Contacts of the strand formed by residues 110 - 115 (chain A) in PDB entry 3C33
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 ILE 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLY* 1.3 72.4 - - - -
111A SER* 1.3 73.2 + - - +
142A THR* 3.7 37.0 - - + +
145A PHE* 3.7 33.0 - - + -
146A PHE* 4.2 1.1 - - + -
188A LEU* 4.0 15.0 - - + -
189A MET 3.7 6.3 - - - +
190A GLU* 4.5 2.5 - - + +
210A LEU* 3.4 1.0 - - - -
211A ILE* 2.9 48.6 + - + +
212A ASP* 2.7 18.1 + - - +
214A LYS* 3.3 28.5 - - - +
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Residues in contact with SER 111 (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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109A GLY 3.6 0.2 + - - -
110A ILE* 1.3 74.6 - - - +
112A ILE* 1.3 72.4 + - - +
188A LEU* 3.4 10.1 - - - +
189A MET 2.9 30.0 + - - -
191A SER* 4.5 2.2 - - - -
194A ILE* 3.6 15.3 - - - -
206A GLN* 3.0 28.8 - - - +
207A ILE 3.3 4.9 + - - -
209A GLY 2.8 24.3 + - - -
210A LEU* 4.5 6.3 - - - -
211A ILE* 5.1 3.8 - - - +
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Residues in contact with ILE 112 (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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111A SER* 1.3 87.3 + - - +
113A LEU* 1.3 69.5 + - - +
114A TYR* 4.2 0.9 - - + -
120A ILE* 5.7 1.1 - - + -
122A SER 3.9 4.3 - - - -
123A ALA* 3.6 39.5 - - + +
126A LEU* 3.8 15.3 - - + -
186A ALA* 4.0 19.7 - - + -
187A LEU 3.5 5.2 - - - +
188A LEU* 3.7 17.3 - - + -
194A ILE* 3.7 4.5 - - - +
206A GLN* 3.3 7.3 - - - -
207A ILE* 2.8 63.8 + - + +
211A ILE* 5.9 3.8 - - + -
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Residues in contact with LEU 113 (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 ILE* 1.3 71.6 - - - +
114A TYR* 1.3 66.1 + - - +
177A ILE* 4.1 26.7 - - + -
180A VAL* 3.9 19.5 - - + +
186A ALA* 3.5 3.3 - - - +
187A LEU* 2.7 46.2 + - + +
189A MET* 4.2 11.7 - - - -
194A ILE* 3.9 20.7 - - + +
197A VAL* 4.1 15.9 - - + -
198A THR* 3.9 28.0 - - + -
204A LEU* 4.0 21.1 - - + -
205A THR 3.7 4.3 - - - +
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Residues in contact with TYR 114 (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 ILE* 4.0 4.9 + - + -
113A LEU* 1.3 75.1 - - - +
115A ARG* 1.3 100.3 + - - +
118A THR* 3.4 32.4 - - + +
120A ILE* 3.7 23.5 - - + +
126A LEU* 5.6 0.4 - - + -
132A ILE* 3.5 29.6 - - + +
180A VAL* 3.9 11.7 - - + -
184A ASP* 2.7 22.1 + - - -
185A TYR 3.3 23.1 - - - -
186A ALA* 3.7 11.0 - - + -
204A LEU* 3.3 6.1 - - - +
205A THR* 2.9 31.6 + - - +
207A ILE* 3.5 20.2 - - + -
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Residues in contact with ARG 115 (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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114A TYR* 1.3 114.2 + - - +
116A LYS* 1.3 69.3 + - - +
117A GLY 3.8 0.3 + - - -
118A THR* 3.5 35.2 + - + +
180A VAL* 4.3 8.5 + - + +
183A THR 4.0 6.8 + - - -
184A ASP* 2.2 49.9 + - - +
203A ASN* 3.6 11.2 - - + +
204A LEU* 4.1 9.4 - - + +
205A THR* 3.7 7.5 - - - +
207A ILE* 4.2 2.8 - - - +
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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