Contacts of the helix formed by residues 202 - 215 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95Q PRO 3.2 12.3 - - - +
96Q ASN 2.7 29.4 + - - +
97Q MSE 3.6 13.8 - - - +
98Q ALA* 3.8 14.7 - - + +
102Q LYS* 4.2 16.6 + - - +
103Q GLY* 4.4 2.2 - - - -
200Q VAL 3.2 2.4 + - - -
201Q VAL* 1.3 69.6 - - - +
203Q TRP* 1.3 53.5 + - - +
204Q ASP* 3.3 20.0 + - - +
205Q ASP* 2.7 48.1 + - - +
206Q VAL* 3.2 7.3 + - - +
208Q ARG* 4.8 4.4 + - - +
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Residues in contact with TRP 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q LYS 5.0 1.2 + - - -
104Q GLY 3.3 24.8 + - - -
105Q GLY 3.8 9.7 + - - -
106Q LYS* 3.4 25.3 - - - +
107Q PRO* 3.8 22.4 - - + +
108Q GLY 4.9 3.0 - - - +
111Q ILE* 3.9 18.9 - - + +
115Q ILE* 4.2 5.8 - - + -
122Q PHE* 3.7 20.8 - + - -
125Q PHE* 3.7 24.5 - + - -
144Q LEU* 5.3 0.7 - - + -
173Q LEU* 3.7 16.2 - - + -
198Q TRP* 4.1 11.9 + + - -
201Q VAL* 2.9 29.8 + - + +
202Q ASN* 1.3 71.3 - - - +
204Q ASP* 1.3 59.5 + - - +
206Q VAL* 3.7 32.6 - - + +
207Q GLU* 3.0 27.2 + - - +
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Residues in contact with ASP 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q LYS* 3.9 20.0 - - - +
202Q ASN* 3.0 13.1 + - - +
203Q TRP* 1.3 76.6 + - - +
205Q ASP* 1.3 64.2 + - - +
207Q GLU* 3.3 8.3 + - - +
208Q ARG* 3.0 36.9 + - - +
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Residues in contact with ASP 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Q PRO* 3.2 29.6 - - - +
96Q ASN* 2.7 32.1 + - - -
202Q ASN* 2.7 20.2 + - + +
204Q ASP* 1.3 79.7 - - - +
206Q VAL* 1.3 60.3 + - - +
207Q GLU 3.0 1.5 + - - -
208Q ARG* 3.1 31.8 + - - +
209Q ARG* 3.0 51.2 + - - +
222Q LEU* 4.8 2.3 - - - +
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Residues in contact with VAL 206 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Q ASN* 4.0 5.6 - - - +
111Q ILE* 3.9 24.7 - - + +
144Q LEU* 4.9 1.1 - - + -
172Q LEU* 3.5 37.6 - - + +
173Q LEU* 3.8 28.0 - - + -
201Q VAL* 4.6 0.2 - - + -
202Q ASN 3.2 12.7 + - - +
203Q TRP* 3.7 28.3 - - + +
204Q ASP 3.4 0.2 - - - -
205Q ASP* 1.3 74.8 - - - +
207Q GLU* 1.3 57.8 + - - +
209Q ARG* 4.0 2.9 - - - +
210Q LEU* 3.2 23.7 + - - +
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Residues in contact with GLU 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q GLY 3.4 10.8 - - - +
109Q GLY* 3.2 9.9 - - - -
110Q LYS* 2.9 26.2 + - - +
111Q ILE* 3.0 30.2 + - + +
203Q TRP 3.0 16.8 + - - +
204Q ASP* 3.5 9.9 - - - +
205Q ASP 3.0 0.4 - - - -
206Q VAL* 1.3 76.9 - - - +
208Q ARG* 1.3 68.2 + - + +
210Q LEU* 3.2 2.4 + - - +
211Q GLN* 2.9 48.3 + - + +
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Residues in contact with ARG 208 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M GLU* 4.6 26.9 - - - +
95Q PRO* 5.2 2.0 + - - +
202Q ASN* 4.8 4.6 + - - +
204Q ASP* 3.0 36.8 + - - +
205Q ASP* 3.1 40.0 + - - +
207Q GLU* 1.3 80.9 - - + +
209Q ARG* 1.3 61.2 + - - +
211Q GLN* 3.1 24.8 + - - +
212Q LYS* 3.3 12.5 + - - +
222Q LEU* 3.2 45.8 + - - +
