Contacts of the helix formed by residues 160 - 175 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D ILE* 1.3 74.2 - - - +
161D TYR* 1.3 56.1 + - - +
162D GLU* 3.3 18.9 + - - +
163D GLN* 3.2 33.9 + - + +
164D ALA* 2.8 27.7 + - - +
195D LYS* 5.4 4.2 + - - +
320D GLN* 3.9 25.5 + - - +
321D LEU 4.6 1.4 + - - -
323D HIS* 4.4 9.4 + - + +
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Residues in contact with TYR 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ALA* 3.2 31.3 + - - -
148D ILE* 3.8 31.4 - - + -
158D THR* 3.6 17.5 - - + +
159D ILE* 2.8 43.3 + - + -
160D ASP* 1.3 72.3 + - - +
162D GLU* 1.3 61.8 + - - +
164D ALA* 4.0 5.5 - - - +
165D ALA* 3.0 26.2 + - - +
191D ILE* 4.1 22.9 - - + -
195D LYS* 3.8 24.2 - - + +
196D LYS* 4.4 5.8 - - + +
274D PHE* 3.8 16.4 - + - -
292D GLN* 3.1 35.2 + - - -
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ASP* 3.2 11.0 + - - +
161D TYR* 1.3 78.1 - - - +
163D GLN* 1.3 63.1 + - - +
165D ALA* 3.7 2.6 - - - +
166D PHE* 3.0 22.0 + - - +
194D ALA 5.1 0.7 - - - +
195D LYS* 3.1 39.1 + - + +
198D LYS* 4.5 10.0 - - + +
199D GLY* 3.0 27.4 + - - +
202D ARG* 3.0 41.0 + - - +
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Residues in contact with GLN 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ASP* 3.2 31.3 + - + +
162D GLU* 1.3 81.5 + - - +
164D ALA* 1.3 60.4 + - - +
165D ALA 3.1 0.2 - - - -
166D PHE* 3.2 7.9 + - - -
167D ASP* 2.5 68.0 + - - +
202D ARG* 2.8 31.5 - - - +
323D HIS* 3.9 11.8 - - + -
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 4.0 9.4 - - + -
160D ASP 2.8 17.7 + - - +
161D TYR 4.0 1.3 - - - +
163D GLN* 1.3 76.7 - - - +
165D ALA* 1.3 63.9 + - - +
167D ASP* 3.4 2.6 + - - +
168D ALA* 3.1 21.8 + - - +
274D PHE* 3.8 13.9 - - + -
290D VAL* 3.7 20.2 - - + +
323D HIS* 3.3 32.7 + - + -
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Residues in contact with ALA 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D TYR 3.0 19.4 + - - +
162D GLU 3.7 4.0 - - - +
164D ALA* 1.3 77.1 - - - +
166D PHE* 1.3 63.7 + - - +
168D ALA* 3.1 12.1 + - - +
169D VAL* 3.1 17.6 + - - +
196D LYS* 3.6 36.3 - - + +
199D GLY* 4.6 1.3 - - - -
200D TYR 4.6 0.7 - - - +
244D PHE* 3.9 25.0 - - + -
274D PHE* 4.1 1.7 - - + -
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Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLU* 3.0 19.3 + - - +
163D GLN* 3.4 13.5 - - - +
165D ALA* 1.3 76.5 - - - +
167D ASP* 1.3 66.4 + - - +
168D ALA 3.1 0.3 + - - -
169D VAL* 3.1 5.8 - - - +
170D GLN* 2.8 67.6 + - + +
199D GLY 3.6 14.3 + - - +
202D ARG* 3.3 41.7 - - + +
203D ALA* 3.5 29.8 - - - +
206D GLU* 3.6 19.3 - - + -
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Residues in contact with ASP 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D GLN* 2.5 42.9 + - - +
164D ALA 3.6 4.3 - - - +
166D PHE* 1.3 76.8 - - - +
168D ALA* 1.3 57.3 + - - +
170D GLN* 3.2 8.6 + - - +
171D SER* 2.9 30.0 + - - -
323D HIS* 3.0 24.6 + - + +
