Contacts of the helix formed by residues 202 - 215 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95T PRO* 3.2 26.7 - - - +
96T ASN 2.5 15.1 + - - +
97T MSE 3.7 11.6 - - - +
98T ALA* 3.8 11.5 - - + +
102T LYS* 3.5 28.5 + - - +
103T GLY* 4.5 3.8 - - - -
200T VAL 3.5 0.6 + - - -
201T VAL* 1.3 73.0 - - - +
203T TRP* 1.3 52.5 + - - +
204T ASP* 3.2 25.1 + - - +
205T ASP* 2.7 38.8 + - - +
206T VAL* 3.2 5.9 + - - +
208T ARG* 4.0 6.4 + - - -
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Residues in contact with TRP 203 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T LYS 5.3 1.0 + - - -
104T GLY 3.5 21.5 + - - -
105T GLY 3.4 15.6 + - - -
106T LYS 3.7 13.2 - - - +
107T PRO* 3.4 34.5 - - + -
108T GLY 5.1 1.8 - - - +
111T ILE* 4.0 20.2 - - + +
115T ILE* 4.1 4.7 - - + -
122T PHE* 3.5 32.3 - + - -
125T PHE* 4.0 11.0 - + - -
144T LEU* 5.4 0.4 - - + -
173T LEU* 3.9 20.9 - - + -
198T TRP* 3.9 15.7 + + - -
201T VAL* 3.3 23.4 + - + +
202T ASN* 1.3 72.7 - - - +
204T ASP* 1.3 59.1 + - - +
205T ASP 3.1 0.2 - - - -
206T VAL* 3.7 24.4 - - + +
207T GLU* 2.9 30.1 + - - +
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Residues in contact with ASP 204 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102T LYS* 3.2 29.3 - - - +
202T ASN* 3.0 9.2 + - - +
203T TRP* 1.3 78.9 - - - +
205T ASP* 1.3 57.8 + - - +
207T GLU* 3.5 6.3 - - - +
208T ARG* 3.1 54.0 + - - +
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Residues in contact with ASP 205 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95T PRO* 3.1 41.1 - - - +
96T ASN* 2.6 30.8 + - - -
202T ASN* 2.7 21.3 + - + +
204T ASP* 1.3 78.3 - - - +
206T VAL* 1.3 62.3 + - - -
208T ARG* 3.3 22.5 + - - +
209T ARG* 2.8 47.3 + - - +
222T LEU 5.0 4.0 - - - +
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Residues in contact with VAL 206 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96T ASN* 4.2 4.5 - - - +
111T ILE* 3.8 28.5 - - + -
144T LEU* 4.6 1.3 - - + -
172T LEU* 3.7 36.0 - - + +
173T LEU* 3.8 28.0 - - + -
201T VAL* 4.4 0.9 - - + -
202T ASN 3.2 13.2 + - - +
203T TRP* 3.4 27.3 + - + +
205T ASP* 1.3 75.0 - - - +
207T GLU* 1.3 57.3 + - - +
209T ARG* 3.1 4.6 + - - +
210T LEU* 2.8 28.5 + - - +
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Residues in contact with GLU 207 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108T GLY 4.1 4.7 - - - +
109T GLY* 3.7 4.8 - - - -
110T LYS* 2.8 36.0 + - - +
111T ILE* 2.7 36.6 + - + +
203T TRP 2.9 18.0 + - - +
204T ASP* 3.5 8.5 - - - +
206T VAL* 1.3 77.7 - - - +
208T ARG* 1.3 59.8 + - + +
210T LEU* 3.2 5.4 + - - +
211T GLN* 2.9 33.7 + - + +
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Residues in contact with ARG 208 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T LYS* 5.2 5.3 - - - +
202T ASN* 4.0 9.3 + - - -
204T ASP* 3.1 45.7 + - - +
205T ASP* 3.3 31.1 + - - +
207T GLU* 1.3 77.5 - - + +
209T ARG* 1.3 62.9 + - - +
211T GLN* 3.3 6.5 + - - +
212T LYS* 3.1 28.2 + - - +
222T LEU* 4.0 40.5 + - - +
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Residues in contact with ARG 209 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92T ILE* 3.8 11.9 - - - +
