Contacts of the helix formed by residues 183 - 199 (chain A) in PDB entry 6S6A
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 ASN 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASN* 5.4 0.4 - - - +
181A ILE* 4.0 1.9 - - - +
182A PRO* 1.3 77.0 + - + +
184A VAL* 1.3 61.9 + - - +
185A GLN* 3.2 12.6 + - - +
186A GLN* 2.9 61.8 + - + +
187A LEU* 3.4 7.8 + - - +
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Residues in contact with VAL 184 (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 TYR* 3.5 55.2 - - + +
181A ILE* 3.7 37.7 - - + +
182A PRO 3.0 4.6 + - - +
183A ASN* 1.3 74.2 - - - +
185A GLN* 1.3 81.1 + - + +
186A GLN 3.5 0.2 - - - -
187A LEU* 3.9 8.5 - - + +
188A GLU* 3.4 24.4 + - - +
214A ILE 4.0 9.2 - - - +
215A SER* 4.9 0.7 - - - +
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Residues in contact with GLN 185 (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 TYR* 5.6 2.2 - - - +
182A PRO 5.5 1.0 + - - -
183A ASN* 3.2 10.3 + - - +
184A VAL* 1.3 98.6 + - + +
186A GLN* 1.3 65.7 - - - +
187A LEU 3.2 1.8 - - - -
188A GLU* 3.2 8.6 + - - +
189A MET* 3.1 31.2 + - + +
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Residues in contact with GLN 186 (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 ASN* 2.9 46.5 + - - +
185A GLN* 1.3 78.9 - - - +
187A LEU* 1.3 57.3 + - - +
189A MET* 3.5 16.1 + - + +
190A ASN* 2.9 40.8 + - - +
300A LEU* 3.7 24.3 - - + +
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Residues in contact with LEU 187 (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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53A LEU* 5.3 3.6 - - + -
181A ILE* 5.1 14.4 - - + -
183A ASN 3.4 8.5 + - - +
184A VAL* 3.9 10.3 - - + +
185A GLN 3.2 0.2 - - - -
186A GLN* 1.3 74.7 - - - +
188A GLU* 1.3 64.3 + - - +
189A MET 3.1 1.6 - - - -
190A ASN* 3.1 7.2 + - + +
191A LEU* 3.0 24.1 + - + +
205A LEU* 4.0 26.7 - - + -
214A ILE* 4.4 15.9 - - + +
215A SER* 3.6 19.5 - - - +
297A PHE* 4.3 20.6 - - + -
300A LEU* 4.6 15.9 - - + +
301A GLU* 6.0 2.0 - - - +
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Residues in contact with GLU 188 (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 TYR* 2.6 40.2 + - + +
184A VAL 3.4 12.0 + - - +
185A GLN* 3.2 11.7 + - - +
187A LEU* 1.3 77.4 - - - +
189A MET* 1.3 55.8 + - - +
191A LEU* 3.8 5.8 + - - +
192A ARG* 3.1 60.3 + - - +
215A SER* 3.6 26.9 - - - +
216A HIS* 3.7 11.9 + - - +
403A 9JE 4.0 6.1 + - - -
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Residues in contact with MET 189 (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 GLN* 3.1 23.1 + - + +
186A GLN* 3.6 19.3 - - + +
188A GLU* 1.3 73.0 - - - +
190A ASN* 1.3 60.3 + - - +
191A LEU 3.1 1.8 - - - -
192A ARG* 2.9 11.2 + - - +
193A ASN* 2.9 39.2 + - - +
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Residues in contact with ASN 190 (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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186A GLN* 2.9 27.1 + - - +
187A LEU* 3.1 7.2 + - - +
189A MET* 1.3 82.4 - - - +
191A LEU* 1.3 56.5 - - - +
193A ASN* 3.3 11.6 + - - +
194A PHE* 3.3 17.8 + - - +
297A PHE* 3.1 30.9 - - + -
300A LEU* 3.0 35.1 - - + +
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Residues in contact with LEU 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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187A LEU* 3.0 16.0 + - + +
188A GLU* 3.9 6.5 - - - +
190A ASN* 1.3 75.8 - - - +
192A ARG* 1.3 64.3 + - - +
193A ASN 3.2 0.4 - - - -
194A PHE* 3.3 8.1 + - + +
