Contacts of the helix formed by residues 198 - 213 (chain A) in PDB entry 3H8E
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 HIS 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PRO 4.2 6.5 - - - +
195A ASN 3.3 25.1 + - - -
196A LEU* 3.2 6.9 + - - -
197A CYS* 1.3 76.2 - - - +
199A PRO* 1.3 80.0 - - + +
200A SER* 3.5 15.8 + - - -
201A PHE* 3.1 49.1 + - + +
202A LEU* 3.1 14.6 + - - +
243A GLN* 3.4 44.8 + - + -
321A GLU* 4.7 3.6 - - - +
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Residues in contact with PRO 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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197A CYS 4.8 0.4 - - - +
198A HIS* 1.3 88.4 - - + +
200A SER* 1.3 58.4 + - - +
202A LEU* 3.1 6.0 + - + +
203A ALA* 2.9 26.9 + - - +
243A GLN* 5.0 2.7 - - + +
244A PRO 3.3 25.4 - - - +
246A ARG* 3.7 15.5 - - + +
248A ILE* 4.5 0.3 - - - +
268A GLY 4.9 2.7 - - - +
269A ILE 6.1 0.9 - - - -
291A MET* 5.2 3.8 - - - -
319A CYS* 3.7 22.4 - - + -
320A ALA* 3.6 36.8 - - - +
321A GLU* 4.1 8.5 - - + +
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Residues in contact with SER 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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198A HIS* 3.2 16.2 + - - -
199A PRO* 1.3 79.3 - - - +
201A PHE* 1.4 57.6 + - - +
203A ALA* 3.2 9.0 + - - +
204A GLU* 2.9 34.8 + - - +
243A GLN* 4.2 4.9 + - - -
244A PRO* 4.0 13.7 + - - +
246A ARG* 3.6 29.1 + - - +
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Residues in contact with PHE 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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143A ARG* 5.9 5.2 - - - -
189A LEU* 3.9 17.5 - - + -
192A LEU* 5.1 14.6 - - + -
196A LEU* 3.3 25.8 - - + +
197A CYS* 3.8 27.4 - - + -
198A HIS* 3.1 21.9 + - + +
200A SER* 1.4 76.9 - - - +
202A LEU* 1.3 64.5 + - + +
204A GLU* 3.1 12.4 + - + +
205A GLN* 2.9 58.7 + - + +
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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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189A LEU* 4.1 21.8 - - + -
197A CYS* 3.9 18.6 - - - -
198A HIS 3.1 16.4 + - - +
199A PRO 3.1 7.2 + - - +
201A PHE* 1.3 81.4 - - + +
203A ALA* 1.3 57.8 + - - +
205A GLN* 3.3 6.3 + - + +
206A ALA* 2.9 28.6 + - - +
248A ILE* 3.6 12.8 - - + -
291A MET* 0.9 88.6 - - + -
298A PHE* 3.6 14.5 - - + -
319A CYS* 3.8 5.8 - - + -
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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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199A PRO 2.9 12.7 + - - +
200A SER* 3.5 10.3 - - - +
202A LEU* 1.3 78.0 - - - +
204A GLU* 1.3 58.9 + - + +
206A ALA* 3.2 3.9 + - - +
207A LYS* 3.0 37.1 + - - +
220A VAL* 3.7 31.9 - - + +
246A ARG* 4.2 9.0 - - + +
248A ILE* 3.5 15.2 - - + +
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Residues in contact with GLU 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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200A SER* 2.9 21.1 + - - +
201A PHE* 3.1 13.4 + - + +
203A ALA* 1.3 78.5 - - - +
205A GLN* 1.3 62.9 + - - +
207A LYS* 2.9 38.9 + - - +
208A GLU* 2.9 40.9 + - - +
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Residues in contact with GLN 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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185A PHE* 3.9 23.8 - - + -
189A LEU* 4.1 11.5 - - + +
201A PHE* 2.9 53.8 + - + +
202A LEU* 3.4 9.6 - - - +