95T PRO* 3.2 32.7 - - - +
96T ASN* 3.7 4.8 - - - +
171T VAL 3.8 11.2 - - - -
172T LEU* 3.4 37.4 - - + +
205T ASP* 2.8 38.2 + - - +
206T VAL 3.1 7.2 + - - +
208T ARG* 1.3 76.7 - - + +
210T LEU* 1.3 62.7 + - - +
212T LYS* 3.4 3.2 + - - +
213T ALA 3.0 16.6 + - - -
219T ALA* 2.9 45.9 + - + +
220T LEU* 3.9 6.5 - - - +
222T LEU* 5.2 11.2 + - - +
320T ACT 3.6 26.6 + - - +
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Residues in contact with LEU 210 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T LYS* 3.7 15.3 - - + +
111T ILE* 3.5 44.6 - - + +
114T LEU* 4.1 22.7 - - + -
146T TYR* 4.5 4.0 - - + -
153T LEU* 4.4 3.8 - - + -
172T LEU* 3.5 28.2 - - + +
206T VAL 2.8 16.5 + - - +
207T GLU* 3.2 5.8 + - - +
209T ARG* 1.3 74.9 - - - +
211T GLN* 1.3 55.1 + - - +
213T ALA* 3.0 8.0 + - + +
214T LEU* 2.7 52.4 + - + +
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Residues in contact with GLN 211 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M GLN* 3.6 24.8 + - - +
187M LYS* 6.6 0.2 - - - -
110T LYS* 3.8 31.4 - - - +
207T GLU* 2.9 20.7 + - + +
208T ARG* 3.7 7.6 - - - +
210T LEU* 1.3 78.1 - - - +
212T LYS* 1.3 63.4 + - + +
214T LEU* 3.3 13.1 + - - +
215T ASN* 2.9 58.1 + - - +
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Residues in contact with LYS 212 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216Q GLY 5.2 2.6 + - - -
208T ARG 3.1 17.2 + - - +
209T ARG* 3.6 8.5 - - - +
210T LEU 3.2 0.2 - - - -
211T GLN* 1.3 76.3 - - + +
213T ALA* 1.3 55.9 + - - +
215T ASN* 3.2 5.9 + - - +
217T GLN* 2.7 71.1 + - - +
218T ILE* 3.0 29.4 + - - +
219T ALA* 4.0 3.6 - - - -
220T LEU 3.0 28.0 + - - +
221T LYS* 4.1 8.2 + - - +
222T LEU* 3.8 16.6 - - - +
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Residues in contact with ALA 213 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218Q ILE* 4.2 1.2 - - - +
146T TYR* 3.5 52.3 + - + -
170T GLN* 4.4 9.0 - - + -
172T LEU* 4.2 4.3 - - + -
209T ARG 3.0 13.5 + - - +
210T LEU* 3.0 11.8 + - - +
212T LYS* 1.3 77.0 - - - +
214T LEU* 1.3 58.7 + - - +
216T GLY* 2.9 21.3 + - - -
217T GLN 3.6 11.6 + - - -
219T ALA* 4.8 1.0 - - - +
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Residues in contact with LEU 214 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M PRO* 3.8 38.0 - - + +
33M TYR* 5.1 0.9 - - - -
196M ASN* 3.2 15.6 + - - -
110T LYS* 3.7 39.7 - - + +
114T LEU* 4.5 11.4 - - + -
146T TYR* 4.4 20.2 + - + -
210T LEU* 2.7 46.0 + - + +
211T GLN* 3.5 21.1 - - - +
213T ALA* 1.3 70.4 - - - +
215T ASN* 1.3 57.1 + - - +
216T GLY* 2.9 9.8 + - - -
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Residues in contact with ASN 215 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M GLN* 2.9 51.5 + - - +
186M TYR* 3.6 26.8 - - + +
187M LYS* 5.8 0.2 - - - +
192M SER* 3.6 19.1 - - - +
196M ASN* 3.7 9.9 + - - +
211T GLN* 2.9 30.9 + - - +
212T LYS* 3.2 2.1 + - - +
214T LEU* 1.3 73.6 - - - +
216T GLY* 1.3 62.3 + - - +
217T GLN* 3.1 32.7 + - + +
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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