Contacts of the helix formed by residues 195 - 207 (chain A) in PDB entry 1QIB
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 LEU 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A THR* 5.2 1.1 - - + -
108A LEU* 4.2 24.2 - - + -
113A VAL* 4.2 25.8 - - + -
116A ALA* 4.6 15.7 - - + -
117A PHE* 4.2 19.5 - - + -
146A PHE* 4.5 11.2 - - + -
180A PHE* 4.0 27.1 - - + -
186A TRP* 3.8 30.1 - - + -
187A SER 3.1 13.3 + - - +
188A LEU* 5.3 1.1 - - + +
193A TYR 3.2 2.6 + - - -
194A SER* 1.3 72.3 - - - +
196A PHE* 1.3 56.6 + - - +
199A ALA* 3.1 32.6 + - - +
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Residues in contact with PHE 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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116A ALA* 3.7 33.2 - - + +
119A ARG* 3.5 60.6 - - + +
120A ALA* 3.6 9.7 - - - +
123A VAL* 4.1 16.4 - - + -
188A LEU* 4.8 5.2 - - + +
194A SER* 3.1 8.2 + - - +
195A LEU* 1.3 79.0 - - - +
197A LEU* 1.3 81.5 + - + +
200A ALA* 3.2 23.0 + - + +
232A PHE* 4.3 22.0 - + + -
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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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194A SER* 3.1 15.4 + - - +
196A PHE* 1.3 103.0 - - + +
198A VAL* 1.3 65.5 + - - +
200A ALA* 3.4 7.0 + - + +
201A HIS* 3.4 19.9 + - - +
218A LEU* 4.4 10.2 - - + +
223A TYR* 4.0 15.9 - - + +
227A THR 3.9 19.1 - - - +
228A TYR* 3.8 31.4 - - + -
229A THR* 4.1 12.1 - - - +
232A PHE* 4.3 26.9 - - + -
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Residues in contact with VAL 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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164A LEU* 4.1 18.4 - - + -
165A ALA* 3.8 28.9 - - + -
180A PHE* 4.0 6.7 - - + -
186A TRP* 3.8 24.9 - - + -
193A TYR* 4.6 1.1 - - + -
194A SER 3.1 15.7 + - - +
195A LEU 4.4 0.7 - - - +
197A LEU* 1.3 75.3 - - - +
199A ALA* 1.3 58.3 + - - +
201A HIS* 3.4 7.8 + - + +
202A GLU* 3.0 38.4 + - - +
223A TYR* 3.9 26.9 - - + -
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Residues in contact with ALA 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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116A ALA 4.8 0.2 - - - +
117A PHE* 3.9 17.5 - - + -
120A ALA* 3.8 17.0 - - + -
180A PHE* 3.8 25.0 - - + -
195A LEU 3.1 21.3 + - - +
196A PHE* 4.0 0.9 - - - +
198A VAL* 1.3 73.8 - - - +
200A ALA* 1.3 65.6 + - - +
201A HIS 3.1 1.3 - - - -
202A GLU 3.2 0.6 + - - +
203A PHE* 3.0 34.6 + - + -
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Residues in contact with ALA 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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120A ALA* 3.7 16.9 - - + +
123A VAL* 4.2 17.5 - - + -
124A TRP* 3.1 27.1 + - - +
196A PHE* 3.2 22.8 + - + +
197A LEU* 3.4 7.4 + - + +
199A ALA* 1.3 79.0 - - - +
201A HIS* 1.3 61.1 + - - +
203A PHE* 4.7 0.4 - - - -
204A GLY 3.4 5.0 + - - -
218A LEU* 3.8 19.5 - - + -
232A PHE* 5.3 2.9 - - + -
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Residues in contact with HIS 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 LEU 3.4 10.3 + - - +
198A VAL* 3.5 10.5 - - + +
199A ALA 3.1 0.2 - - - -
200A ALA* 1.3 77.1 - - - +
202A GLU* 1.3 83.8 + - - +
204A GLY 3.3 8.5 + - - -
205A HIS* 3.6 10.2 + - - -
211A HIS* 3.9 3.1 - - - -
218A LEU* 2.8 34.5 + - + +
219A MET* 3.7 25.5 - - + +
220A ALA 3.3 23.5 + - - -
