Contacts of the helix formed by residues 195 - 213 (chain A) in PDB entry 3SDG
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 PRO 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A SER* 3.7 7.6 - - - +
194A VAL* 1.3 90.8 - - + +
196A GLU* 1.3 58.4 + - - +
197A ALA* 4.3 5.8 - - + +
198A ARG* 2.7 45.1 + - + -
199A VAL* 3.0 9.5 + - - +
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Residues in contact with GLU 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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111A PHE* 3.6 29.8 - - + -
115A GLY* 5.0 2.3 - - - +
118A LYS* 2.8 39.8 + - - -
186A SER* 4.2 19.2 + - - +
187A PHE* 3.8 19.9 - - + +
194A VAL 3.3 2.4 + - - -
195A PRO* 1.3 73.0 - - - +
197A ALA* 1.3 62.8 + - - +
198A ARG 3.2 1.0 + - - -
199A VAL* 3.5 21.3 + - - +
200A LEU 4.7 0.3 + - - -
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Residues in contact with ALA 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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111A PHE* 5.5 1.1 - - - -
195A PRO* 3.1 4.7 - - + +
196A GLU* 1.3 78.4 - - - +
198A ARG* 1.3 71.2 + - + +
200A LEU 5.4 0.2 - - - -
201A ASP* 5.9 1.2 - - - -
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Residues in contact with ARG 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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194A VAL* 3.7 11.2 - - + -
195A PRO* 2.7 34.3 + - + +
197A ALA* 1.3 82.5 + - + +
199A VAL* 1.3 58.3 + - - +
200A LEU 3.5 2.0 - - - -
201A ASP* 3.0 48.1 + - - +
202A THR* 2.7 40.1 + - - +
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 3.6 22.2 - - + -
182A THR* 3.4 37.2 - - + +
183A LEU* 4.2 6.5 - - + -
186A SER* 3.6 22.2 - - - +
187A PHE* 5.5 0.2 - - + -
194A VAL* 3.6 10.5 - - + -
195A PRO 3.0 6.0 + - - +
196A GLU* 3.5 19.4 + - - +
198A ARG* 1.3 80.6 - - - +
200A LEU* 1.4 67.0 + - - +
202A THR* 3.3 1.5 + - - -
203A LEU* 2.9 39.7 + - + +
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Residues in contact with LEU 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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104A ARG* 4.1 30.7 - - + +
107A ILE* 3.5 33.0 - - + +
108A ASN* 3.8 36.8 - - + +
111A PHE* 4.6 23.6 - - + -
183A LEU* 6.0 0.2 - - - -
196A GLU 4.7 1.4 + - - -
197A ALA 5.4 0.8 - - - -
198A ARG 3.5 0.6 - - - -
199A VAL* 1.4 82.3 - - - +
201A ASP* 1.3 59.0 + - - +
203A LEU* 3.9 3.7 - - - -
204A VAL* 2.9 37.2 + - + +
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Residues in contact with ASP 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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104A ARG* 2.5 42.9 + - - +
198A ARG* 3.0 43.8 + - - +
199A VAL 3.4 0.2 - - - -
200A LEU* 1.3 79.2 - - - +
202A THR* 1.3 63.7 + - - +
204A VAL* 4.0 0.9 - - - +
205A HIS* 3.1 24.6 + - - +
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Residues in contact with THR 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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182A THR* 5.6 1.1 - - + -
194A VAL* 3.7 25.0 - - + +
198A ARG* 2.7 32.1 + - - +
199A VAL* 3.6 8.1 - - - -
201A ASP* 1.3 81.5 - - - +
203A LEU* 1.3 68.2 + - + +
205A HIS* 3.4 4.2 + - - +
206A ILE* 3.3 42.4 + - + +
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Residues in contact with LEU 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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107A ILE* 4.2 16.6 - - + -
178A MET* 3.8 31.2 - - + -
179A ASN* 3.4 34.5 - - - +
182A THR* 3.9 17.9 - - + -
183A LEU* 3.8 31.9 - - + -
199A VAL* 2.9 29.5 + - + +
200A LEU* 4.0 2.7 - - - +
202A THR* 1.3 75.1 - - + +
204A VAL* 1.3 66.5 + - - +
206A ILE* 3.2 3.1 + - + -
207A TRP* 2.8 31.1 + - - -
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Residues in contact with VAL 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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100A GLU* 3.8 30.3 - - + +
103A TRP* 5.3 0.4 - - + -
104A ARG* 3.5 61.2 - - + +
107A ILE* 4.0 16.4 - - + -
200A LEU* 2.9 27.6 + - + +
201A ASP 4.0 0.9 - - - +
203A LEU* 1.3 75.4 - - - +
205A HIS* 1.3 59.7 + - - +
