Contacts of the helix formed by residues 197 - 211 (chain A) in PDB entry 1H3F
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 GLN 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ARG* 5.3 2.6 + - - -
179A GLN* 3.2 16.2 - - - +
192A MET 5.8 0.6 + - - -
193A GLY* 4.4 5.4 - - - -
194A GLY 2.9 21.1 + - - +
196A ASP* 1.3 96.6 - - - +
198A ARG* 1.3 63.3 + - - +
199A PHE 3.4 2.4 + - - -
200A ASN* 2.9 29.9 + - - +
201A LEU* 3.2 32.9 + - + +
220A LEU* 4.5 1.3 - - - -
1433A TYE 2.4 43.3 + - - +
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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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21A GLU* 3.0 35.4 + - - -
23A VAL* 4.7 12.8 - - + +
194A GLY 4.0 1.6 + - - -
195A THR 3.6 15.1 + - - +
196A ASP 3.3 2.8 - - - -
197A GLN* 1.3 78.4 - - - +
199A PHE* 1.3 64.9 + - - +
201A LEU* 3.3 3.0 + - - +
202A LEU* 3.1 55.2 + - + +
218A CYS* 5.9 0.2 - - - +
220A LEU* 3.8 23.1 - - + +
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Residues in contact with PHE 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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147A MET* 3.6 28.5 - - + -
151A GLN* 3.8 16.6 - - + -
152A MET* 3.7 32.1 - - + -
154A GLU* 5.2 2.2 - - + -
155A ARG* 3.5 50.9 - - + -
156A GLU* 6.3 0.9 - - + -
176A PRO* 4.3 5.4 - - + -
196A ASP 5.0 2.4 + - - +
197A GLN 3.4 0.8 - - - -
198A ARG* 1.3 79.2 - - - +
200A ASN* 1.3 70.6 + - - +
202A LEU* 3.2 11.9 + - + +
203A VAL* 3.1 40.4 + - + +
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Residues in contact with ASN 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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155A ARG* 2.8 36.7 + - - +
175A TYR* 5.8 0.6 - - - +
176A PRO* 3.4 24.2 - - + +
179A GLN* 2.8 39.6 + - + +
180A ALA* 5.0 0.7 - - - +
191A GLU* 4.9 0.9 - - - +
197A GLN* 2.9 26.5 + - - +
198A ARG 3.4 0.4 - - - -
199A PHE* 1.3 81.2 - - - +
201A LEU* 1.3 64.1 + - - +
203A VAL* 3.2 9.4 + - - +
204A GLY* 3.1 17.3 + - - -
1433A TYE 3.6 3.8 + - - -
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Residues in contact with LEU 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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179A GLN* 3.6 15.7 - - - +
191A GLU* 3.5 57.7 - - + +
192A MET 4.1 12.6 - - - +
193A GLY* 4.2 2.0 - - - +
197A GLN* 3.2 23.3 + - + +
198A ARG* 3.7 4.7 - - - +
200A ASN* 1.3 75.6 - - - +
202A LEU* 1.3 62.4 + - - +
204A GLY 3.1 9.0 + - - -
205A ARG 3.3 3.8 + - - -
216A GLN* 3.2 14.7 + - - -
218A CYS* 3.4 24.1 - - + -
219A PHE 4.5 0.4 - - - +
220A LEU* 3.5 29.4 - - + -
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Residues in contact with LEU 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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23A VAL* 4.6 13.9 - - + -
198A ARG* 3.1 55.1 + - + +
199A PHE* 3.2 11.2 + - + +
201A LEU* 1.3 72.6 - - - +
203A VAL* 1.3 67.6 + - + +
205A ARG* 3.1 35.3 + - - +
206A GLU* 3.2 12.0 + - - +
218A CYS* 4.4 8.1 - - + -
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Residues in contact with VAL 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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147A MET* 4.1 16.8 - - + -
152A MET* 5.6 0.9 - - - -
176A PRO* 3.9 17.3 - - + +
177A PHE* 4.1 20.9 - - + -
180A ALA* 3.9 14.1 - - + -
199A PHE* 3.1 46.1 + - + +
200A ASN 3.2 7.6 + - - +
202A LEU* 1.3 76.4 - - + +
204A GLY* 1.3 62.3 + - - +
206A GLU* 3.2 8.0 + - + +
207A VAL* 2.9 30.0 + - + +
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Residues in contact with GLY 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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180A ALA* 3.6 24.0 - - - +
