Contacts of the helix formed by residues 160 - 175 (chain P) in PDB entry 1SXG
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 ASP 160 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159P ILE* 1.3 72.3 - - - +
161P TYR* 1.3 62.5 + - - +
162P GLU* 3.3 13.9 + - - +
163P GLN* 3.2 38.8 + - + +
164P ALA* 3.0 21.8 + - - +
195P LYS* 5.5 4.1 + - - +
320P GLN* 3.2 38.1 + - - +
321P LEU 4.1 2.4 + - - +
323P HIS* 4.4 8.3 + - - +
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Residues in contact with TYR 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P PHE* 5.2 0.2 - - - -
75P TYR* 5.2 0.5 + - - -
146P ALA* 3.2 30.9 + - - +
148P ILE* 4.0 23.3 - - + -
158P THR* 3.1 21.7 + - - -
159P ILE* 3.1 19.4 + - + -
160P ASP* 1.3 72.3 + - - +
162P GLU* 1.3 60.8 + - - +
164P ALA* 3.7 4.9 - - - +
165P ALA* 3.2 22.2 + - - +
191P ILE* 3.5 35.8 - - + +
195P LYS* 3.6 25.9 - - + +
196P LYS* 4.3 11.1 - - + +
274P PHE* 3.9 12.7 - + - -
292P GLN* 3.1 42.6 + - - -
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Residues in contact with GLU 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P ASP* 3.2 11.3 + - - +
161P TYR* 1.3 78.4 - - - +
163P GLN* 1.3 68.5 + - + +
165P ALA 3.3 0.9 + - - -
166P PHE* 2.9 24.4 + - - +
194P ALA 5.2 0.4 - - - +
195P LYS* 3.4 36.4 - - + +
198P LYS* 4.1 10.0 - - + +
199P GLY* 3.4 21.4 + - - -
202P ARG* 2.5 49.8 + - - +
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Residues in contact with GLN 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P ASP* 3.2 30.6 + - + +
162P GLU* 1.3 85.0 - - + +
164P ALA* 1.3 59.2 + - - +
166P PHE* 3.7 11.1 - - - -
167P ASP* 2.9 51.7 + - - +
202P ARG* 3.0 25.5 + - - +
323P HIS* 3.8 9.2 - - + -
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Residues in contact with ALA 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159P ILE* 3.8 10.1 - - + -
160P ASP 3.0 16.8 + - - +
161P TYR 3.7 2.7 - - - +
162P GLU 3.1 0.2 - - - -
163P GLN* 1.3 75.2 - - - +
165P ALA* 1.3 63.7 + - - +
167P ASP* 4.2 1.2 - - - +
168P ALA* 3.4 21.8 + - - +
274P PHE* 3.4 30.5 - - + -
290P VAL* 3.9 11.6 - - + +
323P HIS* 3.6 21.4 + - + -
325P ILE* 4.8 0.3 - - - +
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Residues in contact with ALA 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P TYR 3.2 15.4 + - - +
162P GLU 3.6 4.7 - - - +
164P ALA* 1.3 78.6 - - - +
166P PHE* 1.3 65.4 + - - +
168P ALA* 3.3 2.9 + - - +
169P VAL* 3.1 29.5 + - - +
196P LYS* 3.4 34.1 - - + +
199P GLY* 4.0 4.5 - - - -
200P TYR 4.0 1.6 - - - +
244P PHE* 3.9 21.8 - - + -
274P PHE* 4.2 0.6 - - - -
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Residues in contact with PHE 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P GLU* 2.9 23.8 + - - +
163P GLN* 3.8 12.6 - - - +
164P ALA 3.4 0.2 - - - -
165P ALA* 1.3 77.7 - - - +
167P ASP* 1.3 65.5 + - - +
169P VAL* 3.2 2.1 + - - +
170P GLN* 2.6 67.6 + - + +
199P GLY 3.6 13.2 - - - +
202P ARG* 3.1 26.9 - - - -
203P ALA* 3.3 31.7 - - - +
206P GLU* 3.3 37.9 - - + -
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Residues in contact with ASP 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P GLN* 2.9 28.9 + - - +
164P ALA 4.2 0.7 - - - +
165P ALA 3.4 0.2 - - - -
166P PHE* 1.3 81.2 - - - +
168P ALA* 1.3 54.5 + - - +
170P GLN* 3.5 6.9 - - - +
171P SER* 2.8 35.5 + - - -
323P HIS* 2.5 34.9 + - - +