207A TRP* 3.2 1.2 + - - +
208A VAL* 2.8 42.4 + - + +
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Residues in contact with HIS 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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100A GLU* 6.4 0.4 - - - -
201A ASP 3.1 18.1 + - - +
202A THR* 3.6 5.6 - - - +
203A LEU 3.3 0.2 - - - -
204A VAL* 1.3 80.0 - - - +
206A ILE* 1.3 66.2 + - + +
208A VAL* 4.3 2.8 - - - +
209A THR* 2.8 66.2 + - + +
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Residues in contact with ILE 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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175A LEU* 4.2 7.6 - - + -
178A MET* 3.5 42.6 - - + -
202A THR* 3.3 30.9 + - + +
203A LEU* 3.2 4.3 + - + +
205A HIS* 1.3 84.1 - - + +
207A TRP* 1.3 63.3 + - - +
209A THR* 3.4 5.6 + - - -
210A SER* 2.9 33.8 + - - +
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Residues in contact with TRP 207 (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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103A TRP* 3.7 31.2 - + + -
107A ILE* 3.7 16.2 - - + -
149A THR* 3.4 23.8 - - + -
175A LEU* 3.6 35.2 + - + +
176A ASN* 3.7 22.0 - - - -
178A MET* 3.5 13.9 - - + +
179A ASN* 2.8 42.6 + - - +
203A LEU 2.8 29.4 + - - +
204A VAL* 3.8 3.6 - - - +
206A ILE* 1.3 78.1 - - - +
208A VAL* 1.3 59.9 + - + +
210A SER* 3.3 4.5 + - - -
211A ILE* 2.9 48.4 + - + +
217A 3SE 3.6 21.5 - - + -
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Residues in contact with VAL 208 (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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99A ARG* 4.3 17.0 - - + +
100A GLU* 3.9 37.9 - - + +
103A TRP* 4.3 17.9 - - + -
204A VAL* 2.8 34.5 + - + +
205A HIS* 4.3 2.9 - - - +
207A TRP* 1.3 69.6 - - - +
209A THR* 1.3 70.7 + - + +
212A TYR* 3.0 49.0 + - + +
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Residues in contact with THR 209 (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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205A HIS* 2.8 53.6 + - + +
206A ILE* 3.4 8.7 + - - -
208A VAL* 1.3 80.2 - - + +
210A SER* 1.3 58.3 + - - +
212A TYR* 5.4 0.4 - - - -
213A GLY* 2.9 30.6 + - - +
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Residues in contact with SER 210 (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 THR* 4.6 6.6 + - - -
171A LEU* 3.8 22.5 - - - +
175A LEU* 3.5 25.3 - - - +
206A ILE* 2.9 25.0 + - - -
207A TRP 3.3 4.3 + - - -
208A VAL 3.3 0.2 - - - -
209A THR* 1.3 77.8 + - - +
211A ILE* 1.3 65.9 + - - +
213A GLY 4.4 7.0 + - - +
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Residues in contact with ILE 211 (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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103A TRP* 3.8 26.2 - - + +
153A ILE* 4.1 25.2 - - + +
156A GLU* 5.5 0.7 - - + -
157A ARG* 5.3 2.6 + - - -
162A ALA* 3.8 11.3 - - + +
163A PRO* 3.6 18.2 - - - +
165A THR* 5.1 1.7 + - - -
171A LEU* 4.1 14.6 - - + +
175A LEU* 3.9 16.2 - - + -
207A TRP* 2.9 50.0 + - + +
210A SER* 1.3 81.4 - - - +
212A TYR* 1.3 87.2 + - + +
213A GLY 3.6 0.7 - - - -
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Residues in contact with TYR 212 (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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99A ARG* 3.6 54.0 + - + +
102A MET* 4.2 0.7 - - - +
103A TRP* 2.9 38.4 + + - -
156A GLU* 2.5 33.9 + - - +
161A ALA* 3.4 26.5 - - + -
162A ALA* 3.9 15.3 - - + -
163A PRO* 3.3 17.9 - - - +
208A VAL* 3.0 38.3 + - + +
209A THR* 5.4 0.2 - - - -
211A ILE* 1.3 85.2 - - + +
213A GLY* 1.4 60.8 + - - +
214A GLU* 4.0 7.4 + - - -
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Residues in contact with GLY 213 (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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163A PRO* 3.5 11.2 - - - +
165A THR* 3.8 8.7 - - - +
209A THR* 2.9 23.9 + - - +
210A SER* 4.5 6.4 - - - +
211A ILE 3.6 0.4 - - - -
212A TYR* 1.4 78.7 - - - +
214A GLU* 1.3 57.4 + - - -
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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