183A SER* 4.8 0.4 - - - -
191A GLU* 5.2 0.7 - - - -
200A ASN 3.1 8.3 + - - -
201A LEU 3.1 9.4 + - - -
202A LEU 3.1 1.2 - - - -
203A VAL* 1.3 78.4 - - - +
205A ARG* 1.3 55.7 + - - +
207A VAL* 3.5 1.2 + - - +
208A GLN* 2.9 35.7 + - - +
216A GLN* 3.8 15.3 - - - -
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Residues in contact with ARG 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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23A VAL 4.5 3.8 - - - -
24A PRO* 3.4 19.3 - - - +
27A GLU* 2.9 24.4 + - - -
201A LEU 3.3 2.7 + - - +
202A LEU* 3.1 24.9 + - + +
204A GLY* 1.3 76.4 - - - +
206A GLU* 1.3 61.5 + - - +
208A GLN* 3.4 6.4 + - - +
209A ARG* 3.0 60.8 + - - +
215A PRO* 3.3 28.8 + - + +
216A GLN* 2.8 48.6 + - + +
218A CYS* 3.7 24.0 - - - -
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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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146A LEU* 4.5 29.9 - - + +
147A MET* 5.1 11.0 - - + -
202A LEU 3.2 7.9 + - - +
203A VAL* 3.2 13.0 + - + +
205A ARG* 1.3 79.4 - - - +
207A VAL* 1.3 63.5 + - + +
209A ARG* 3.2 35.1 + - - +
210A ALA* 3.1 21.5 + - - +
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Residues in contact with VAL 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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143A LEU* 3.7 28.0 - - + -
146A LEU* 4.1 21.1 - - + -
177A PHE* 4.4 7.6 - - + +
180A ALA* 3.5 29.4 - - + +
181A TYR* 4.4 2.0 - - - +
184A VAL* 3.7 19.1 - - + -
203A VAL* 2.9 27.6 + - + +
204A GLY 3.9 1.3 - - - +
206A GLU* 1.3 74.1 - - + +
208A GLN* 1.3 66.8 + - - +
210A ALA* 3.1 2.1 + - - +
211A TYR* 3.0 28.1 + - + -
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Residues in contact with GLN 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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183A SER* 3.5 21.5 - - - +
184A VAL* 4.0 17.0 - - + +
187A ARG 4.3 0.3 - - - -
188A ALA 3.0 20.5 + - - +
204A GLY 2.9 17.1 + - - +
205A ARG 3.7 3.4 - - - +
207A VAL* 1.3 77.2 - - - +
209A ARG* 1.3 61.3 + - - +
211A TYR* 3.1 8.0 + - - -
213A GLN* 2.8 53.1 + - + +
214A SER 3.7 15.6 - - - +
215A PRO* 3.7 1.3 - - + +
216A GLN* 2.6 50.5 - - - +
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Residues in contact with ARG 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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202A LEU 5.5 0.2 + - - -
205A ARG* 3.0 64.1 + - - +
206A GLU* 3.2 43.4 + - - +
207A VAL 3.2 0.2 - - - -
208A GLN* 1.3 75.2 - - - +
210A ALA* 1.3 58.8 + - - +
212A GLY* 2.9 19.8 + - - -
213A GLN 3.8 7.2 - - - -
215A PRO* 4.1 22.0 - - + +
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Residues in contact with ALA 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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146A LEU* 3.7 34.1 - - + -
206A GLU 3.1 13.1 + - - +
207A VAL 3.4 8.5 - - - +
209A ARG* 1.3 75.3 - - - +
211A TYR* 1.3 66.9 + - + +
212A GLY 3.5 0.5 + - - -
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Residues in contact with TYR 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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139A GLU* 4.5 15.7 + - - +
142A ARG* 5.8 2.4 - - - +
143A LEU* 3.8 33.3 - - + +
146A LEU* 5.7 0.4 - - + -
181A TYR* 3.7 28.6 - + - -
184A VAL* 3.9 26.7 - - + -
207A VAL* 3.0 27.7 + - + +
208A GLN 3.1 3.7 + - - +
210A ALA* 1.3 83.2 - - + +
212A GLY* 1.3 61.7 + - - +
213A GLN* 3.3 9.0 + - - +
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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