Contacts of the helix formed by residues 195 - 206 (chain F) 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 LYS 195 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148F ILE* 4.3 30.3 - - + +
150F SER* 5.4 6.7 - - - -
160F ASP* 5.2 2.2 - - - +
161F TYR* 3.9 22.0 - - + +
162F GLU* 3.5 34.6 - - + +
190F PRO 4.4 4.7 - - - +
191F ILE* 3.0 18.7 + - - +
193F HIS 3.6 1.2 - - - -
194F ALA* 1.3 96.0 + - - +
196F LYS* 1.3 58.0 + - - +
197F VAL 3.4 0.7 - - - -
198F LYS* 3.2 3.7 + - - +
199F GLY* 2.7 33.1 + - - -
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Residues in contact with LYS 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F TYR* 4.4 7.2 - - + +
165F ALA* 3.4 19.7 - - + +
182F PHE* 3.5 19.0 - - + -
191F ILE* 3.2 37.7 + - + +
192F ASN* 3.5 25.7 + - - +
195F LYS* 1.3 80.2 - - + +
197F VAL* 1.3 58.8 + - - +
200F TYR* 2.8 30.7 + - - +
221F TYR* 6.1 2.6 - - - -
244F PHE* 4.9 0.7 - - + -
246F GLY* 2.9 36.8 + - - -
274F PHE* 3.6 33.4 - - + -
275F ASP* 5.0 2.0 + - - -
292F GLN* 5.7 0.2 - - - +
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F PHE* 3.5 17.1 - - + -
187F LEU* 5.1 7.9 - - + -
192F ASN 2.9 20.8 + - - +
193F HIS* 3.1 33.4 - - + +
196F LYS* 1.3 71.7 - - - +
198F LYS* 1.3 74.7 + - + +
200F TYR* 3.2 3.8 - - - +
201F LYS* 2.8 62.3 + - + +
216F ILE* 4.6 21.8 - - + -
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Residues in contact with LYS 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F GLU* 4.1 11.2 - - + +
193F HIS 3.5 6.0 + - - -
194F ALA* 2.9 44.2 - - - +
195F LYS 3.2 4.7 + - - +
196F LYS 3.2 0.4 - - - -
197F VAL* 1.3 87.5 - - + +
199F GLY* 1.3 67.9 + - - +
200F TYR 3.0 1.9 + - - -
201F LYS* 3.0 10.0 + - + +
202F ARG* 2.7 25.7 + - - +
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Residues in contact with GLY 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F GLU* 3.2 38.9 + - - -
165F ALA* 4.0 1.1 - - - -
166F PHE* 3.5 18.6 - - - -
195F LYS 2.7 17.9 + - - -
196F LYS 3.8 1.1 - - - -
198F LYS* 1.3 72.5 - - - +
200F TYR* 1.3 61.8 + - - +
202F ARG* 3.3 2.5 + - - +
203F ALA 3.1 18.5 + - - -
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Residues in contact with TYR 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F ALA* 4.0 1.4 - - - +
169F VAL* 3.8 23.5 - - + +
180F ILE* 2.6 28.2 + - + -
181F ALA 3.4 20.9 - - - -
182F PHE* 3.4 22.7 - + + -
196F LYS 2.8 14.2 + - - +
197F VAL* 3.2 14.4 - - + +
199F GLY* 1.3 76.0 - - - +
201F LYS* 1.3 83.2 + - + +
202F ARG 3.1 0.7 + - - -
203F ALA* 3.2 12.8 + - - +
204F LEU* 3.3 35.5 + - + +
211F VAL* 4.6 1.8 - - + -
212F ARG 5.2 1.9 + - - -
215F TYR* 3.6 10.6 + - - +
216F ILE* 3.2 40.4 - - + +
244F PHE* 4.7 9.0 - + + -
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Residues in contact with LYS 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F VAL* 2.8 49.1 + - + +
198F LYS* 3.8 7.4 - - + +
200F TYR* 1.3 81.1 - - + +
202F ARG* 1.3 56.9 + - - +
204F LEU* 3.3 1.7 - - - +
205F THR* 2.9 35.9 + - + +
211F VAL* 3.6 42.8 - - + -
213F ASP* 5.6 4.8 + - - -
216F ILE* 5.2 5.2 - - - -
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Residues in contact with ARG 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F GLU* 2.7 34.1 + - - +
163F GLN* 2.9 38.0 + - - +
166F PHE* 3.2 26.4 - - + +
198F LYS 2.7 17.3 + - - +
199F GLY 3.5 3.8 - - - +
201F LYS* 1.3 74.4 - - - +
203F ALA* 1.3 61.9 + - - +
204F LEU 3.0 1.6 - - - -
205F THR* 4.2 4.7 - - - -
206F GLU* 2.7 56.3 + - + +
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Residues in contact with ALA 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F PHE* 3.3 33.5 - - + +
169F VAL* 3.3 39.9 - - + -
170F GLN* 3.9 12.3 + - - +
173F ILE* 4.5 4.2 - - - +
199F GLY 3.1 6.4 + - - +
200F TYR 3.2 0.4 + - - +
202F ARG* 1.3 77.2 - - - +
204F LEU* 1.3 59.6 + - - +
206F GLU* 4.1 1.2 - - - +
207F SER* 3.1 26.9 + - - -
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Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F VAL* 3.9 21.8 - - + -
173F ILE* 4.1 8.1 - - + -
178F LYS 5.3 2.0 - - - +
180F ILE* 4.0 21.1 - - + +
200F TYR* 3.3 45.6 + - + +
201F LYS 3.3 7.6 - - - +
202F ARG 3.0 0.6 - - - -
203F ALA* 1.3 75.5 - - - +
205F THR* 1.3 57.4 + - - +
206F GLU 3.1 0.9 - - - -
207F SER* 2.7 25.9 + - - -
208F GLY 3.2 7.1 + - - -
209F LEU* 3.3 23.5 + - + +
210F PRO 3.8 22.7 - - - +
211F VAL* 4.0 13.5 - - + -
212F ARG 5.5 0.2 - - - +
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Residues in contact with THR 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F LYS* 2.9 14.6 + - + +
202F ARG* 4.1 3.6 + - - -
204F LEU* 1.3 78.4 - - - +
206F GLU* 1.3 59.2 + - - +
207F SER 3.1 4.2 + - - -
208F GLY* 3.2 11.4 + - - -
209F LEU 3.4 13.9 - - - +
210F PRO* 5.0 0.9 - - + -
211F VAL* 3.7 28.0 - - + +
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Residues in contact with GLU 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F PHE* 3.5 24.0 - - + -
170F GLN* 5.1 4.1 + - - +
202F ARG* 2.7 51.3 + - + +
203F ALA 4.3 1.8 - - - +
205F THR* 1.3 79.3 + - - +
207F SER* 1.3 58.4 + - - +
208F GLY 3.6 0.2 - - - -
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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