Contacts of the helix formed by residues 202 - 215 (chain X) in PDB entry 1P7G
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 ASN 202 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95X PRO 3.3 20.4 - - - +
96X ASN 2.7 20.7 + - - +
97X MSE 3.7 12.1 - - - +
98X ALA* 3.8 8.8 - - + +
102X LYS* 3.1 36.8 + - - +
103X GLY* 4.7 1.3 - - - -
200X VAL 3.4 1.2 + - - -
201X VAL* 1.3 69.5 - - - +
203X TRP* 1.3 56.3 + - - +
204X ASP* 3.2 15.4 + - - +
205X ASP* 2.8 30.4 + - - +
206X VAL* 3.2 10.8 + - - +
208X ARG* 3.7 7.8 + - - -
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Residues in contact with TRP 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X LYS 5.4 1.2 + - - -
104X GLY 3.9 12.7 + - - +
105X GLY 3.1 28.3 + - - -
106X LYS 3.9 2.7 - - - +
107X PRO* 3.4 37.4 - - + +
108X GLY 5.1 1.7 + - - +
111X ILE* 4.1 12.6 - - + +
115X ILE* 4.1 4.9 - - + -
122X PHE* 3.2 29.1 - + - -
125X PHE* 3.7 17.3 - + - -
144X LEU* 5.0 1.1 - - + -
173X LEU* 3.6 18.2 - - + -
198X TRP* 4.0 14.3 + + - -
201X VAL* 3.2 23.6 + - + +
202X ASN* 1.3 73.3 - - - +
204X ASP* 1.3 59.0 + - - +
206X VAL* 3.6 38.7 - - + +
207X GLU* 3.0 27.0 + - - +
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Residues in contact with ASP 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X LYS* 3.1 30.8 - - - +
202X ASN* 2.9 8.9 + - - +
203X TRP* 1.3 76.8 - - - +
205X ASP* 1.3 61.8 + - - +
207X GLU* 3.5 6.7 + - - +
208X ARG* 3.0 42.1 + - - +
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Residues in contact with ASP 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X PRO* 3.5 21.7 - - - +
96X ASN* 3.1 16.1 + - - -
202X ASN* 2.8 25.0 + - - +
204X ASP* 1.3 75.3 - - - +
206X VAL* 1.3 66.3 + - - +
208X ARG* 3.0 30.9 + - - +
209X ARG* 2.7 54.8 + - - +
222X LEU* 3.7 12.5 - - - +
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Residues in contact with VAL 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96X ASN* 4.4 4.3 - - - +
111X ILE* 3.8 18.6 - - + -
144X LEU* 4.8 1.3 - - + -
172X LEU* 3.9 30.0 - - + +
173X LEU* 3.9 28.7 - - + -
201X VAL* 4.4 0.7 - - + -
202X ASN 3.6 13.7 - - - +
203X TRP* 3.6 42.4 - - + +
205X ASP* 1.3 78.4 + - - +
207X GLU* 1.3 56.2 + - - +
209X ARG* 3.4 3.0 + - - +
210X LEU* 2.9 27.3 + - - +
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Residues in contact with GLU 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X GLY 5.3 0.9 - - - +
109X GLY* 3.6 10.2 - - - -
110X LYS* 2.9 31.8 + - - +
111X ILE* 2.8 41.6 + - + +
203X TRP 3.0 18.8 + - - +
204X ASP* 3.5 9.0 - - - +
206X VAL* 1.3 74.2 - - - +
208X ARG* 1.3 66.8 + - - +
210X LEU* 3.1 6.4 + - - +
211X GLN* 2.9 33.0 + - + +
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Residues in contact with ARG 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X LYS* 4.6 6.5 - - - +
202X ASN* 3.7 11.7 + - - +
204X ASP* 3.0 30.8 + - - +
205X ASP* 3.0 41.7 + - - +
207X GLU* 1.3 76.6 - - + +
209X ARG* 1.3 62.2 + - - +
211X GLN* 3.2 7.7 + - - +
212X LYS* 3.1 27.4 + - + +
