Contacts of the helix formed by residues 160 - 174 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159I ILE* 1.3 74.3 - - - +
161I TYR* 1.3 50.0 + - - +
162I GLU* 3.1 11.2 + - - +
163I GLN* 2.6 45.5 + - + +
164I ALA* 2.7 30.9 + - - +
320I GLN* 3.6 23.4 + - + +
321I LEU 4.4 2.8 + - - -
323I HIS* 4.3 10.3 + - + +
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Residues in contact with TYR 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I ALA* 3.1 31.6 + - - -
147I SER* 5.1 0.4 - - - -
148I ILE* 3.7 21.3 - - + -
158I THR* 2.9 27.3 + - - -
159I ILE* 3.1 21.0 + - + -
160I ASP* 1.3 71.2 - - - +
162I GLU* 1.3 58.0 + - - +
164I ALA* 3.6 5.1 - - - +
165I ALA* 2.8 31.7 + - - +
191I ILE* 3.2 38.1 - - + -
195I LYS* 4.0 10.1 - - + -
196I LYS* 4.4 9.5 - - + +
274I PHE* 3.7 17.7 - + - -
292I GLN* 2.5 36.3 + - - -
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Residues in contact with GLU 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I ASP* 3.1 8.2 + - - +
161I TYR* 1.3 75.7 - - - +
163I GLN* 1.3 76.1 + - - +
165I ALA* 3.3 3.8 + - - +
166I PHE* 2.9 20.1 + - - +
194I ALA 5.1 0.4 - - - +
195I LYS* 3.4 45.8 - - + +
198I LYS* 3.9 8.6 - - + +
199I GLY* 3.4 17.5 - - - +
202I ARG* 2.7 47.6 + - - -
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Residues in contact with GLN 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I ASP* 2.6 36.0 + - + +
162I GLU* 1.3 72.1 + - - +
164I ALA* 1.3 57.8 + - - +
166I PHE* 2.9 20.1 + - - +
167I ASP* 2.7 70.4 + - - +
202I ARG* 3.2 20.9 + - - +
323I HIS* 3.8 9.9 - - + -
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Residues in contact with ALA 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I ILE* 4.2 3.4 - - + -
160I ASP 2.7 17.9 + - - +
161I TYR* 3.6 6.3 - - - +
163I GLN* 1.3 75.6 - - - +
165I ALA* 1.3 65.2 + - - +
166I PHE 3.0 0.3 + - - -
167I ASP* 3.1 2.0 + - - +
168I ALA* 3.0 22.4 + - - +
274I PHE* 3.7 24.7 - - + -
290I VAL* 3.7 17.4 - - + +
323I HIS* 3.5 24.5 + - + -
325I ILE* 5.2 0.4 - - - +
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Residues in contact with ALA 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I TYR 2.8 21.3 + - - +
162I GLU 3.5 5.2 - - - +
164I ALA* 1.3 73.1 - - - +
166I PHE* 1.3 57.2 + - - +
168I ALA* 3.5 3.1 - - - +
169I VAL* 2.9 27.9 + - - +
196I LYS* 3.4 35.7 - - + +
199I GLY* 4.0 3.8 - - - -
244I PHE* 3.6 30.2 - - + -
274I PHE* 4.2 0.8 - - - -
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Residues in contact with PHE 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I GLU 2.9 13.1 + - - +
163I GLN* 2.9 16.8 + - - +
165I ALA* 1.3 72.3 - - - +
167I ASP* 1.3 81.3 + - - +
168I ALA 3.1 1.7 + - - -
169I VAL* 3.2 4.3 - - - +
170I GLN* 2.9 55.9 + - + +
199I GLY 3.2 12.8 - - - +
202I ARG* 2.9 44.0 - - + +
203I ALA* 3.2 34.2 - - - +
206I GLU* 3.6 18.4 - - + -
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Residues in contact with ASP 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I GLN* 2.7 46.1 + - - +
164I ALA 3.8 2.9 - - - +
166I PHE* 1.3 78.8 - - - +
168I ALA* 1.3 56.5 + - - +
170I GLN* 3.4 5.7 + - - +
