Contacts of the strand formed by residues 109 - 115 (chain A) in PDB entry 7B8E
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 THR 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PRO* 3.3 37.5 - - + -
108A SER* 1.3 74.5 - - - +
110A THR* 1.3 73.5 + - - +
111A VAL* 3.8 0.9 - - - +
140A GLU* 3.0 25.2 + - - +
142A VAL* 3.8 15.7 - - + +
188A GLY 3.1 7.0 + - - +
190A ASP* 2.9 28.7 + - - +
478A LYS* 5.3 4.4 - - - +
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Residues in contact with THR 110 (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 THR* 1.3 81.1 + - - +
111A VAL* 1.3 64.8 + - - +
112A MET* 5.2 0.9 - - + -
141A VAL* 3.4 20.1 - - - +
142A VAL* 2.9 24.6 + - - -
193A THR* 3.3 33.8 - - + +
474A ALA 5.5 0.7 - - - -
477A ALA* 3.5 32.5 - - + +
478A LYS* 3.1 34.0 - - - +
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Residues in contact with VAL 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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110A THR* 1.3 77.8 - - - +
112A MET* 1.3 67.8 + - - +
113A VAL* 4.1 13.5 - - + -
142A VAL* 3.3 14.1 - - + +
144A VAL* 4.1 20.0 - - + -
180A VAL* 4.3 7.6 - - + -
184A ILE* 3.8 18.4 - - + -
189A GLY* 3.7 29.2 - - - -
190A ASP 3.7 15.0 - - - +
193A THR 3.2 12.4 + - - +
194A VAL* 4.1 8.1 - - + -
195A THR* 2.9 25.5 + - - -
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Residues in contact with MET 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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110A THR* 4.3 0.6 - - + -
111A VAL* 1.3 77.3 - - - +
113A VAL* 1.3 57.2 + - - +
135A LEU* 4.7 8.7 - - + -
141A VAL* 4.2 22.0 - - + -
142A VAL 3.0 7.2 + - - +
143A LEU* 3.5 22.1 - - + +
144A VAL* 2.7 34.5 + - - +
195A THR* 3.3 7.6 - - + +
197A PHE* 4.0 24.2 - - + -
223A ILE* 4.2 13.0 - - + -
473A TRP* 3.8 33.7 - - + +
474A ALA* 4.3 13.0 - - - -
477A ALA* 3.9 22.0 - - + -
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Residues in contact with VAL 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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111A VAL* 4.1 7.2 - - + -
112A MET* 1.3 76.2 - - - +
114A TRP* 1.3 62.3 + - - +
115A ILE* 4.3 2.1 - - + +
144A VAL* 3.2 28.7 - - + +
146A LEU* 3.9 32.1 - - + -
177A LEU* 4.0 17.3 - - + -
180A VAL* 4.5 11.0 - - + -
194A VAL* 3.8 25.1 - - + -
195A THR 2.9 11.5 + - - +
196A ILE* 3.4 6.3 - - + +
197A PHE* 2.8 31.0 + - - +
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Residues in contact with TRP 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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113A VAL* 1.3 72.3 - - - +
115A ILE* 1.3 67.0 + - - +
116A TYR* 3.7 16.1 + + + +
117A GLY 5.1 0.2 - - - -
125A SER* 5.7 0.7 - - - -
130A TYR* 3.4 58.2 - + + -
143A LEU* 5.1 1.3 - - + -
144A VAL 2.7 15.3 + - - +
145A SER* 3.7 14.3 - - - -
146A LEU* 3.2 28.6 + - - +
197A PHE* 3.3 54.7 - + + -
198A GLY* 3.6 14.8 - - - -
199A GLU* 3.6 30.1 - - + -
225A GLN* 3.9 13.7 - - - -
444A ILE* 4.1 11.0 - - + -
448A PHE* 3.5 24.5 - + + -
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Residues in contact with ILE 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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113A VAL* 4.3 6.1 - - + +
114A TRP* 1.3 79.7 - - - +
116A TYR* 1.3 70.2 + - - +
146A LEU* 4.1 24.7 - - + -
148A TYR* 3.8 10.5 - - + -
173A GLN* 3.7 39.9 - - + +
177A LEU* 5.2 2.0 - - + -
196A ILE* 4.8 9.9 - - + -
197A PHE 2.7 17.1 + - - +
198A GLY* 3.1 19.4 - - - -
199A GLU 3.7 1.7 + - - -
202A GLY* 3.4 9.8 - - - +
205A SER* 4.1 10.3 - - - -
206A VAL* 4.3 15.3 - - + -
209A HIS* 4.3 15.7 - - + +
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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