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Residues in contact with ARG 209 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q ILE* 4.1 19.4 - - - +
95Q PRO* 3.6 13.5 - - - +
96Q ASN* 3.9 3.4 - - - +
171Q VAL 3.6 13.0 + - - -
172Q LEU* 3.5 34.7 - - + +
205Q ASP* 3.0 43.9 + - - +
206Q VAL 4.1 2.9 - - - +
208Q ARG* 1.3 77.2 - - - +
210Q LEU* 1.3 61.4 + - - +
211Q GLN 3.3 0.2 + - - -
212Q LYS* 3.4 2.1 + - - -
213Q ALA* 3.1 21.3 + - - +
219Q ALA* 3.2 41.6 + - + +
222Q LEU* 4.7 12.9 + - - +
317Q ACT 2.9 45.8 + - - +
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Residues in contact with LEU 210 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q LYS* 3.3 14.1 - - + +
111Q ILE* 3.2 44.4 - - + +
114Q LEU* 3.4 28.7 - - + -
146Q TYR* 4.3 11.4 - - + -
153Q LEU* 4.4 0.4 - - + -
172Q LEU* 3.5 28.6 - - + +
206Q VAL 3.2 16.7 + - - +
207Q GLU* 3.2 7.5 + - - +
209Q ARG* 1.3 78.0 - - - +
211Q GLN* 1.3 54.9 + - - +
213Q ALA* 4.4 1.1 - - + -
214Q LEU* 2.8 51.3 + - + +
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Residues in contact with GLN 211 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q LYS* 3.2 32.5 - - - +
207Q GLU* 2.9 40.8 + - + +
208Q ARG* 3.1 14.5 + - + +
210Q LEU* 1.3 77.7 - - - +
212Q LYS* 1.3 66.3 + - + +
214Q LEU* 3.4 16.4 + - - +
215Q ASN* 3.5 8.0 + - - +
217Q GLN* 4.8 0.3 + - - -
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Residues in contact with LYS 212 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M LYS* 5.6 1.4 - - - +
195M ASP* 2.9 42.0 + - - +
196M ASN* 6.0 0.2 + - - -
208Q ARG 3.3 12.8 + - - +
209Q ARG* 3.4 4.9 + - - +
211Q GLN* 1.3 74.7 - - + +
213Q ALA* 1.3 66.6 + - - +
215Q ASN* 2.7 15.2 + - - +
217Q GLN* 3.0 36.1 + - + +
218Q ILE 3.7 26.7 + - - +
219Q ALA* 4.2 10.3 - - + -
221Q LYS* 4.0 23.0 - - - +
222Q LEU* 4.4 26.5 - - + +
216T GLY 5.8 0.4 - - - -
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Residues in contact with ALA 213 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146Q TYR* 3.0 52.5 - - + -
170Q GLN* 4.3 12.8 - - + -
172Q LEU* 4.4 5.4 - - + -
209Q ARG 3.1 14.7 + - - +
210Q LEU* 3.8 3.4 - - - +
212Q LYS* 1.3 76.9 - - - +
214Q LEU* 1.3 57.3 + - - +
216Q GLY* 2.9 18.4 + - - -
217Q GLN 3.4 15.3 + - - +
219Q ALA* 4.6 0.8 - - + +
218T ILE* 6.0 0.2 - - - -
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Residues in contact with LEU 214 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q LYS* 3.6 48.0 - - + -
114Q LEU* 3.4 31.2 - - + -
146Q TYR* 4.2 19.2 + - + +
151Q GLU* 5.2 4.5 - - - +
210Q LEU* 2.8 36.7 + - + +
211Q GLN* 3.5 12.8 - - - +
212Q LYS 3.1 0.2 - - - -
213Q ALA* 1.3 73.2 - - - +
215Q ASN* 1.3 56.9 + - - +
216Q GLY 3.2 2.4 + - - -
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Residues in contact with ASN 215 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M ASP* 3.0 35.2 + - - +
191M GLY* 4.0 7.8 - - - -
211Q GLN 3.5 5.1 + - - +
212Q LYS 2.7 7.9 + - - +
214Q LEU* 1.3 73.9 - - - +
216Q GLY* 1.3 62.7 + - - +
217Q GLN* 3.0 31.9 + - - +
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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