 48.7 - - + +
69A VAL* 4.0 12.1 - - + -
185A LEU* 3.5 33.7 - - + -
246A THR 3.6 0.4 - - - -
247A SER* 1.3 81.3 + - - +
249A GLU* 1.3 57.7 + - - +
251A PHE* 3.4 2.0 + - + +
252A MET* 3.0 58.7 + - + +
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 4.9 1.9 - - - +
243A THR 4.5 1.8 - - - +
244A HIS* 2.8 52.6 + - + +
245A GLN* 3.9 5.2 + - - -
246A THR* 3.4 26.3 + - - +
247A SER 3.3 0.6 - - - -
248A LEU* 1.3 80.7 - - - +
250A LEU* 1.3 55.9 + - - +
252A MET* 3.6 9.6 + - - +
253A TYR* 3.1 26.3 + - - +
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 4.1 7.0 - - + -
232A PRO* 3.9 36.1 - - + +
233A VAL* 3.5 35.7 - - - +
234A LYS* 3.8 4.3 - - - +
235A VAL* 3.9 16.3 - - + +
244A HIS* 3.7 26.2 - - + +
246A THR 3.0 26.5 + - - +
247A SER* 3.4 9.6 - - - +
249A GLU* 1.3 74.2 - - - +
251A PHE* 1.3 72.4 + - + +
253A TYR* 3.4 3.3 + - - +
254A LEU* 2.9 37.9 + - + +
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Residues in contact with PHE 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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69A VAL* 4.4 13.0 - - + -
73A ILE* 3.8 39.3 - - + -
74A TRP* 3.9 15.0 - + + -
77A ILE* 5.1 0.2 - - + -
185A LEU* 3.6 35.4 - - + -
186A MET* 4.0 14.8 - - + -
247A SER 3.2 19.5 + - - +
248A LEU* 3.6 5.6 - - - +
250A LEU* 1.3 79.7 - - - +
252A MET* 1.3 57.8 + - - +
254A LEU* 3.1 7.9 + - - +
255A ASN* 2.9 35.4 + - - +
286A ALA* 3.6 15.7 - - + +
287A GLY* 4.4 7.4 - - - -
290A LEU* 3.8 28.7 - - + -
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Residues in contact with MET 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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185A LEU* 4.0 17.3 - - + -
248A LEU* 3.0 50.9 + - + +
249A GLU* 4.0 7.2 - - - +
250A LEU 3.4 0.2 - - - -
251A PHE* 1.3 75.1 - - - +
253A TYR* 1.3 58.9 + - - +
255A ASN* 3.1 12.7 + - - +
256A GLU* 2.9 33.2 + - - +
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Residues in contact with TYR 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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223A LEU* 4.1 8.3 - - + -
235A VAL* 3.8 27.8 - - + -
237A ASN* 2.8 38.5 + - + +
240A ASP* 4.4 1.6 + - - -
242A THR* 4.0 22.9 + - + -
244A HIS* 3.4 32.8 - + + +
249A GLU 3.1 17.9 + - - +
250A LEU 3.6 3.4 - - - +
252A MET* 1.3 76.5 - - - +
254A LEU* 1.3 58.5 + - + +
256A GLU* 3.3 31.9 + - - +
257A VAL* 2.8 57.1 + - + +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU* 3.6 31.6 - - + -
225A ILE* 4.3 7.6 - - + -
235A VAL* 3.8 31.4 - - + -
250A LEU* 2.9 22.5 + - + +
251A PHE* 3.5 7.2 - - - +
253A TYR* 1.3 76.1 - - + +
255A ASN* 1.3 58.7 - - - +
257A VAL* 4.4 2.2 - - - -
258A ALA* 2.9 32.2 + - - +
286A ALA* 3.7 13.8 - - + +
289A ILE* 3.9 12.9 - - + +
290A LEU* 3.5 40.8 - - + -
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Residues in contact with ASN 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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185A LEU* 2.8 33.2 + - - +
186A MET 4.6 1.6 - - - +
209A LYS* 3.8 17.0 + - - +
251A PHE* 2.9 23.5 + - - +
252A MET* 3.1 14.6 + - - +
254A LEU* 1.3 75.9 - - - +
256A GLU* 1.3 54.8 + - - +
259A GLY* 2.8 31.5 + - - -
285A PRO* 3.7 15.6 - - + +
