Contacts of the helix formed by residues 195 - 207 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ILE* 3.5 33.9 - - + +
150A SER* 4.2 10.4 + - - +
160A ASP* 5.4 3.1 - - - +
161A TYR* 3.9 23.3 - - + +
162A GLU* 3.3 30.6 - - + +
190A PRO 3.5 11.2 + - - +
191A ILE* 3.5 15.3 - - - +
192A ASN 3.5 1.0 + - - -
194A ALA* 1.3 93.5 + - - +
196A LYS* 1.3 62.0 + - - +
197A VAL 3.4 0.7 - - - -
198A LYS* 3.5 2.0 + - - -
199A GLY 2.9 23.9 + - - -
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Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 4.1 21.0 - - + +
165A ALA* 3.5 18.6 - - + +
182A PHE* 3.9 17.7 - - + -
191A ILE* 3.0 35.6 + - + +
192A ASN* 3.8 18.9 - - - +
195A LYS* 1.3 74.8 - - - +
197A VAL* 1.3 66.2 + - - +
199A GLY 3.5 0.2 + - - -
200A TYR* 3.1 24.6 + - - +
221A TYR* 6.0 1.2 - - - -
244A PHE* 5.0 1.6 - - + -
246A GLY* 3.1 32.7 + - - +
247A THR* 4.6 6.3 - - - +
274A PHE* 3.7 38.6 - - + -
275A ASP* 4.9 2.0 + - - -
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PHE* 3.8 23.3 - - + -
187A LEU* 3.8 22.9 - - + -
192A ASN* 2.9 34.2 + - + +
193A HIS* 3.8 10.1 - - - +
196A LYS* 1.3 75.0 - - - +
198A LYS* 1.3 59.2 + - + +
200A TYR* 3.4 3.9 + - + +
201A LYS* 3.0 50.5 + - + +
216A ILE* 4.9 16.2 - - + -
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 3.3 12.3 - - - +
193A HIS 3.7 17.3 - - - +
194A ALA* 3.5 28.0 - - - +
195A LYS 3.5 4.7 + - - +
196A LYS 3.2 0.8 - - - -
197A VAL* 1.3 76.7 - - + +
199A GLY* 1.3 59.3 + - - +
200A TYR 3.1 1.6 - - - -
201A LYS* 4.1 10.6 - - + +
202A ARG* 2.9 29.8 + - - +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 3.0 37.8 + - - -
165A ALA* 4.0 0.9 - - - -
166A PHE* 3.0 26.6 - - - +
195A LYS 2.9 16.4 + - - -
196A LYS 4.0 0.2 - - - -
197A VAL 3.5 0.2 - - - -
198A LYS* 1.3 71.4 - - - +
200A TYR* 1.3 63.8 + - - +
202A ARG* 4.2 0.4 - - - -
203A ALA* 3.2 12.8 + - - +
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Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ALA* 4.0 0.8 - - - +
169A VAL* 3.5 32.3 - - + +
180A ILE* 2.7 32.2 + - + -
181A ALA 3.9 6.3 - - - -
182A PHE* 3.6 37.5 - + + -
196A LYS 3.1 19.2 + - - +
197A VAL* 3.4 6.3 - - + +
199A GLY* 1.3 75.5 - - - +
201A LYS* 1.3 93.5 + - + +
203A ALA* 3.1 13.2 + - - +
204A LEU* 3.2 32.5 + - + +
211A VAL* 5.3 5.6 - - + -
212A ARG 5.1 1.9 + - - -
215A TYR* 3.3 22.0 + - - +
216A ILE* 4.7 12.8 - - + -
244A PHE* 4.7 4.9 - + + -
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A VAL* 3.0 38.0 + - + +
198A LYS* 4.1 9.1 - - + +
200A TYR* 1.3 88.5 - - + +
202A ARG* 1.3 67.2 + - - +
204A LEU* 3.3 1.9 + - - +
205A THR* 2.9 33.7 + - + +
211A VAL* 4.0 34.3 - - + -
216A ILE* 6.3 2.0 - - + -
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Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 2.4 39.6 + - - +
163A GLN* 3.3 28.2 + - - +
166A PHE* 3.3 42.7 - - + +
198A LYS 2.9 18.9 + - - +
199A GLY 3.8 2.0 - - - +
200A TYR 3.2 0.2 - - - -
201A LYS* 1.3 76.9 - - - +
203A ALA* 1.3 54.1 + - - +
205A THR* 3.3 7.0 + - - +
206A GLU* 2.7 64.8 + - + +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.3 28.0 - - + +
169A VAL* 3.6 27.4 - - + -
170A GLN* 4.0 9.3 - - - +
173A ILE* 4.4 3.4 - - + +
199A GLY 3.2 12.0 + - - +
200A TYR 3.1 9.8 + - - +
202A ARG* 1.3 79.5 - - - +
204A LEU* 1.3 64.0 + - - +
206A GLU* 3.6 1.7 + - - +
207A SER* 3.3 22.3 + - - -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A VAL* 4.2 5.4 - - + -
173A ILE* 3.8 2.5 - - + -
178A LYS 4.2 4.5 - - - +
179A ASN* 6.2 0.4 - - - -
180A ILE* 3.5 33.0 - - + +
200A TYR* 3.2 44.1 + - + +
201A LYS 3.8 4.5 - - - +
203A ALA* 1.3 75.5 - - - +
205A THR* 1.3 68.4 + - - +
207A SER* 2.9 13.0 + - - -
209A LEU* 2.9 54.1 + - + +
210A PRO 3.8 16.4 - - - +
211A VAL* 4.1 14.8 - - + -
212A ARG 6.0 0.2 - - - +
215A TYR* 6.0 0.9 - - + -
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Residues in contact with THR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LYS* 2.9 21.9 + - + +
202A ARG* 3.3 11.6 + - - +
204A LEU* 1.3 72.0 - - - +
206A GLU* 1.3 62.9 + - - +
208A GLY* 2.8 19.8 + - - -
209A LEU 4.2 8.3 - - - +
211A VAL* 3.7 20.9 - - + -
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.3 28.8 - - + -
170A GLN* 5.7 0.9 - - - +
202A ARG* 2.7 54.2 + - + +
203A ALA 4.0 3.4 - - - +
205A THR* 1.3 76.7 + - - +
207A SER* 1.3 58.4 + - - +
208A GLY 3.4 2.6 + - - -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLN* 3.9 13.0 + - - -
173A ILE* 3.5 29.7 - - - +
203A ALA 3.3 15.7 + - - -
204A LEU 2.9 5.9 + - - -
206A GLU* 1.3 74.9 - - - +
208A GLY* 1.3 64.3 + - - +
209A LEU* 3.2 13.7 + - - +
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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