204A GLU* 1.3 75.5 - - - +
206A ALA* 1.3 58.0 + - - +
208A GLU* 3.4 25.1 + - - +
209A LEU* 3.0 28.4 + - - +
298A PHE* 4.1 14.4 - - + -
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Residues in contact with ALA 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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202A LEU 2.9 14.1 + - - +
203A ALA 3.6 3.8 - - - +
204A GLU 3.2 0.2 - - - -
205A GLN* 1.3 75.2 - - - +
207A LYS* 1.3 66.1 + - - +
209A LEU* 3.2 2.9 + - - +
210A GLY 2.9 19.2 + - - -
218A VAL* 3.4 14.7 - - + +
248A ILE* 3.4 33.0 - - + -
250A LEU* 3.8 14.8 - - + +
298A PHE* 3.8 13.2 - - + -
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Residues in contact with LYS 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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203A ALA* 3.0 19.9 + - - +
204A GLU* 2.9 44.7 + - - +
206A ALA* 1.3 73.3 - - - +
208A GLU* 1.3 64.5 + - + +
210A GLY* 3.4 1.4 + - - -
211A LYS* 3.1 38.6 + - - +
218A VAL* 4.2 12.6 - - + +
220A VAL* 4.0 25.1 - - + +
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Residues in contact with GLU 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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204A GLU* 2.9 33.0 + - + +
205A GLN* 3.4 25.6 + - - +
207A LYS* 1.3 77.7 - - + +
209A LEU* 1.3 61.5 + - - +
211A LYS* 3.2 22.2 + - - +
212A ALA* 3.3 13.5 + - - +
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Residues in contact with LEU 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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185A PHE* 4.9 5.8 - - + -
205A GLN 3.0 17.3 + - - +
206A ALA 3.2 4.7 + - - +
208A GLU* 1.3 76.1 - - - +
210A GLY* 1.3 63.2 + - - +
212A ALA* 3.0 12.3 + - + -
213A HIS* 3.2 44.2 + - + +
216A LEU* 3.9 10.5 - - + +
250A LEU* 4.2 3.6 - - + -
298A PHE* 4.2 24.0 - - + +
301A LEU* 3.8 31.0 - - + -
302A ARG* 3.9 32.3 - - + +
305A LEU* 4.3 6.1 - - + -
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Residues in contact with GLY 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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206A ALA 2.9 11.5 + - - -
207A LYS 3.7 3.8 - - - -
208A GLU 3.3 0.4 - - - -
209A LEU* 1.3 75.9 - - - +
211A LYS* 1.3 62.3 + - - +
212A ALA 3.2 0.7 + - - -
213A HIS 3.3 19.4 - - - +
216A LEU* 3.7 19.9 - - - +
218A VAL* 3.8 22.2 - - - -
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Residues in contact with LYS 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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207A LYS* 3.1 30.4 + - - +
208A GLU* 3.2 12.3 + - + +
210A GLY* 1.3 76.8 - - - +
212A ALA* 1.3 60.1 + - - +
213A HIS 3.6 1.7 + - - -
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Residues in contact with ALA 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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208A GLU 3.3 10.1 + - - +
209A LEU* 3.0 12.7 + - + +
211A LYS* 1.3 75.8 - - - +
213A HIS* 1.4 77.6 + - + +
214A LYS 4.3 0.6 + - - -
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Residues in contact with HIS 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 LEU* 3.2 46.1 - - + +
210A GLY 3.3 15.0 + - - +
211A LYS 3.4 2.5 - - - -
212A ALA* 1.4 93.5 + - + +
214A LYS* 1.3 66.9 + - - +
215A ALA 3.3 1.1 - - - +
216A LEU* 3.1 28.8 + - + +
302A ARG* 5.7 1.8 + - - -
305A LEU* 3.8 37.9 + - + +
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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