195A ALA* 3.0 24.3 + - - +
203A VAL* 3.5 43.5 - - + +
205A LEU* 3.9 30.1 - - + -
215A SER* 3.9 13.0 - - - +
216A HIS* 3.8 25.1 - - - +
217A TYR* 4.2 3.4 - - + +
266A PHE* 4.9 1.1 - - + -
272A VAL* 5.1 0.2 - - + -
297A PHE* 3.7 18.5 - - + -
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Residues in contact with ARG 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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188A GLU* 3.1 50.2 + - - +
189A MET* 2.9 15.0 + - - +
191A LEU* 1.3 74.3 - - - +
193A ASN* 1.3 57.9 + - - +
195A ALA* 3.4 2.8 + - - +
196A GLN* 3.0 51.4 + - - +
216A HIS* 2.8 30.7 + - - -
217A TYR* 3.5 36.8 - - + +
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Residues in contact with ASN 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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189A MET* 2.9 16.3 + - - +
190A ASN* 3.3 17.0 + - - +
192A ARG* 1.3 71.1 - - - +
194A PHE* 1.3 66.7 + - - +
196A GLN* 3.1 10.2 + - - +
197A ILE* 3.0 50.1 + - + +
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Residues in contact with PHE 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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190A ASN 3.3 13.1 + - - +
191A LEU* 3.7 11.9 - - + +
193A ASN* 1.3 78.3 - - - +
195A ALA* 1.3 59.6 + - - +
197A ILE* 3.2 8.7 + - + +
198A ILE* 2.9 61.5 + - + +
203A VAL* 4.1 26.7 - - + -
266A PHE* 4.2 17.5 - + - -
272A VAL* 4.4 4.5 - - + -
274A VAL* 4.2 9.9 - - + -
289A ASN* 4.0 12.1 - - + -
290A ILE* 3.9 17.0 - - + -
293A ALA* 3.5 29.4 - - + -
297A PHE* 4.0 12.3 - + + -
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Residues in contact with ALA 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 LEU 3.0 18.0 + - - +
192A ARG 3.6 1.6 - - - +
194A PHE* 1.3 78.3 - - - +
196A GLN* 1.3 58.0 + - - +
198A ILE* 3.2 8.5 - - - +
199A GLU* 2.9 22.7 + - - -
200A ALA* 3.1 13.2 + - + +
203A VAL* 3.7 19.5 - - + -
217A TYR* 3.3 39.5 - - + -
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Residues in contact with GLN 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 ARG* 3.0 37.2 + - - +
193A ASN* 3.7 5.1 + - - +
195A ALA* 1.3 75.2 - - - +
197A ILE* 1.3 64.0 + - + +
199A GLU* 3.2 24.6 + - - +
217A TYR* 4.1 27.3 + - + +
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Residues in contact with ILE 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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193A ASN* 3.0 48.3 + - + +
194A PHE* 3.7 8.1 - - + +
196A GLN* 1.3 77.2 - - + +
198A ILE* 1.3 62.4 + - + +
199A GLU* 3.6 9.2 + - - +
289A ASN* 4.7 13.9 + - + +
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Residues in contact with ILE 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 PHE* 2.9 50.6 + - + +
195A ALA* 3.2 14.8 - - - +
197A ILE* 1.3 74.1 - - + +
199A GLU* 1.3 68.3 + - - +
200A ALA* 3.8 14.6 - - + -
203A VAL* 4.9 1.6 - - + -
274A VAL* 4.2 10.8 - - + -
276A MET* 3.8 10.5 - - - +
281A ILE* 5.0 5.2 - - - +
286A THR* 4.0 26.4 + - + +
289A ASN* 3.8 29.1 + - + +
290A ILE* 3.9 18.2 - - + -
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Residues in contact with GLU 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 ALA 2.9 7.8 + - - -
196A GLN* 3.2 15.9 + - - +
197A ILE 4.4 7.6 - - - +
198A ILE* 1.3 81.7 - - - +
200A ALA* 1.3 59.0 + - - +
201A ASP* 4.1 3.5 + - - +
276A MET* 2.8 22.4 - - + +
279A PRO* 5.4 7.4 - - + +
281A ILE* 4.8 15.3 - - + +
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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