Contacts of the helix formed by residues 190 - 205 (chain A) in PDB entry 3HF8
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 CYS 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ALA* 1.3 77.5 - - - +
191A ARG* 1.3 66.9 + - - +
192A GLU* 3.6 11.4 - - - -
193A TYR* 3.2 23.6 + - - +
194A LEU* 3.2 17.5 + - - +
280A LEU* 4.0 2.5 - - - -
321A CYS* 3.6 23.6 - - - -
323A GLN* 3.5 16.6 - - - +
328A ARG* 3.8 7.0 - - - +
329A VAL 3.1 12.1 + - - +
330A PHE* 3.7 23.6 - - - -
379A PHE* 4.0 9.2 - - - -
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Residues in contact with ARG 191 (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 ALA 3.9 0.6 + - - -
190A CYS* 1.3 71.6 - - - +
192A GLU* 1.3 75.4 + - + +
194A LEU* 3.3 11.2 + - - +
195A LYS* 2.9 30.2 + - - +
323A GLN* 2.9 43.0 + - - +
324A ASP* 3.4 36.3 + - - +
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Residues in contact with GLU 192 (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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190A CYS* 3.6 6.2 - - - -
191A ARG* 1.3 79.1 + - + +
193A TYR* 1.3 65.3 + - - +
195A LYS* 3.3 10.1 + - + +
196A ASN* 3.2 30.9 + - - -
280A LEU* 3.9 7.4 - - + -
283A GLU* 3.9 28.7 - - + +
285A SER* 5.2 1.0 + - - +
323A GLN* 2.8 29.8 + - - -
378A SER* 6.0 1.4 - - - -
379A PHE* 3.5 39.7 + - + +
380A GLU* 5.4 2.9 - - - +
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Residues in contact with TYR 193 (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 TYR* 3.0 38.0 + + - -
189A ALA* 3.7 18.8 - - + -
190A CYS* 3.2 25.3 + - - +
192A GLU* 1.3 78.3 - - - +
194A LEU* 1.3 68.1 + - + +
196A ASN* 3.2 4.0 + - - +
197A LEU* 3.0 51.3 + - + +
275A LEU* 2.5 32.7 + - - +
276A GLY 4.2 1.3 - - - -
279A PRO* 3.4 28.5 - - + +
280A LEU* 3.8 15.1 - - + +
335A LEU* 3.7 24.5 - - + -
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Residues in contact with LEU 194 (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 TYR* 3.6 41.7 - - + +
186A PRO* 3.9 20.4 - - + +
189A ALA* 3.7 22.0 - - + +
190A CYS 3.2 10.0 + - - +
191A ARG* 3.3 10.7 + - - +
193A TYR* 1.3 83.6 - - + +
195A LYS* 1.3 62.1 + - - +
197A LEU* 4.2 7.7 - - + +
198A PRO* 3.1 21.7 - - - +
328A ARG* 4.3 2.9 - - - +
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Residues in contact with LYS 195 (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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191A ARG 2.9 16.4 + - - +
192A GLU* 3.5 8.5 - - + +
193A TYR 3.2 0.2 - - - -
194A LEU* 1.3 77.0 - - - +
196A ASN* 1.3 62.7 + - - +
198A PRO* 3.5 7.2 - - - +
199A LEU* 3.2 22.6 - - + +
283A GLU* 4.3 25.2 + - - +
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Residues in contact with ASN 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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192A GLU 3.2 13.8 + - - +
193A TYR 3.2 3.6 + - - +
195A LYS* 1.3 83.8 - - - +
197A LEU* 1.3 66.1 + - - +
198A PRO* 3.4 1.8 - - - -
199A LEU* 3.2 25.3 + - + +
200A LEU* 3.4 14.7 + - + +
220A PHE* 5.1 1.8 - - + -
224A ARG* 5.1 6.1 - - - -
279A PRO* 3.0 32.6 + - + +
282A ALA* 3.9 19.8 - - + +
283A GLU* 3.1 36.6 + - - +
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Residues in contact with LEU 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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178A PHE* 5.7 2.5 - - + -