222X LEU* 3.7 26.5 - - + +
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Residues in contact with ARG 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X ILE* 3.9 12.6 - - - +
95X PRO* 3.4 25.3 - - - +
96X ASN* 3.9 3.6 - - - +
171X VAL 3.8 11.4 - - - -
172X LEU* 3.7 29.2 - - + -
205X ASP* 2.7 43.8 + - - +
206X VAL 3.7 6.7 - - - +
208X ARG* 1.3 76.2 - - - +
210X LEU* 1.3 63.3 + - - +
212X LYS* 3.3 2.4 + - - +
213X ALA* 3.1 19.9 + - - +
219X ALA* 2.9 43.5 + - + +
220X LEU* 4.0 2.8 - - - +
222X LEU* 3.9 17.9 - - + +
324X ACT 2.8 37.7 + - - +
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Residues in contact with LEU 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X LYS* 3.8 19.3 - - + -
111X ILE* 4.1 19.3 - - + +
114X LEU* 3.8 23.8 - - + -
146X TYR* 3.9 17.9 - - + -
153X LEU* 4.3 1.1 - - + -
172X LEU* 3.7 29.3 - - + +
206X VAL 2.9 18.3 + - - +
207X GLU* 3.1 11.2 + - - +
209X ARG* 1.3 75.8 - - - +
211X GLN* 1.3 58.3 + - + +
213X ALA* 3.3 0.9 + - - +
214X LEU* 2.9 52.2 + - + +
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Residues in contact with GLN 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X LYS* 3.9 13.9 - - - +
207X GLU* 2.9 25.9 + - + +
208X ARG* 3.5 11.2 - - - +
209X ARG 3.2 0.2 - - - -
210X LEU* 1.3 75.8 - - + +
212X LYS* 1.3 66.7 + - + +
214X LEU* 3.0 22.9 + - + +
215X ASN* 2.9 41.5 + - - +
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Residues in contact with LYS 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216U GLY 5.4 0.6 + - - -
208X ARG* 3.1 16.3 + - + +
209X ARG 3.3 5.6 + - - +
211X GLN* 1.3 75.7 - - + +
213X ALA* 1.3 55.2 + - - +
215X ASN* 3.0 8.1 + - - +
217X GLN* 2.7 76.5 + - - +
218X ILE 3.5 21.4 + - - +
219X ALA* 4.2 2.2 - - - -
220X LEU 4.4 4.0 + - - +
221X LYS 4.9 0.4 - - - -
222X LEU* 3.3 50.5 - - + +
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Residues in contact with ALA 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218U ILE* 4.3 5.0 - - - +
146X TYR* 3.6 43.4 - - + -
170X GLN* 4.1 16.6 - - + -
172X LEU* 4.4 1.3 - - + -
209X ARG 3.1 13.2 + - - +
210X LEU* 3.5 10.1 - - - +
212X LYS* 1.3 76.5 - - - +
214X LEU* 1.3 58.1 + - - +
216X GLY* 2.9 20.3 + - - -
217X GLN 3.4 11.6 + - - -
219X ALA* 5.0 0.6 - - + +
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Residues in contact with LEU 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X LYS* 4.2 14.8 - - + -
114X LEU* 4.1 12.1 - - + -
146X TYR* 3.3 39.5 - - + +
210X LEU* 2.9 44.4 + - + +
211X GLN* 3.0 27.8 + - - +
213X ALA* 1.3 77.1 - - - +
215X ASN* 1.3 61.0 + - - +
216X GLY 3.1 1.0 + - - -
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Residues in contact with ASN 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217U GLN* 5.8 0.9 - - - +
211X GLN* 2.9 35.9 + - - +
212X LYS* 3.0 11.1 + - - +
214X LEU* 1.3 78.6 - - - +
216X GLY* 1.3 61.0 + - - +
217X GLN* 3.0 32.2 + - - +
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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