221A PRO* 5.0 2.6 + - + +
501A ZN 2.4 35.5 - - - -
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Residues in contact with GLU 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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164A LEU* 5.7 0.2 - - - +
165A ALA* 3.6 40.9 + - + +
166A HIS* 3.2 23.3 - - - +
167A ALA* 3.4 16.8 + - + +
178A SER* 4.5 11.2 - - - +
180A PHE* 4.3 9.4 - - + -
198A VAL* 3.0 23.1 + - - +
199A ALA 3.2 4.0 + - - +
201A HIS* 1.3 92.7 - - - +
203A PHE* 1.3 60.2 + - + +
205A HIS* 2.9 37.4 + - - +
206A ALA 3.1 4.9 + - - -
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Residues in contact with PHE 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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117A PHE* 3.8 33.2 - + - -
120A ALA* 3.7 30.3 - - + -
121A PHE* 3.8 40.8 - + + -
124A TRP* 3.9 19.2 + - + +
142A ILE* 4.9 2.0 - - + -
144A ILE* 3.8 19.7 - - + -
178A SER* 3.6 27.8 - - - -
180A PHE* 4.8 3.8 - + - -
199A ALA* 3.0 24.8 + - + +
201A HIS 3.3 0.2 - - - -
202A GLU* 1.3 72.9 - - + +
204A GLY* 1.3 63.8 + - - +
206A ALA* 3.5 8.9 + - + +
207A MET* 3.3 30.2 + - - +
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Residues in contact with GLY 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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124A TRP* 3.7 25.8 - - - +
200A ALA 3.4 4.9 + - - -
201A HIS 3.3 8.2 + - - -
202A GLU 3.1 2.0 - - - -
203A PHE* 1.3 78.6 - - - +
205A HIS* 1.3 59.6 + - - +
207A MET* 3.4 5.6 + - - +
208A GLY 3.4 4.7 + - - -
209A LEU* 2.9 39.4 + - - +
219A MET* 4.3 3.6 - - - -
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Residues in contact with HIS 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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167A ALA* 3.8 22.3 + - + +
168A PHE 3.9 7.0 - - - +
169A ALA* 3.9 7.3 - - - +
201A HIS 3.6 19.6 + - - -
202A GLU* 2.9 21.6 + - - +
204A GLY* 1.3 73.1 - - - +
206A ALA* 1.3 58.4 + - - +
207A MET 3.0 4.7 - - - -
208A GLY* 2.8 22.2 + - - -
209A LEU 3.1 22.4 + - - +
210A GLU* 4.6 13.1 + - - -
211A HIS* 3.5 15.0 + + - -
219A MET* 3.6 14.3 - - + +
501A ZN 2.3 35.2 - - - -
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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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92A TRP* 2.9 25.5 + - - -
142A ILE* 4.1 15.3 - - + -
167A ALA* 4.3 1.7 - - + +
168A PHE 3.4 12.7 + - - +
170A PRO* 3.5 8.7 - - - +
176A GLY* 3.4 27.4 - - - +
178A SER* 4.5 5.6 - - - +
202A GLU 3.1 8.4 + - - +
203A PHE* 3.9 11.4 - - + +
204A GLY 3.4 0.4 - - - -
205A HIS* 1.3 77.4 - - - +
207A MET* 1.3 60.4 + - - +
208A GLY 3.4 0.2 - - - -
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Residues in contact with MET 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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91A LYS* 4.5 1.4 - - - -
92A TRP* 3.3 33.7 - - + +
97A ILE* 3.8 16.2 - - + -
121A PHE* 5.5 2.7 - - - -
124A TRP* 5.6 6.5 - - + -
130A LEU* 3.8 25.6 - - + -
132A PHE* 3.7 34.8 - - + -
142A ILE* 4.5 9.0 - - + -
170A PRO* 3.4 6.6 - - - +
203A PHE* 3.3 19.8 + - - +
204A GLY* 3.8 6.1 - - - +
205A HIS 3.0 1.2 + - - -
206A ALA* 1.3 81.2 - - - +
208A GLY* 1.3 58.2 + - - +
242A ILE* 3.9 19.7 - - + -
245A LEU* 4.1 4.5 - - - +
246A TYR* 2.8 29.6 + - + -
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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