182A ASN* 3.4 26.5 - - - +
185A TYR* 3.6 21.1 - - + -
193A TYR* 3.0 44.6 + - + +
194A LEU* 4.2 7.9 - - + +
196A ASN* 1.3 76.1 - - - +
198A PRO* 1.4 68.1 - - + +
200A LEU* 3.3 20.6 + - + +
201A SER* 3.3 13.2 + - - -
206A TYR* 4.7 8.0 - - + +
275A LEU* 4.6 15.0 - - + -
279A PRO* 4.0 12.3 - - + +
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Residues in contact with PRO 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 LEU 3.1 19.7 - - - +
195A LYS* 3.5 8.3 - - - +
196A ASN 3.4 4.5 - - - -
197A LEU* 1.4 89.2 - - + +
199A LEU* 1.3 61.6 + - + +
201A SER* 3.2 10.1 + - - +
202A LYS* 3.0 27.7 + - - +
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Residues in contact with LEU 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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195A LYS* 3.2 28.0 - - + +
196A ASN* 3.2 18.7 + - - +
198A PRO* 1.3 81.8 - - + +
200A LEU* 1.3 56.8 + - - +
202A LYS* 3.3 4.8 + - + -
203A TYR* 2.9 55.5 + - + +
220A PHE* 3.8 23.1 - - + -
224A ARG* 4.8 13.9 - - - +
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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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196A ASN* 3.4 10.7 + - + +
197A LEU* 3.3 10.1 + - + +
198A PRO 3.2 0.6 - - - -
199A LEU* 1.3 75.5 - - - +
201A SER* 1.3 59.3 + - - +
204A CYS* 3.0 32.9 + - - -
205A GLY 3.4 1.9 + - - -
206A TYR* 3.2 45.0 - - + -
217A VAL* 4.6 0.9 - - + -
220A PHE* 3.7 28.9 - - + -
278A VAL* 3.6 26.0 - - + -
279A PRO* 3.7 41.5 - - + -
282A ALA* 5.9 0.2 - - + -
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 4.5 7.4 - - - -
197A LEU 3.3 9.3 + - - -
198A PRO* 3.2 13.2 + - - +
200A LEU* 1.3 80.0 - - - +
202A LYS* 1.3 62.6 + - - +
205A GLY* 3.8 11.8 + - - -
206A TYR* 3.0 34.2 + - - +
207A ARG* 5.2 4.2 + - - +
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Residues in contact with LYS 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 PRO 3.0 16.1 + - - +
199A LEU* 3.6 6.7 - - + +
200A LEU 3.3 0.2 - - - -
201A SER* 1.3 77.9 - - - +
203A TYR* 1.3 97.4 + - + +
205A GLY 5.1 0.5 + - - -
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Residues in contact with TYR 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 LEU* 2.9 43.0 + - + +
202A LYS* 1.3 105.1 - - + +
204A CYS* 1.3 64.1 + - - +
205A GLY 3.7 1.1 - - - -
216A ASP* 5.3 3.6 - - - +
220A PHE* 4.0 28.9 - + + -
223A GLU* 6.2 0.2 - - - -
224A ARG* 6.0 2.5 - - - -
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Residues in contact with CYS 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 LEU* 3.0 19.3 + - - +
203A TYR* 1.3 81.3 - - - +
205A GLY* 1.3 63.4 + - - +
206A TYR* 3.4 16.4 - - + -
210A ASN* 4.8 0.7 + - - -
212A PRO* 3.6 19.6 - - - +
213A GLN 4.7 2.1 + - - -
216A ASP* 3.8 25.5 - - + +
217A VAL* 3.9 15.7 - - + -
220A PHE* 3.5 39.5 - - - -
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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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200A LEU 3.4 1.2 + - - -
201A SER 3.8 7.0 + - - -
202A LYS 5.0 0.4 + - - -
203A TYR 3.7 1.4 - - - -
204A CYS* 1.3 79.5 - - - +
206A TYR* 1.3 60.5 + - - +
207A ARG* 3.0 31.1 + - - +
210A ASN* 3.0 31.8 + - - +
212A PRO* 4.2 2.2 - - - +
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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