Contacts of the helix formed by residues 203 - 216 (chain A) in PDB entry 4HH3
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 ARG 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ALA* 3.4 6.3 - - - -
197A GLN* 6.4 0.9 - - - -
201A GLY 4.2 3.8 + - - +
202A ARG* 1.3 79.3 - - - +
204A ARG* 1.3 67.8 + - - +
205A GLY* 3.3 3.1 + - - +
206A GLU* 2.9 20.4 + - + +
207A PHE* 2.9 22.3 + - - +
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A SER 5.4 1.0 + - - -
169A THR* 3.2 36.6 + - - +
170A GLY* 4.3 5.4 - - - +
171A ARG* 5.4 7.7 - - - +
194A ALA* 6.0 7.4 - - + -
195A ILE* 6.3 0.9 - - + -
196A ALA* 3.4 17.3 - - + +
197A GLN* 6.1 3.1 - - - +
203A ARG* 1.3 72.9 - - - +
205A GLY* 1.3 66.1 + - - +
208A MET* 2.9 44.9 + - + +
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Residues in contact with GLY 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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203A ARG* 3.4 2.6 - - - +
204A ARG* 1.3 79.8 - - - +
206A GLU* 1.3 62.1 + - - +
208A MET* 4.1 2.8 - - - +
209A GLU* 3.1 25.9 + - - +
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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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201A GLY 4.3 1.5 - - - +
202A ARG* 2.7 48.3 + - - +
203A ARG* 2.9 40.1 + - + +
205A GLY* 1.3 74.7 - - - +
207A PHE* 1.3 64.9 + - - +
209A GLU* 3.8 7.9 - - - +
210A THR* 2.8 40.6 + - - +
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Residues in contact with PHE 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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195A ILE* 3.8 34.5 - - + -
196A ALA* 4.0 11.2 - - + -
199A PHE* 3.8 33.4 - + - -
202A ARG* 3.8 36.6 - - + +
203A ARG 2.9 18.7 + - - +
204A ARG 3.9 1.6 - - - +
206A GLU* 1.3 86.7 - - - +
208A MET* 1.3 63.5 + - - +
210A THR* 3.3 1.4 + - - -
211A MET* 2.9 62.3 + - + +
225A VAL* 4.6 7.2 - - + -
236A VAL* 5.5 3.4 - - + -
249A LEU* 4.7 7.4 - - + -
251A CYS* 5.4 5.2 - - - -
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Residues in contact with MET 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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165A VAL* 4.3 4.9 - - + -
166A SER 3.9 18.4 - - - +
167A MET* 3.8 40.2 - - + +
170A GLY* 4.1 7.6 - - - -
195A ILE* 3.9 26.5 - - + -
204A ARG* 2.9 37.0 + - + +
205A GLY* 4.1 2.2 - - - +
207A PHE* 1.3 82.7 - - + +
209A GLU* 1.3 55.7 + - - +
211A MET* 3.5 1.9 + - - +
212A THR* 2.7 38.9 + - - +
249A LEU* 4.2 18.8 - - + -
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Residues in contact with GLU 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 GLY 3.1 18.1 + - - +
206A GLU* 3.9 6.7 - - - +
208A MET* 1.3 76.9 - - - +
210A THR* 1.3 59.2 + - - +
212A THR* 3.8 4.7 - - - -
213A ASN* 2.9 55.3 + - - +
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Residues in contact with THR 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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202A ARG* 3.9 15.9 + - - +
206A GLU* 2.8 27.9 + - - +
207A PHE 3.3 3.8 + - - -
209A GLU* 1.3 78.9 + - - +
211A MET* 1.3 73.4 + - + +
213A ASN* 4.0 5.4 - - - +
214A LEU* 3.0 31.4 + - + +
223A VAL* 5.2 6.3 - - + -
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Residues in contact with MET 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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202A ARG* 4.4 2.5 - - - +
207A PHE* 2.9 58.4 + - + +
208A MET 4.1 2.0 - - - +
210A THR* 1.3 105.9 - - + +
212A THR* 1.3 59.0 + - - +
214A LEU* 3.4 0.4 + - - -
215A ALA* 2.9 31.2 + - - +
223A VAL* 3.7 38.8 - - + -
236A VAL* 4.5 9.4 - - - -
238A PRO* 3.7 30.2 - - + +
249A LEU* 4.0 21.0 - - + +
251A CYS* 5.3 1.6 - - - -
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Residues in contact with THR 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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167A MET* 3.5 33.2 - - + +
208A MET* 2.7 25.5 + - - +
209A GLU* 3.8 5.6 - - - -
211A MET* 1.3 78.1 - - - +
213A ASN* 1.3 65.8 + - - +
215A ALA* 3.5 3.1 + - - +
216A ALA* 3.3 21.6 + - + +
240A VAL* 4.4 15.9 - - + +
247A ARG* 4.8 12.3 - - - +
249A LEU* 5.2 0.9 - - - +
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Residues in contact with ASN 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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209A GLU* 2.9 43.9 + - - +
210A THR* 4.0 4.7 - - - +
212A THR* 1.3 80.3 - - - +
214A LEU* 1.3 62.7 + - - +
216A ALA* 3.2 16.6 + - - +
217A THR* 3.3 17.6 + - - +
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Residues in contact with LEU 214 (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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210A THR* 3.0 22.4 + - + +
211A MET* 3.8 3.6 - - - +
213A ASN* 1.3 73.8 - - - +
215A ALA* 1.3 64.3 + - - +
217A THR* 2.7 28.7 + - + +
220A ALA* 3.7 26.7 - - + +
221A ALA 3.5 19.1 - - - +
223A VAL* 3.4 31.6 - - + -
238A PRO* 3.8 20.4 - - + -
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Residues in contact with ALA 215 (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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211A MET 2.9 19.4 + - - +
212A THR 3.8 1.8 - - - +
214A LEU* 1.3 76.4 - - - +
216A ALA* 1.3 58.7 + - - +
217A THR 3.1 12.9 + - - +
238A PRO* 3.7 25.5 - - - +
239A ARG* 4.0 1.5 - - - -
240A VAL* 3.8 35.2 - - + +
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Residues in contact with ALA 216 (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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212A THR* 3.3 11.5 + - + +
213A ASN* 3.2 13.7 + - - +
214A LEU 3.2 0.8 - - - -
215A ALA* 1.3 79.5 - - - +
217A THR* 1.3 59.3 + - + +
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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