Contacts of the helix formed by residues 200 - 218 (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 LEU 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A MET* 3.8 46.0 - - + -
104A CYS* 4.1 13.0 - - - -
142A ALA* 3.2 26.8 + - + +
145A HIS* 3.3 14.3 + - - +
154A ASN* 3.6 9.8 + - + +
155A LEU* 4.1 16.2 - - + -
158A TRP* 4.2 17.9 - - + -
199A GLY* 1.3 70.0 - - - -
201A SER* 1.3 57.5 + - - +
202A GLY 3.4 2.2 - - - -
203A VAL* 3.2 26.6 + - + +
204A VAL* 3.0 28.3 + - + +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A HIS* 4.9 1.4 + - - -
154A ASN* 3.6 20.4 + - - +
199A GLY 3.3 2.5 + - - -
200A LEU* 1.3 75.4 - - - +
202A GLY* 1.3 61.6 + - - +
203A VAL 3.2 0.2 - - - -
204A VAL* 3.6 8.8 - - - +
205A TYR* 2.9 37.0 + - - -
236A TRP* 4.1 10.5 - - - -
247A MET* 3.9 21.0 + - - -
249A MET* 4.1 7.4 - - - +
254A HIS* 2.6 30.3 + - - -
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A SER* 4.5 2.9 - - - -
185A SER* 3.8 28.5 - - - -
199A GLY 4.6 1.0 + - - -
200A LEU 3.4 0.6 - - - -
201A SER* 1.3 80.6 + - - +
203A VAL* 1.3 63.3 + - - +
205A TYR* 3.5 2.3 + - - +
206A ALA* 3.2 17.3 + - - +
249A MET* 4.4 6.3 - - - -
253A ALA 4.9 0.2 - - - -
254A HIS* 4.0 10.7 - - - -
257A GLY* 3.6 14.2 - - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 5.0 2.7 - - + -
158A TRP* 3.8 33.9 - - + -
177A ILE* 5.5 0.4 - - + -
178A THR* 3.8 26.7 - - + +
181A SER* 3.4 24.5 - - - +
182A ALA* 3.8 16.4 - - + +
200A LEU* 3.2 29.3 + - + +
202A GLY* 1.3 76.3 - - - +
204A VAL* 1.3 57.5 + - - +
206A ALA* 3.4 3.6 + - - +
207A LEU* 3.0 30.0 + - + +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 3.6 29.4 - - + +
157A TRP* 3.6 25.8 - - + -
158A TRP* 4.3 11.2 - - + +
161A LEU* 4.9 1.3 - - + -
200A LEU* 3.0 23.0 + - + +
201A SER* 3.3 5.8 + - - +
202A GLY 3.2 0.4 - - - -
203A VAL* 1.3 74.9 - - + +
205A TYR* 1.3 52.9 + - - +
207A LEU* 3.0 10.5 + - + +
208A MET* 2.8 46.6 + - + +
236A TRP* 3.5 25.4 - - + -
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A SER 2.9 25.2 + - - -
202A GLY 3.7 7.2 - - - +
204A VAL* 1.3 72.7 - - - +
206A ALA* 1.3 59.3 + - - +
208A MET* 4.4 6.7 - - - -
209A GLY 2.9 25.8 + - - -
236A TRP* 3.2 29.0 + + - -
237A ILE* 3.5 55.7 + - + +
240A GLY* 4.9 2.4 - - - -
241A TRP* 4.6 9.9 + + - +
247A MET* 4.9 1.1 - - - +
251A ASN* 5.7 0.2 + - - -
254A HIS* 3.2 68.5 + + + +
255A ILE* 5.2 0.9 - - + -
258A LEU* 3.3 29.5 - - + +
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Residues in contact with ALA 206 (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* 4.0 12.8 - - + -
181A SER* 3.4 31.0 - - - +
202A GLY 3.2 4.0 + - - +
203A VAL 3.5 6.3 - - - +
205A TYR* 1.3 78.0 - - - +
207A LEU* 1.3 57.8 + - - +
210A TYR* 2.9 26.9 + - - +
257A GLY 3.1 21.4 + - - +
260A VAL* 4.6 0.4 - - + -
261A GLY* 3.1 20.3 - - - +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TRP 5.0 0.2 - - - +
158A TRP* 3.7 38.4 - - + -
161A LEU* 4.0 18.4 - - + +
162A GLY* 3.9 17.5 - - - +
165A VAL* 4.2 21.1 - - + -
174A LEU* 3.9 21.1 - - + -
177A ILE* 4.3 19.5 - - + -
203A VAL* 3.0 22.3 + - + +
204A VAL* 3.0 10.7 + - - +
206A ALA* 1.3 73.7 - - - +
208A MET* 1.3 59.0 + - - +
210A TYR* 4.3 1.1 - - + -
211A VAL* 2.9 37.1 + - + +
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Residues in contact with MET 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TRP* 3.3 47.1 - - + +
161A LEU* 3.8 13.7 - - + +
204A VAL* 2.8 26.5 + - + +
205A TYR* 3.7 6.7 - - - +
207A LEU* 1.3 72.7 - - - +
209A GLY* 1.3 62.3 + - - +
211A VAL* 4.1 1.6 - - - +
212A TRP* 3.0 28.4 + - - +
225A LEU* 4.4 12.0 - - + +
233A ALA* 3.9 21.8 - - + -
236A TRP* 3.4 35.7 - - + -
