Contacts of the helix formed by residues 198 - 212 (chain A) in PDB entry 5H1C
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 ASP 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASN* 3.1 7.3 - - + +
197A THR* 1.3 88.6 + - - +
199A HIS* 1.3 61.3 + - - +
200A GLN 3.2 0.2 - - - -
201A THR* 2.2 37.5 + - - +
202A GLN* 3.6 5.4 + - - +
232A TYR* 4.7 3.3 + - - -
244A HIS* 3.6 20.3 + - - -
56B PRO* 6.2 0.4 - - - -
57B LYS* 3.2 34.8 + - + +
58B LYS 5.1 0.5 + - - -
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Residues in contact with HIS 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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193A ARG 3.4 13.9 - - - -
194A ALA* 3.3 6.6 - - + -
195A PHE* 3.3 20.1 + - - +
196A ASN* 3.1 29.2 + - + +
198A ASP* 1.3 80.4 - - - +
200A GLN* 1.3 62.5 + - - +
202A GLN* 3.1 25.4 + - + -
203A LEU* 3.0 33.9 + - + +
84B MET* 3.2 56.0 + - + +
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Residues in contact with GLN 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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160A ILE* 5.4 5.7 - - + +
162A THR* 3.4 19.3 - - + +
194A ALA* 4.0 16.8 - - + -
197A THR 3.4 9.8 + - - +
198A ASP 3.2 0.2 - - - -
199A HIS* 1.3 77.7 - - - +
201A THR* 1.3 58.1 + - + +
203A LEU* 3.3 11.2 + - + +
204A LEU* 2.9 33.1 + - - +
221A VAL* 5.2 1.2 - - - +
223A SER 3.9 3.4 + - - -
224A ALA* 3.7 18.3 + - - +
227A LEU* 3.3 28.8 - - + +
228A TYR* 3.6 27.4 + - - -
248A PHE* 3.9 26.2 - - + -
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Residues in contact with THR 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 THR 4.3 0.4 - - - +
198A ASP* 2.2 31.2 + - - +
200A GLN* 1.3 75.3 - - + +
202A GLN* 1.3 69.5 + - - +
204A LEU* 2.8 26.9 + - + +
205A TYR* 2.9 32.9 + - - -
244A HIS* 3.8 33.7 - - + +
248A PHE* 5.2 7.0 - - + -
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Residues in contact with GLN 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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198A ASP 4.3 5.8 - - - +
199A HIS* 3.1 25.1 + - + +
201A THR* 1.3 89.0 + - - +
203A LEU* 1.3 58.8 + - + +
205A TYR* 3.3 9.3 + - + +
206A GLN* 2.9 39.2 + - - +
84B MET* 6.0 0.5 - - - +
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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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160A ILE* 4.2 23.6 - - + +
192A ALA* 4.5 11.2 - - + -
193A ARG 4.6 2.0 - - - +
194A ALA* 3.6 34.5 - - + +
199A HIS* 3.0 40.8 + - + +
200A GLN* 3.5 10.1 - - - +
202A GLN* 1.3 79.2 - - + +
204A LEU* 1.3 58.2 + - - +
206A GLN* 3.9 13.5 - - - +
207A ALA* 2.9 27.0 + - - +
84B MET 3.7 15.3 - - - +
86B PHE* 3.4 22.2 - - + -
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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
----------------------------------------------------------
160A ILE* 4.6 16.8 - - + -
200A GLN 2.9 17.3 + - - +
201A THR* 2.8 14.7 + - + +
203A LEU* 1.3 75.6 - - - +
205A TYR* 1.3 67.2 + - + +
207A ALA* 3.0 6.3 + - + +
208A SER* 2.9 22.7 + - - -
219A LEU* 5.2 2.9 - - + -
221A VAL* 6.3 0.2 - - + -
248A PHE* 3.6 36.3 - - + +
251A MET* 3.8 37.7 - - + -
252A LEU* 3.8 23.8 - - + -
255A LEU* 4.4 15.7 - - + +
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Residues in contact with TYR 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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44A ALA 3.4 27.1 - - - -
45A GLY* 3.8 15.1 - - - -
47A HIS* 4.7 2.1 + - - -
59A GLU* 4.7 9.5 + - - -
