Contacts of the strand formed by residues 192 - 199 (chain A) in PDB entry 4QGC
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LYS* 4.1 29.2 - - - -
142A ILE 3.2 13.9 - - - +
143A THR* 4.5 3.1 - - - +
144A LEU* 5.5 0.7 - - - -
165A CYS* 3.5 5.3 - - - -
187A GLN* 5.3 3.8 - - + -
188A LYS 5.4 0.2 - - - -
189A GLY* 2.8 48.2 + - - +
190A ALA 4.3 1.8 - - - -
191A ASP* 1.3 103.0 - - - +
193A LEU* 1.3 80.7 + - - +
194A VAL* 3.9 19.7 - - + -
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Residues in contact with LEU 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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141A LYS* 3.3 4.9 - - - +
142A ILE* 2.6 53.3 + - + +
164A ILE* 4.1 32.8 - - + +
165A CYS* 4.2 15.7 - - - -
168A VAL* 4.0 21.1 - - + -
174A ILE* 4.2 14.1 - - + -
185A VAL* 4.1 8.7 - - + -
187A GLN 3.6 12.6 - - - +
188A LYS* 3.9 22.4 - - + -
192A PHE* 1.3 85.1 - - - +
194A VAL* 1.3 62.7 + - - +
195A THR* 4.0 8.3 - - + -
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Residues in contact with VAL 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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139A THR* 3.9 25.4 - - + +
140A LEU 3.8 2.5 - - - +
141A LYS* 4.5 9.2 - - + +
185A VAL* 3.7 0.9 - - - +
186A LYS* 2.7 36.5 + - + -
187A GLN* 3.0 47.2 + - + +
192A PHE* 3.9 22.2 - - + -
193A LEU* 1.3 75.9 - - - +
195A THR* 1.3 60.4 + - - +
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Residues in contact with THR 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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139A THR* 3.4 8.5 + - - +
140A LEU* 2.7 58.7 + - - +
142A ILE* 4.1 25.2 - - + +
174A ILE* 4.6 1.1 - - + -
183A LEU* 3.8 25.2 - - + +
184A GLN 3.3 9.0 - - - -
185A VAL* 4.1 22.0 - - + +
186A LYS* 4.2 4.3 - - - +
193A LEU* 4.5 4.9 - - + -
194A VAL* 1.3 79.9 - - - +
196A GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 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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137A GLY* 3.8 32.4 - - - +
138A ALA 3.5 4.7 - - - +
139A THR* 5.3 1.6 - - - +
183A LEU* 3.7 2.0 - - - -
184A GLN* 3.0 31.4 + - + +
186A LYS* 4.0 33.6 + - + +
195A THR* 1.3 75.1 - - - +
197A VAL* 1.3 70.0 + - - +
198A GLU* 3.2 10.9 + - + +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.2 22.4 - - + -
135A LYS 3.2 24.9 - - - +
136A LYS* 3.6 1.4 - - - -
137A GLY* 2.8 28.1 + - - -
138A ALA* 3.0 21.0 + - + +
139A THR 5.4 0.2 - - - -
140A LEU* 4.5 9.9 - - + -
181A ILE* 4.8 0.2 - - + -
182A SER 4.2 2.0 - - - +
183A LEU* 3.8 23.1 - - + -
196A GLU* 1.3 71.7 - - - +
198A GLU* 1.3 61.4 + - - +
199A ASN 3.5 29.6 - - - +
200A GLY* 3.7 9.9 - - - +
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Residues in contact with GLU 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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136A LYS* 3.4 28.5 - - - +
173A LYS* 3.3 32.4 + - - +
182A SER* 2.9 21.2 + - - +
183A LEU 4.6 0.4 - - - -
184A GLN* 2.9 36.8 + - + +
196A GLU* 3.2 16.1 + - + +
197A VAL* 1.3 72.8 - - - +
199A ASN* 1.3 69.3 + - - +
200A GLY 4.0 0.2 - - - -
339D ARG* 5.9 1.0 + - - -
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Residues in contact with ASN 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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136A LYS* 4.8 3.0 + - - +
175A TYR* 5.4 3.0 - - - -
180A LEU 4.4 9.8 - - - +
181A ILE* 3.4 24.8 - - - +
182A SER* 3.1 33.1 + - - +
197A VAL* 3.5 5.0 - - - +
198A GLU* 1.3 79.8 - - - +
200A GLY* 1.3 65.9 + - - +
337D LYS* 3.3 40.0 - - - +
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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