Contacts of the helix formed by residues 250 - 270 (chain A) in PDB entry 4NJP
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 ALA 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLN* 2.8 22.9 + - - +
192A PHE* 6.2 4.7 - - + -
193A SER* 4.8 8.1 - - - +
243A ASP* 6.0 1.1 - - - -
248A SER 4.0 0.2 + - - -
249A MET* 1.3 76.2 - - - +
251A ASN* 1.3 69.2 + - - +
252A GLY* 3.4 3.6 - - - +
253A ALA* 3.3 6.3 + - - +
254A HIS* 3.1 20.8 + - - -
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Residues in contact with ASN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 5.7 0.2 + - - -
240A GLY 3.7 7.4 - - - +
241A TRP* 3.1 79.7 + - + +
243A ASP* 4.4 5.0 + - - +
249A MET 5.0 1.2 - - - +
250A ALA* 1.3 77.1 - - - +
252A GLY* 1.3 64.7 + - - +
254A HIS* 3.1 12.0 + - - +
255A ILE* 3.1 31.2 + - + +
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Residues in contact with GLY 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 3.6 15.0 - - - +
192A PHE* 4.7 11.6 - - - -
250A ALA* 3.4 2.0 - - - +
251A ASN* 1.3 79.0 - - - +
253A ALA* 1.3 59.5 + - - +
255A ILE* 3.6 14.5 - - - +
256A ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 3.3 23.5 - - - +
188A VAL* 3.6 13.2 - - - +
189A GLN* 3.3 31.1 + - - +
192A PHE* 5.3 1.2 - - - -
249A MET* 3.4 23.3 - - + -
250A ALA* 3.3 7.1 + - - +
251A ASN 3.3 0.2 - - - -
252A GLY* 1.3 76.0 - - - +
254A HIS* 1.3 61.1 + - - +
256A ALA* 3.4 1.8 - - - +
257A GLY 3.2 15.6 + - - -
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Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A SER* 2.6 32.8 + - - -
202A GLY* 4.0 7.4 - - - -
205A TYR* 3.2 62.4 + + + +
240A GLY* 5.7 3.9 - - - -
241A TRP* 6.2 1.8 - - + -
247A MET* 4.1 17.9 - - + -
249A MET* 3.1 38.2 + - + +
250A ALA 3.1 10.4 + - - -
251A ASN* 3.1 13.5 + - - +
253A ALA* 1.3 73.6 - - - +
255A ILE* 1.3 55.4 + - + +
257A GLY* 3.2 2.2 + - - +
258A LEU* 2.7 29.6 + - - +
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 4.8 0.9 - - + -
241A TRP* 3.7 32.8 - - + -
251A ASN 3.1 18.3 + - - +
252A GLY* 3.6 12.8 - - - +
254A HIS* 1.3 74.7 - - - +
256A ALA* 1.3 57.1 + - - +
257A GLY 3.2 0.2 - - - -
258A LEU* 3.5 14.5 - - + +
259A ALA* 2.7 41.7 + - + +
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 3.5 25.5 - - + +
185A SER* 4.2 6.3 - - - -
188A VAL* 3.8 21.1 - - + -
252A GLY 3.2 11.2 + - - +
253A ALA 3.4 11.4 - - - +
255A ILE* 1.3 77.8 - - - +
257A GLY* 1.3 63.2 + - - +
259A ALA* 3.6 4.7 - - - +
260A VAL* 3.2 27.9 + - - +
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Residues in contact with GLY 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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181A SER* 4.6 7.6 - - - -
185A SER* 4.4 6.0 - - - -
202A GLY 3.6 19.7 - - - -
206A ALA* 3.1 27.8 - - - +
253A ALA 3.2 7.6 + - - -
254A HIS 3.2 7.7 + - - -
255A ILE 3.2 0.4 - - - -
256A ALA* 1.3 80.7 - - - +
258A LEU* 1.3 63.7 + - - +
259A ALA 3.2 0.3 + - - -
260A VAL* 3.4 2.5 + - - +
261A GLY 3.3 6.1 + - - -
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 3.3 38.3 - - + +
208A MET* 5.0 2.9 - - + -
209A GLY* 3.5 24.0 - - - +
237A ILE* 5.8 6.7 - - + -
254A HIS 2.7 17.8 + - - +
255A ILE* 3.1 16.6 + - + +
257A GLY* 1.3 72.6 - - - +
259A ALA* 1.3 53.1 + - - +
261A GLY* 3.0 4.3 + - - -
262A LEU* 2.8 54.1 + - + +
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 5.6 2.2 - - + -
255A ILE* 2.7 24.9 + - + +
256A ALA* 3.6 7.9 - - - +
258A LEU* 1.3 72.5 - - - +
260A VAL* 1.3 59.5 + - + +
262A LEU* 3.1 13.2 + - - +
263A ALA* 2.9 30.9 + - - +
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Residues in contact with VAL 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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177A ILE 4.5 1.8 - - - +
180A ILE* 3.8 32.3 - - + -
181A SER* 4.1 20.4 - - - +
184A LEU* 3.6 25.4 - - + -