325P ILE* 4.1 15.2 - - + +
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Residues in contact with ALA 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P ALA 3.4 12.0 + - - +
165P ALA 3.3 6.7 + - - +
166P PHE 3.2 0.4 - - - -
167P ASP* 1.3 78.3 - - - +
169P VAL* 1.3 61.6 + - - +
171P SER* 3.0 23.0 + - - -
172P LEU* 3.4 12.6 + - - +
244P PHE* 3.3 35.4 - - + -
272P ILE* 4.3 9.1 - - + +
290P VAL* 3.9 11.0 - - + -
325P ILE* 4.4 10.0 - - - +
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Residues in contact with VAL 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P ALA 3.1 15.2 + - - +
168P ALA* 1.3 74.6 - - - +
170P GLN* 1.3 60.9 + - - +
172P LEU* 3.2 12.9 + - - +
173P ILE* 3.0 35.2 + - + +
180P ILE* 4.4 12.3 - - + -
200P TYR* 3.7 46.2 - - + +
203P ALA* 3.5 24.5 - - + -
204P LEU* 4.5 7.2 - - + -
244P PHE* 3.9 17.7 - - + -
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Residues in contact with GLN 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P PHE* 2.6 50.1 + - + +
167P ASP* 3.5 11.4 - - - +
169P VAL* 1.3 71.3 - - - +
171P SER* 1.3 59.8 + - - +
173P ILE* 3.2 17.8 + - - +
174P ASP* 2.4 71.6 + - - +
203P ALA* 4.4 2.3 - - + +
206P GLU* 5.5 1.4 - - - +
207P SER* 3.8 16.6 + - - -
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Residues in contact with SER 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P ASP 2.8 17.9 + - - -
168P ALA* 3.0 12.6 + - - -
170P GLN* 1.3 72.5 - - - +
172P LEU* 1.3 64.3 + - - +
174P ASP* 3.4 13.4 + - - +
175P SER* 3.1 25.5 + - - -
272P ILE* 5.2 3.1 - - - +
325P ILE* 6.2 0.7 - - - -
327P PHE* 3.9 33.5 - - - -
331P THR* 5.9 0.3 - - - +
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Residues in contact with LEU 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ALA 3.7 11.2 - - - +
169P VAL* 3.2 12.8 + - - +
171P SER* 1.3 83.3 + - - +
173P ILE* 1.3 61.0 - - - +
175P SER* 3.2 9.5 + - - -
177P HIS* 3.0 47.9 + - + -
180P ILE* 4.1 24.5 - - + -
242P ALA* 3.9 20.0 - - + -
243P ILE 4.7 5.8 - - - +
244P PHE* 4.7 6.1 - - + -
270P GLU* 3.9 15.5 - - + +
272P ILE* 3.2 37.0 - - + -
331P THR* 4.5 2.5 - - + -
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Residues in contact with ILE 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P VAL* 3.0 21.5 + - + +
170P GLN* 3.2 21.7 + - - +
172P LEU* 1.3 74.6 - - - +
174P ASP* 1.3 60.3 + - - +
175P SER 3.0 1.6 - - - -
176P GLY* 2.8 20.3 + - - -
177P HIS 3.8 8.9 + - - +
180P ILE* 4.3 9.0 - - + -
203P ALA* 3.5 23.8 - - + +
204P LEU* 4.3 1.3 - - + +
207P SER* 3.4 36.6 - - - +
209P LEU* 4.0 21.3 - - + -
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Residues in contact with ASP 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170P GLN* 2.4 46.7 + - - +
171P SER* 3.7 13.3 - - - +
172P LEU 3.3 0.2 - - - -
173P ILE* 1.3 77.1 - - - +
175P SER* 1.3 59.8 + - - +
176P GLY* 3.0 1.6 + - - -
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Residues in contact with SER 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171P SER 3.1 14.6 + - - -
172P LEU* 3.2 15.9 - - - -
173P ILE 3.0 0.2 - - - -
174P ASP* 1.3 76.8 - - - +
176P GLY* 1.3 57.1 + - - +
177P HIS* 4.1 7.7 + - - -
270P GLU* 3.7 22.7 + - - -
332P LYS* 4.4 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
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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