Contacts of the helix formed by residues 202 - 215 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95U PRO 3.0 17.1 - - - +
96U ASN 2.7 19.1 + - - +
97U MSE 3.5 19.5 - - - +
98U ALA* 3.7 8.0 - - + +
102U LYS* 3.5 27.7 + - - +
103U GLY* 4.3 1.8 - - - -
200U VAL 3.2 1.2 + - - -
201U VAL* 1.3 70.0 - - - +
203U TRP* 1.3 53.3 + - - +
204U ASP* 3.2 32.4 + - - +
205U ASP* 2.7 41.3 + - - +
206U VAL* 3.3 5.4 + - - +
208U ARG* 5.4 1.9 + - - -
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Residues in contact with TRP 203 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U LYS 4.9 2.8 + - - -
104U GLY 3.7 14.4 - - - +
105U GLY 2.9 28.5 + - - -
106U LYS 3.9 7.9 - - - +
107U PRO* 3.4 29.5 - - + +
108U GLY 5.2 2.2 - - - +
111U ILE* 3.9 25.4 - - + +
115U ILE* 4.0 7.6 - - + -
122U PHE* 3.6 23.0 - + - -
125U PHE* 3.8 24.9 - + - -
144U LEU* 5.1 0.7 - - + -
173U LEU* 3.9 11.2 - - + -
198U TRP* 3.8 15.0 + + - -
201U VAL* 3.2 22.9 + - + +
202U ASN* 1.3 73.5 - - - +
204U ASP* 1.3 59.1 + - - +
206U VAL* 3.8 29.3 - - + +
207U GLU* 3.0 27.2 + - - +
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Residues in contact with ASP 204 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102U LYS* 3.7 27.6 - - - +
202U ASN* 2.8 17.8 + - - +
203U TRP* 1.3 79.4 + - - +
205U ASP* 1.3 62.0 + - - +
207U GLU* 3.6 6.6 - - - +
208U ARG* 3.0 45.8 + - - +
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Residues in contact with ASP 205 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U PRO* 3.1 32.7 - - - +
96U ASN* 2.8 28.6 + - - -
202U ASN* 2.7 18.0 + - - +
204U ASP* 1.3 78.0 - - - +
206U VAL* 1.3 65.2 + - - +
207U GLU 3.2 0.2 - - - -
208U ARG* 3.4 20.2 + - - +
209U ARG* 2.8 53.3 + - - +
222U LEU 4.5 7.3 - - - +
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Residues in contact with VAL 206 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U ASN* 4.7 4.0 - - - +
111U ILE* 3.7 29.8 - - + -
144U LEU* 4.5 3.8 - - + -
172U LEU* 3.8 32.2 - - + +
173U LEU* 3.8 28.0 - - + -
201U VAL* 4.4 1.6 - - + -
202U ASN 3.3 10.5 + - - +
203U TRP* 3.5 28.5 + - + +
204U ASP 3.4 0.2 - - - -
205U ASP* 1.3 75.8 - - - +
207U GLU* 1.3 63.8 + - - +
209U ARG* 3.1 4.3 + - - +
210U LEU* 2.9 21.2 + - - +
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Residues in contact with GLU 207 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108U GLY 5.1 0.7 - - - -
109U GLY* 3.5 11.0 - - - -
110U LYS* 2.8 22.7 + - - +
111U ILE* 2.9 34.2 + - + +
203U TRP 3.0 18.5 + - - +
204U ASP* 3.6 9.9 - - - +
205U ASP 3.2 0.2 - - - -
206U VAL* 1.3 76.0 - - - +
208U ARG* 1.3 64.9 + - + +
210U LEU* 3.0 4.7 + - - +
211U GLN* 2.9 54.7 + - + +
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Residues in contact with ARG 208 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U LYS* 4.9 13.1 - - - +
202U ASN* 5.4 1.4 + - - -
204U ASP* 3.0 40.9 + - - +
205U ASP* 3.8 17.9 + - - +
206U VAL 3.4 0.4 - - - -
207U GLU* 1.3 80.8 - - + +
209U ARG* 1.3 58.8 + - - +
211U GLN* 3.8 7.3 + - - +
212U LYS* 3.1 30.8 + - - +
222U LEU* 3.9 32.1 + - + +