286A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 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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252A MET* 2.9 14.0 + - - +
253A TYR* 3.3 37.2 + - + +
255A ASN* 1.3 75.1 - - - +
257A VAL* 1.3 61.5 + - + +
259A GLY* 5.2 0.4 - - - -
260A LYS* 3.1 28.2 + - - +
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Residues in contact with VAL 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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221A ASP* 3.9 27.6 - - + +
223A LEU* 3.9 23.8 - - + -
253A TYR* 2.8 59.4 + - + +
254A LEU* 4.1 5.8 - - - +
256A GLU* 1.3 76.3 - - + +
258A ALA* 1.3 65.4 + - - +
260A LYS* 3.4 13.6 - - + +
261A HIS* 3.2 25.4 - - + -
289A ILE* 4.8 0.4 - - + -
353A VAL* 4.0 9.9 - - + -
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Residues in contact with ALA 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 LEU 2.9 20.0 + - - +
257A VAL* 1.3 77.3 - - - +
259A GLY* 1.3 60.9 + - - +
261A HIS 3.3 1.4 + - - -
262A GLY 3.1 4.3 + - - -
263A VAL* 2.9 39.5 + - + +
285A PRO* 3.4 34.1 - - + +
289A ILE* 3.4 16.4 - - + -
353A VAL* 4.2 4.3 - - - -
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Residues in contact with GLY 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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209A LYS 3.6 20.8 - - - +
210A THR* 3.5 5.3 - - - -
211A GLN* 2.8 30.5 + - - +
255A ASN 2.8 22.8 + - - -
256A GLU* 4.2 1.1 - - - -
258A ALA* 1.3 73.5 - - - +
260A LYS* 1.3 58.5 + - - +
262A GLY 3.4 1.9 + - - -
285A PRO* 3.9 6.8 - - - +
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Residues in contact with LYS 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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211A GLN* 3.6 15.0 - - - +
217A PRO* 3.1 46.3 - - + +
221A ASP* 3.7 16.3 + - - +
256A GLU 3.1 20.6 + - - +
257A VAL* 3.4 7.0 - - + +
259A GLY* 1.3 76.8 - - - +
261A HIS* 1.3 76.3 + - + +
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Residues in contact with HIS 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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213A PRO* 4.7 0.2 - - - +
216A ALA* 3.5 11.0 - - - +
217A PRO* 3.8 23.0 + - + +
219A THR 3.4 24.7 - - - -
220A PRO 4.0 0.2 - - - -
221A ASP* 3.1 30.4 + - + +
257A VAL 3.2 20.8 + - - +
258A ALA 3.3 2.7 + - - +
259A GLY 3.2 0.6 - - - -
260A LYS* 1.3 86.0 - - + +
262A GLY* 1.3 53.5 + - - +
263A VAL* 3.4 2.5 - - + -
353A VAL* 3.2 50.1 + - + +
354A LEU* 3.9 7.2 - - - +
355A LYS* 3.4 12.9 + - - +
356A GLY 2.7 30.5 + - - -
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Residues in contact with GLY 262 (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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210A THR* 3.9 9.4 - - - -
211A GLN* 2.9 36.6 + - - +
213A PRO* 4.2 8.6 - - - +
258A ALA 3.1 2.6 + - - -
259A GLY 3.4 4.4 + - - -
260A LYS 3.5 0.8 + - - -
261A HIS* 1.3 80.0 - - - +
263A VAL* 1.3 60.2 - - - +
264A GLY 3.9 1.4 + - - -
265A ARG* 4.1 10.4 - - - +
356A GLY* 3.4 13.4 - - - +
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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