Contacts of the strand formed by residues 196 - 203 (chain A) in PDB entry 3QIC
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 GLU 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LYS 4.6 3.0 + - - -
141A HIS 6.1 0.4 - - - +
142A LYS 3.7 2.5 + - - +
143A LYS* 3.4 52.7 + - + +
189A ILE* 4.9 1.8 - - - -
193A GLY 5.2 4.8 - - - +
195A PHE* 1.3 82.6 - - - +
197A MET* 1.3 82.2 + - - +
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Residues in contact with MET 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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75A LEU* 3.5 33.2 - - + -
134A LEU* 3.9 29.4 - - + -
139A MET 5.2 0.7 - - - +
142A LYS* 4.2 12.3 - - + +
143A LYS* 4.1 4.4 - - - +
144A LEU* 3.6 32.3 - - + +
146A LEU* 4.2 23.1 - - + -
186A ARG* 4.8 4.5 + - - +
189A ILE* 4.4 15.6 - - + +
195A PHE* 3.8 17.5 - - + -
196A GLU* 1.3 87.9 - - - +
198A ASP* 1.3 66.1 + - - +
199A VAL* 3.7 8.1 + - + +
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Residues in contact with ASP 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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143A LYS* 3.2 32.9 + - - +
144A LEU 3.0 15.7 + - - +
145A PRO* 3.5 4.9 - - + +
146A LEU* 3.0 21.4 + - - -
186A ARG* 4.5 4.9 - - - +
197A MET* 1.3 72.6 - - - +
199A VAL* 1.3 65.0 + - - +
200A VAL* 3.1 18.2 + - + +
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Residues in contact with VAL 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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146A LEU* 3.7 27.8 - - + -
148A PHE* 4.9 2.2 - - + -
160A ASP* 4.7 2.9 - - + +
182A VAL* 3.6 27.6 - - + +
185A LEU* 4.0 25.1 - - + -
186A ARG* 3.1 52.7 + - + +
189A ILE* 4.8 9.0 - - + -
197A MET 3.7 6.0 + - - +
198A ASP* 1.3 67.3 - - - +
200A VAL* 1.3 63.7 + - - +
201A ALA 4.3 12.8 - - - +
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Residues in contact with VAL 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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145A PRO* 4.2 3.6 - - + -
146A LEU 3.1 15.6 + - - +
159A ILE* 4.1 2.8 - - - +
160A ASP* 3.2 22.0 - - - +
198A ASP* 3.2 25.8 - - + +
199A VAL* 1.3 76.8 - - - +
201A ALA* 1.3 61.3 + - - +
453A SER* 3.6 34.1 - - - +
456A ALA* 3.7 20.5 - - + +
457A CYS* 4.1 21.5 - - - -
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Residues in contact with ALA 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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146A LEU 3.7 2.1 + - - +
147A GLY* 3.8 2.4 - - - -
148A PHE* 3.0 25.5 + - - +
159A ILE* 3.7 9.4 - - + +
160A ASP* 4.3 2.6 - - - +
182A VAL* 5.4 0.2 - - - -
199A VAL* 3.7 6.5 - - - +
200A VAL* 1.3 84.9 - - - +
202A MET* 1.3 64.2 + - - +
203A VAL* 5.4 1.3 - - + -
449A ALA 4.8 0.9 - - - +
452A VAL* 3.6 30.5 - - + +
453A SER* 3.9 21.5 - - - +
456A ALA* 4.7 0.9 - - + -
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Residues in contact with MET 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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148A PHE* 3.2 20.0 - - + +
150A PHE* 3.9 20.9 - - + +
154A VAL* 3.5 36.6 - - + -
156A HIS* 3.2 31.1 - - + +
159A ILE* 3.0 16.9 + - - +
160A ASP* 5.2 0.4 - - - -
161A LYS 4.7 0.2 - - - -
162A GLY* 3.7 24.0 - - - +
181A VAL* 3.8 27.6 - - + -
182A VAL* 4.1 19.3 - - + -
201A ALA* 1.3 77.4 - - - +
203A VAL* 1.3 72.1 + - - +
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Residues in contact with VAL 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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60A THR* 6.4 0.4 - - - -
62A VAL* 4.6 0.9 - - + -
148A PHE 3.0 6.2 + - - +
149A THR* 3.3 20.6 - - - +
150A PHE 2.9 27.9 + - - +
156A HIS* 4.8 3.8 - - - -
159A ILE* 4.2 8.7 - - + -
201A ALA* 5.4 1.3 - - + -
202A MET* 1.3 83.9 - - - +
204A ASN* 1.3 69.6 + - - +
207A VAL* 4.3 16.8 - - + -
208A ALA* 4.0 11.2 - - + -
448A GLY 5.3 0.2 - - - -
449A ALA* 4.2 13.5 - - + -
452A VAL* 4.1 33.2 - - + -
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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