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Residues in contact with ARG 209 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92U ILE* 3.9 23.8 + - - +
95U PRO* 3.2 25.9 - - - +
96U ASN* 3.2 6.8 - - - +
171U VAL 3.7 12.3 - - - -
172U LEU* 3.5 30.5 - - + -
205U ASP* 2.8 40.6 + - - +
206U VAL 3.1 8.5 + - - +
208U ARG* 1.3 75.9 - - - +
210U LEU* 1.3 59.7 + - - +
212U LYS 3.5 1.2 + - - -
213U ALA* 3.0 23.4 + - - +
219U ALA* 3.1 48.3 + - + +
220U LEU* 3.8 3.6 + - - +
222U LEU* 4.5 11.2 + - - +
321U ACT 3.3 22.0 + - - -
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Residues in contact with LEU 210 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U LYS* 3.6 11.0 - - + +
111U ILE* 3.4 46.9 - - + +
114U LEU* 3.8 16.8 - - + -
146U TYR* 3.7 24.9 - - + -
153U LEU* 4.1 0.2 - - + -
172U LEU* 3.7 28.4 - - + +
206U VAL 2.9 12.7 + - - +
207U GLU* 3.7 8.3 - - - +
209U ARG* 1.3 73.9 - - - +
211U GLN* 1.3 57.8 + - - +
213U ALA* 3.0 2.9 + - + -
214U LEU* 2.7 53.1 + - + +
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Residues in contact with GLN 211 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U LYS* 2.9 45.1 - - - +
207U GLU* 2.9 42.5 + - + +
208U ARG* 3.9 8.5 - - + +
210U LEU* 1.3 78.0 - - - +
212U LYS* 1.3 64.5 + - + +
214U LEU* 3.4 16.0 + - - +
215U ASN* 3.5 12.0 + - - +
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Residues in contact with LYS 212 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208U ARG* 3.1 14.8 - - + +
209U ARG 3.5 5.6 + - - +
210U LEU 3.1 0.2 - - - -
211U GLN* 1.3 76.2 - - + +
213U ALA* 1.3 65.6 + - - +
215U ASN* 3.1 6.8 + - - -
217U GLN* 2.9 57.6 + - + +
218U ILE 3.5 22.4 + - - +
219U ALA* 4.3 3.8 - - - -
221U LYS* 2.6 32.9 + - - +
222U LEU* 3.3 24.2 + - + +
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Residues in contact with ALA 213 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146U TYR* 3.7 46.0 - - + -
170U GLN* 4.5 8.5 - - + -
172U LEU* 4.2 5.6 - - + -
209U ARG 3.0 13.7 + - - +
210U LEU* 3.0 11.4 + - + +
212U LYS* 1.3 77.3 - - - +
214U LEU* 1.3 62.9 + - - +
216U GLY* 2.9 16.5 + - - -
217U GLN 3.6 13.6 + - - +
219U ALA* 4.8 0.2 - - - +
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Residues in contact with LEU 214 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U LYS* 3.9 41.1 - - + -
114U LEU* 3.6 31.4 - - + -
146U TYR* 3.8 24.2 + - + +
151U GLU* 5.0 6.8 - - - +
210U LEU* 2.7 32.5 + - + +
211U GLN* 3.5 14.1 - - - +
213U ALA* 1.3 71.9 - - - +
215U ASN* 1.3 56.9 + - - +
216U GLY 3.3 2.5 + - - -
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Residues in contact with ASN 215 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211U GLN 3.5 7.3 + - - +
212U LYS 3.1 3.8 + - - +
213U ALA 3.0 1.4 + - - -
214U LEU* 1.3 77.2 - - + +
216U GLY* 1.3 62.0 + - - +
217U GLN* 2.9 34.2 + - - +
217X GLN* 5.8 4.8 + - - +
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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
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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