237A ILE* 4.2 15.7 - - + -
258A LEU* 5.0 3.6 - - + -
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Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR 2.9 16.6 + - - -
206A ALA 4.0 0.9 - - - -
208A MET* 1.3 72.4 - - - +
210A TYR* 1.3 60.4 + - - +
212A TRP* 4.3 4.4 - - - +
213A LEU* 3.2 26.7 + - - +
258A LEU* 3.5 23.8 - - - +
261A GLY 4.1 2.8 - - - +
262A LEU* 3.5 18.6 - - - +
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 4.4 10.8 - - + -
169A LEU* 3.5 27.8 - - + +
173A LYS* 3.7 6.0 - - + -
177A ILE* 4.1 20.0 - - + -
206A ALA 2.9 22.8 + - - +
207A LEU* 3.7 7.0 - - - +
208A MET 3.3 0.2 - - - -
209A GLY* 1.3 73.9 - - - +
211A VAL* 1.3 70.7 + - + +
214A ARG* 2.9 57.6 + - + +
223A ILE* 4.6 2.2 - - + -
261A GLY* 3.4 13.4 + - - +
264A MET* 3.7 11.9 - - + -
265A ALA* 3.3 33.8 - - - +
268A ASP* 2.3 33.0 + - - -
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.3 28.7 - - + +
164A ALA* 5.6 3.1 - - + -
165A VAL* 3.8 28.5 - - + -
207A LEU 2.9 22.0 + - - +
208A MET 4.2 1.8 - - - +
210A TYR* 1.3 74.2 - - + +
212A TRP* 1.3 66.0 + - - +
215A GLY 3.2 16.3 + - - -
223A ILE* 3.9 22.5 - - + +
224A TYR* 3.5 33.6 - - - +
225A LEU* 3.7 6.5 - - + +
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Residues in contact with TRP 212 (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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208A MET 3.0 19.5 + - - +
209A GLY* 4.3 4.9 - - - -
211A VAL* 1.3 78.7 - - - +
213A LEU* 1.3 92.0 + - + +
215A GLY* 3.5 0.9 + - - -
216A GLU* 3.1 53.0 + - + +
225A LEU* 4.1 24.0 + - + +
230A ILE* 3.8 35.3 - - + +
262A LEU* 4.4 12.6 - - + -
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Residues in contact with LEU 213 (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 GLY 3.2 16.7 + - - +
212A TRP* 1.3 97.3 - - + +
214A ARG* 1.3 67.7 + - - +
216A GLU* 4.1 10.3 - - + -
217A ARG* 2.9 60.3 + - + +
262A LEU* 3.6 33.7 - - + +
265A ALA* 3.8 4.9 - - + -
266A PHE* 3.8 22.7 - - + +
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.8 21.8 - - - +
173A LYS* 4.2 6.1 - - - +
210A TYR* 2.9 54.3 + - + +
213A LEU* 1.3 76.7 - - - +
215A GLY* 1.3 57.3 + - - +
217A ARG* 5.1 1.1 - - - -
218A ASP* 2.9 65.5 + - - +
221A SER* 3.2 26.4 - - - +
223A ILE* 3.7 20.6 - - + +
265A ALA* 3.8 11.8 - - + +
268A ASP* 3.7 25.9 + - - +
269A SER* 4.5 5.2 - - - -
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Residues in contact with GLY 215 (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 VAL 3.2 6.7 + - - -
212A TRP 3.9 1.3 - - - -
213A LEU 3.2 0.4 - - - -
214A ARG* 1.3 76.2 - - - +
216A GLU* 1.3 65.4 + - - +
219A PRO* 3.3 29.1 - - - +
223A ILE 2.9 21.5 + - - -
224A TYR* 3.6 19.9 - - - +
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TRP* 3.1 44.6 + - + +
213A LEU* 3.7 17.7 - - + +
215A GLY* 1.3 77.8 - - - +
217A ARG* 1.3 64.4 + - + +
218A ASP 3.8 0.2 + - - -
219A PRO* 4.5 4.3 - - - +
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 2.9 49.9 + - + +
214A ARG 4.5 0.2 - - - +
216A GLU* 1.3 80.6 - - + +
218A ASP* 1.3 62.7 + - - +
219A PRO* 3.9 3.0 - - - +
266A PHE* 4.0 28.8 - - - -
269A SER* 3.4 31.6 + - - +
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ARG* 2.9 40.3 + - - +
217A ARG* 1.3 83.4 - - - +
219A PRO* 1.3 66.0 - - - +
220A GLN* 3.8 14.4 - - - +
221A SER* 2.7 37.9 + - - -
268A ASP 4.4 1.6 - - - +
269A SER* 4.0 26.4 - - - +
272A ALA* 5.4 10.8 + - - +
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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
------------------------------------------------------------
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