325D ILE* 3.8 18.4 - - + +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA 3.1 10.1 + - - +
165D ALA 3.2 5.2 - - - +
167D ASP* 1.3 79.5 - - - +
169D VAL* 1.3 61.4 + - - +
170D GLN 3.1 0.3 + - - -
171D SER* 2.7 25.9 + - - -
172D LEU* 3.4 6.6 + - - +
244D PHE* 3.2 36.3 - - + -
272D ILE* 3.9 10.5 - - + +
290D VAL* 3.6 13.7 - - + -
325D ILE* 4.0 10.1 - - - +
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ALA 3.1 9.6 + - - +
166D PHE* 3.1 16.4 - - - +
168D ALA* 1.3 77.6 - - - +
170D GLN* 1.3 56.2 + - - +
172D LEU* 3.3 12.9 - - - +
173D ILE* 3.0 25.3 + - + +
180D ILE* 3.8 30.7 - - + -
200D TYR* 3.8 32.1 - - + -
203D ALA* 3.2 22.2 - - + -
204D LEU* 4.0 12.3 - - + -
244D PHE* 4.6 8.6 - - + -
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Residues in contact with GLN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 2.8 46.3 + - + +
167D ASP* 3.3 11.2 - - - +
169D VAL* 1.3 75.4 - - - +
171D SER* 1.3 67.5 + - - +
172D LEU 3.0 1.1 - - - -
173D ILE* 2.8 30.2 + - - +
174D ASP* 2.8 39.1 + - - +
203D ALA* 4.1 10.7 + - - +
207D SER* 5.0 4.7 - - - -
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ASP 2.9 12.1 + - - -
168D ALA* 2.7 14.0 + - - -
170D GLN* 1.3 76.5 - - - +
172D LEU* 1.3 77.3 + - - +
174D ASP* 3.2 19.6 + - - +
175D SER* 3.2 15.4 + - - -
272D ILE* 4.4 7.6 - - - +
325D ILE* 4.6 4.2 - - - +
327D PHE* 4.1 33.2 - - - -
331D THR* 5.6 2.0 + - - +
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ALA 3.4 5.4 + - - +
169D VAL* 3.3 17.0 + - - +
170D GLN 3.0 0.2 - - - -
171D SER* 1.3 80.5 + - - +
173D ILE* 1.3 66.6 + - - +
175D SER* 3.1 8.6 + - - +
177D HIS* 3.1 37.9 + - + +
180D ILE* 3.6 30.5 - - + -
242D ALA* 3.8 26.0 - - + -
243D ILE 4.4 13.2 - - - +
244D PHE* 4.5 4.3 - - + +
270D GLU* 3.9 11.9 - - + +
272D ILE* 3.3 36.1 - - + -
331D THR* 4.8 3.1 - - + +
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Residues in contact with ILE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 3.0 16.7 + - + +
170D GLN* 2.8 33.4 + - - +
172D LEU* 1.3 72.0 - - - +
174D ASP* 1.3 59.0 + - - +
176D GLY* 2.8 23.2 + - - -
177D HIS 3.4 11.7 + - - +
180D ILE* 3.5 15.5 - - + -
203D ALA* 4.3 10.1 - - + +
204D LEU* 3.9 9.6 - - + -
207D SER* 3.1 24.9 - - - +
209D LEU* 3.3 30.3 - - + -
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Residues in contact with ASP 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLN* 2.8 36.6 + - - +
171D SER* 3.3 12.8 - - - +
173D ILE* 1.3 71.8 - - - +
175D SER* 1.3 58.2 + - - +
176D GLY* 2.8 11.6 + - - -
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Residues in contact with SER 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D SER 3.2 12.3 + - - -
172D LEU* 3.1 10.8 + - - +
174D ASP* 1.3 74.2 - - - +
176D GLY* 1.3 60.5 + - - +
177D HIS* 3.5 19.6 + - - -
270D GLU* 4.5 8.4 + - - +
331D THR* 5.2 7.6 - - - +
332D LYS* 5.0 6.8 + - - -
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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