201A THR* 2.9 43.5 + - - -
202A GLN* 3.9 8.3 - - + +
204A LEU* 1.3 77.9 - - + +
206A GLN* 1.3 58.3 + - + +
208A SER* 2.5 23.4 + - - +
209A ALA* 2.9 14.4 + - - +
251A MET* 4.5 30.2 - - + +
254A ARG* 5.0 4.7 - - - -
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Residues in contact with GLN 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 GLN* 2.9 25.4 + - + +
203A LEU* 3.9 17.4 - - - +
205A TYR* 1.3 75.0 - - + +
207A ALA* 1.3 59.7 + - - +
209A ALA* 3.2 10.3 + - + +
210A MET* 2.9 31.4 + - + +
84B MET 5.0 2.0 + - - -
85B GLY* 3.6 28.0 - - - +
86B PHE* 3.7 13.8 + - + -
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Residues in contact with ALA 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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158A MET* 4.8 12.7 - - - +
160A ILE* 5.4 1.3 - - + -
203A LEU 2.9 15.6 + - - +
204A LEU* 3.0 14.5 + - + +
206A GLN* 1.3 77.4 - - - +
208A SER* 1.3 59.2 + - - +
210A MET* 2.8 19.9 + - - +
211A MET* 2.9 19.7 + - + +
219A LEU* 4.8 9.4 - - + -
255A LEU* 4.7 12.6 - - + -
86B PHE* 3.5 17.9 - - + -
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Residues in contact with SER 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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45A GLY* 3.3 21.4 + - - -
47A HIS* 3.8 9.7 - - - +
48A THR* 5.9 0.2 - - - +
204A LEU 2.9 9.7 + - - -
205A TYR* 2.5 29.9 + - - -
207A ALA* 1.3 75.8 - - - +
209A ALA* 1.3 60.5 + - - +
211A MET* 3.3 24.5 + - - +
212A VAL* 3.9 7.4 - - - +
251A MET* 6.4 2.2 - - - -
255A LEU* 3.9 19.0 - - - +
259A PHE* 5.1 3.4 - - - -
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Residues in contact with ALA 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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47A HIS* 3.5 26.9 - - + +
205A TYR 2.9 14.3 + - - +
206A GLN* 3.3 14.8 - - + +
207A ALA 3.1 0.2 - - - -
208A SER* 1.3 78.7 + - - +
210A MET* 1.3 62.9 + - + +
211A MET 3.5 0.3 + - - -
212A VAL* 3.8 15.2 + - - +
213A GLU* 4.7 7.4 - - - +
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Residues in contact with MET 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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158A MET* 5.1 1.1 - - + -
206A GLN* 2.9 15.7 + - + +
207A ALA 2.8 8.9 + - - +
209A ALA* 1.3 76.3 - - + +
211A MET* 1.3 66.1 + - - +
212A VAL 3.1 3.7 + - - -
213A GLU* 3.5 40.0 + - + +
214A SER* 4.2 7.1 + - - +
216A TYR* 4.6 28.6 - - + +
86B PHE* 3.6 29.2 - - + -
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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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158A MET* 3.2 37.2 - - + +
207A ALA* 2.9 20.8 + - - +
208A SER* 3.5 15.5 - - - +
209A ALA 3.3 0.8 - - - -
210A MET* 1.3 78.3 - - - +
212A VAL* 1.3 63.4 + - - +
213A GLU 3.3 0.5 + - - -
214A SER 4.0 13.8 + - - +
215A ARG* 4.8 2.9 + - - +
216A TYR* 4.2 7.2 - - + +
219A LEU* 5.8 6.3 - - + -
255A LEU* 4.7 10.1 - - + -
259A PHE* 3.4 57.1 - - + -
261A VAL* 4.1 19.1 - - + -
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Residues in contact with VAL 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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24A PRO* 4.8 15.5 - - + -
47A HIS* 3.5 42.4 - - + +
48A THR* 4.4 12.3 - - + -
208A SER 3.9 4.5 - - - +
209A ALA 3.9 14.4 - - - +
210A MET 3.1 0.6 - - - -
211A MET* 1.3 79.1 - - + +
213A GLU* 1.3 67.2 + - + +
259A PHE* 6.0 0.2 - - - -
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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