171I SER* 2.9 28.9 + - - -
323I HIS* 2.7 28.5 + - - +
325I ILE* 3.9 20.6 - - + +
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Residues in contact with ALA 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ALA 3.0 10.7 + - - +
165I ALA 3.5 9.4 - - - +
166I PHE 3.1 0.2 - - - -
167I ASP* 1.3 76.0 - - - +
169I VAL* 1.3 64.5 + - - +
171I SER* 2.9 23.2 - - - -
172I LEU* 3.3 4.1 + - - +
244I PHE* 3.6 28.3 - - + -
272I ILE* 3.5 19.2 - - + +
290I VAL* 3.9 14.8 - - + -
325I ILE* 4.4 7.1 - - - +
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Residues in contact with VAL 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I ALA 2.9 20.9 - - - +
166I PHE* 3.2 12.8 - - - +
168I ALA* 1.3 76.1 - - - +
170I GLN* 1.3 53.4 + - - +
172I LEU* 2.7 37.5 + - + +
173I ILE* 2.9 23.4 + - + +
180I ILE* 4.8 7.4 - - + -
199I GLY 4.0 4.7 - - - +
200I TYR* 4.0 22.0 - - + +
203I ALA* 3.3 23.1 - - + -
204I LEU* 4.0 20.6 - - + +
244I PHE* 5.1 6.2 - - + -
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Residues in contact with GLN 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I PHE* 2.9 51.0 + - + +
167I ASP* 3.5 8.3 - - - +
169I VAL* 1.3 76.3 - - - +
171I SER* 1.3 63.5 + - - +
173I ILE* 3.1 19.4 + - - +
174I ASP* 2.6 62.1 + - - +
203I ALA* 4.1 11.9 + - + +
206I GLU* 5.8 2.4 - - - +
207I SER* 5.2 5.8 - - - -
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Residues in contact with SER 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I ASP 2.9 14.4 + - - -
168I ALA* 2.9 17.0 - - - -
170I GLN* 1.3 76.1 - - - +
172I LEU* 1.3 60.2 + - - +
174I ASP* 3.9 8.1 + - - +
175I SER* 3.6 18.7 + - - -
272I ILE* 3.7 11.1 - - - +
325I ILE* 5.5 1.3 - - - -
327I PHE* 3.3 33.9 - - - -
331I THR* 5.0 2.6 + - - -
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Residues in contact with LEU 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ALA 3.7 7.2 - - - +
169I VAL* 2.7 24.2 + - - +
171I SER* 1.3 76.1 - - - +
173I ILE* 1.3 62.7 + - - +
175I SER* 3.0 10.7 + - - -
176I GLY 3.5 0.3 + - - -
177I HIS* 3.3 26.5 - - + +
180I ILE* 3.4 40.4 - - + -
242I ALA* 3.7 21.1 - - + -
243I ILE 4.6 4.5 - - - +
244I PHE* 4.5 11.7 - - + -
270I GLU* 4.4 23.1 - - + +
272I ILE* 3.8 24.7 - - + -
331I THR* 4.8 2.7 - - - +
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Residues in contact with ILE 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I VAL* 2.9 23.5 + - + +
170I GLN* 3.1 22.8 + - - +
172I LEU* 1.3 70.9 - - - +
174I ASP* 1.3 59.0 + - - +
175I SER 2.9 4.7 - - - -
176I GLY* 2.8 21.8 + - - -
177I HIS 3.8 12.8 + - - +
178I LYS* 6.5 0.4 - - + -
180I ILE* 4.2 8.7 - - + -
203I ALA 3.1 32.8 - - - +
204I LEU* 4.4 0.7 - - - -
207I SER* 3.3 24.2 - - - +
209I LEU* 3.8 23.3 - - + -
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Residues in contact with ASP 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I GLN* 2.6 47.9 + - - +
171I SER* 4.1 8.1 - - - +
173I ILE* 1.3 76.3 - - - +
175I SER* 1.3 56.9 + - - +
176I GLY 3.3 1.7 + - - -
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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