Contacts of the strand formed by residues 196 - 205 (chain A) in PDB entry 1QF6
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 PHE 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A CYS* 4.4 11.9 - - + -
78A LEU* 3.7 11.0 - - + -
102A PHE* 5.1 3.4 - + + -
121A GLU* 3.5 8.4 - - + +
124A MET* 3.4 42.2 - - + -
125A HIS* 3.2 60.3 + + - -
128A ALA* 4.4 1.3 - - + -
193A CYS 3.3 28.5 - - - -
194A HIS 3.4 4.8 + - - -
195A HIS* 1.3 76.3 - - - +
197A LYS* 1.3 71.2 + - - +
198A LEU* 4.9 3.6 - - + -
221A THR 3.2 17.7 - - - +
222A ALA* 3.8 9.9 - - + +
229A LEU* 3.6 12.4 - - - +
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Residues in contact with LYS 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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121A GLU* 3.4 17.7 + - - +
196A PHE* 1.3 80.0 - - - +
198A LEU* 1.3 77.7 + - - +
199A MET* 3.6 23.9 + - - +
220A GLY* 3.3 0.2 - - - -
221A THR* 2.9 31.8 + - - +
229A LEU* 4.7 11.6 - - + +
233A LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 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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79A LEU* 4.5 6.1 - - + -
102A PHE* 4.2 14.4 - - + -
117A VAL* 3.9 28.9 - - + +
120A LEU* 3.4 33.0 - - + -
121A GLU* 2.8 34.5 + - + +
124A MET* 4.2 14.8 - - + -
196A PHE* 4.9 2.2 - - + -
197A LYS* 1.3 91.7 + - - +
199A MET* 1.3 62.1 + - - +
218A ILE* 4.0 13.0 - - + -
219A TYR 3.4 12.3 - - - +
220A GLY* 4.1 8.1 - - - -
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Residues in contact with MET 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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117A VAL* 4.6 10.2 - - - +
197A LYS* 3.7 25.8 - - - +
198A LEU* 1.3 84.6 - - - +
200A LYS* 1.3 76.1 + - + +
201A THR* 4.7 0.9 - - - +
219A TYR* 2.8 17.3 + - + +
220A GLY* 4.4 4.9 - - - -
221A THR* 3.6 25.6 - - - +
232A TYR* 4.6 2.2 - - + +
233A LEU* 3.5 26.7 - - + -
236A LEU* 3.8 22.4 - - + -
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Residues in contact with LYS 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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199A MET* 1.3 85.4 - - + +
201A THR* 1.3 75.1 + - - +
202A ALA* 6.2 0.4 - - + -
218A ILE* 4.5 0.5 - - - +
219A TYR* 3.1 57.8 + - + +
474A LEU* 6.3 0.4 - - - +
70B G 3.0 48.6 + - - +
71B G 3.2 19.6 + - - +
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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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112A LEU* 4.6 13.3 + - + -
117A VAL* 3.8 31.5 - - + +
199A MET 4.7 0.9 - - - +
200A LYS* 1.3 84.5 - - - +
202A ALA* 1.3 65.1 + - - +
216A GLN* 5.7 5.3 + - - -
217A ARG 3.2 12.1 - - - -
218A ILE* 4.0 21.5 - - + -
219A TYR* 4.6 1.8 - - - -
4B G 5.5 7.1 + - - +
70B G 3.7 11.4 + - - +
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Residues in contact with ALA 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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200A LYS* 6.2 0.7 - - + -
201A THR* 1.3 77.1 - - - +
203A GLY* 1.3 62.9 + - - +
216A GLN* 3.6 4.2 - - - +
217A ARG* 2.7 39.9 + - - +
219A TYR* 4.9 4.2 - - + -
3B C 3.9 4.0 - - - -
4B G 5.9 1.1 - - - -
70B G 3.2 22.9 - - + +
71B G 3.6 36.8 - - - +
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Residues in contact with GLY 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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202A ALA* 1.3 76.7 - - - +
204A ALA* 1.3 59.0 + - - +
214A MET* 3.5 24.5 - - - -
215A LEU 3.1 10.5 - - - -
216A GLN* 4.7 0.7 - - - -
3B C 3.2 22.0 + - - -
71B G 3.1 18.9 + - - +
72B C 3.2 11.8 - - - +
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Residues in contact with ALA 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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105A ASP* 4.1 9.7 - - - +
203A GLY* 1.3 75.3 - - - +
205A TYR* 1.3 63.8 + - - +
206A TRP 3.5 0.2 + - - -
214A MET* 3.4 4.1 - - - +
215A LEU* 2.7 38.8 + - - +
217A ARG* 3.6 43.7 - - + +
72B C 3.3 13.2 - - - +
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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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105A ASP* 5.1 4.0 - - - +
204A ALA* 1.3 77.7 - - - +
206A TRP* 1.3 65.5 + - - +
207A ARG 3.5 0.5 + - - -
208A GLY* 3.4 10.0 + - - -
209A ASP 3.3 31.4 - - - +
210A SER* 3.6 34.8 + - - -
212A ASN 3.8 13.5 - - - -
213A LYS 3.4 4.7 - - - -
214A MET* 3.7 17.5 - - + +
217A ARG* 5.3 1.6 + - - -
1B G 3.0 30.2 + - - -
2B C 3.1 26.9 + - - -
72B C 3.0 24.0 + - - +
73B A 3.3 29.8 - - - -
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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