206A ALA* 4.6 1.3 - - + -
256A ALA 3.2 14.1 + - - +
257A GLY 3.5 8.5 - - - +
259A ALA* 1.3 75.0 - - - +
261A GLY* 1.3 66.6 + - - +
263A ALA* 3.3 6.2 + - - +
264A MET* 3.1 40.5 + - + +
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 5.2 2.7 - - - -
206A ALA* 3.1 30.5 - - - +
210A TYR* 3.4 22.0 - - - -
257A GLY 3.3 4.0 + - - -
258A LEU 3.0 6.8 + - - -
260A VAL* 1.3 79.6 - - - +
262A LEU* 1.3 62.8 + - - +
264A MET* 3.6 2.9 + - - -
265A ALA 3.0 19.1 + - - -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLY* 3.5 29.8 - - - +
212A TRP* 4.4 12.6 - - + -
213A LEU* 3.6 24.2 - - + +
258A LEU* 2.8 39.8 + - + +
259A ALA* 3.1 10.7 + - - +
261A GLY* 1.3 76.8 - - - +
263A ALA* 1.3 57.3 + - - +
265A ALA 3.4 0.3 + - - -
266A PHE* 2.9 31.4 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA 2.9 16.2 + - - +
260A VAL* 3.7 7.9 - - - +
262A LEU* 1.3 74.9 - - - +
264A MET* 1.3 61.4 + - + +
266A PHE* 3.1 9.4 - - - +
267A VAL* 2.9 35.0 + - + +
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Residues in contact with MET 264 (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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173A LYS* 4.6 9.6 - - + +
176A VAL* 3.6 28.9 - - + -
177A ILE* 3.4 41.7 - - + +
180A ILE* 4.5 11.4 - - + -
210A TYR* 3.7 14.4 - - + -
260A VAL* 3.1 28.8 + - + +
261A GLY 4.6 0.2 - - - -
263A ALA* 1.3 79.8 - - + +
265A ALA* 1.3 59.7 + - - +
267A VAL* 3.7 6.6 - - + +
268A ASP* 2.8 38.7 + - - +
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Residues in contact with ALA 265 (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 TYR* 3.3 39.6 - - + +
213A LEU* 3.8 15.3 - - + -
214A ARG* 3.8 16.2 - - + +
261A GLY 3.0 17.5 + - - +
262A LEU 3.8 1.1 - - - +
264A MET* 1.3 71.5 - - - +
266A PHE* 1.3 66.8 + - - +
268A ASP* 3.2 3.8 + - - +
269A SER* 2.9 29.1 + - - -
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Residues in contact with PHE 266 (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 LEU* 3.8 8.9 - - + +
217A ARG* 4.0 31.4 - - - -
262A LEU 2.9 15.5 + - - +
263A ALA* 3.1 13.7 - - - +
265A ALA* 1.3 77.7 - - - +
267A VAL* 1.3 72.3 + - + +
269A SER* 3.0 6.2 + - - -
270A LEU* 2.9 52.0 + - + +
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Residues in contact with VAL 267 (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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263A ALA* 2.9 22.1 + - + +
264A MET* 3.7 7.9 - - + +
266A PHE* 1.3 80.8 - - + +
268A ASP* 1.3 74.6 + - - +
270A LEU* 3.1 28.2 - - + +
271A ASN* 3.7 9.4 - - - +
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Residues in contact with ASP 268 (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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173A LYS* 2.6 30.3 + - - +
210A TYR* 2.3 38.5 + - - +
214A ARG* 3.7 20.6 + - - +
218A ASP* 4.4 1.4 - - - +
264A MET* 2.8 28.1 + - - +
265A ALA 3.6 4.0 - - - +
267A VAL* 1.3 82.8 - - - +
269A SER* 1.3 59.2 + - - +
271A ASN* 3.6 21.7 + - - +
272A ALA 5.2 0.2 + - - -
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ARG* 4.5 6.1 - - - -
217A ARG* 3.4 41.6 - - - +
218A ASP* 4.0 26.6 - - - +
265A ALA 2.9 13.1 + - - -
266A PHE* 3.0 11.1 + - - -
268A ASP* 1.3 74.0 - - - +
270A LEU* 1.3 61.9 + - - +
271A ASN 3.1 6.3 + - - -
272A ALA* 4.1 14.1 + - - +
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Residues in contact with LEU 270 (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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266A PHE* 2.9 48.3 + - + +
267A VAL* 3.1 21.8 - - + +
269A SER* 1.3 75.2 + - - +
271A ASN* 1.3 64.2 + - - +
272A ALA 4.3 3.5 - - - +
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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
------------------------------------------------------------
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