Contacts of the strand formed by residues 109 - 114 (chain F) in PDB entry 6GJH
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 LEU 109 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F VAL* 3.8 29.2 - - + -
104F PHE* 3.9 19.7 - - + -
105F ALA 3.8 13.7 - - - +
106F PRO* 3.4 14.8 + - + +
107F ASP 3.4 3.0 - - - +
108F GLU* 1.3 81.4 - - - +
110F THR* 1.3 66.7 + - - +
111F VAL* 5.6 1.8 - - + -
120F ILE* 4.9 5.6 - - + -
121F THR 3.4 12.1 - - - +
122F GLY* 4.0 10.1 - - - -
138F PHE* 4.1 17.3 - - + -
157F LEU* 4.2 19.3 - - + -
163F LEU* 4.8 17.5 - - + -
130H GLU 4.5 4.2 - - - +
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Residues in contact with THR 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LEU* 1.3 77.6 + - - +
111F VAL* 1.3 67.4 + - - +
112F LYS* 4.0 27.6 - - + +
119F GLU 3.6 0.9 - - - +
120F ILE* 3.3 6.1 - - - +
121F THR* 2.9 48.2 + - + +
129H ASP 4.8 0.2 - - - +
130H GLU* 3.5 38.9 + - + +
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Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LEU* 5.6 2.2 - - + -
110F THR* 1.3 82.4 - - - +
112F LYS* 1.3 67.6 + - - +
113F THR* 5.0 0.2 - - - +
118F VAL* 4.0 24.9 - - + -
119F GLU 3.4 3.1 - - - +
120F ILE* 4.1 15.7 - - + -
153F VAL* 4.8 8.1 - - + -
155F SER* 3.8 35.2 - - - +
163F LEU* 4.1 17.7 - - + -
165F VAL* 4.5 9.4 - - + -
128H GLN* 4.3 4.7 - - - +
129H ASP 5.5 1.2 - - - +
130H GLU 5.3 0.2 + - - -
131H HIS 6.1 0.5 - - - -
132H GLY* 5.8 4.3 + - - -
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Residues in contact with LYS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F THR* 4.0 18.6 - - + -
111F VAL* 1.3 78.5 - - - +
113F THR* 1.3 62.6 + - - +
114F LYS* 5.7 2.5 - - + -
117F VAL 3.9 0.2 - - - +
118F VAL* 3.5 4.2 - - - +
119F GLU* 2.8 51.0 + - + +
128H GLN* 3.8 32.6 + - + +
129H ASP* 3.6 32.4 - - - +
130H GLU* 4.3 2.0 - - - +
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Residues in contact with THR 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F VAL* 5.0 1.0 - - - +
112F LYS* 1.3 77.8 + - - +
114F LYS* 1.3 66.6 + - - +
116F GLY* 5.2 2.7 - - - +
117F VAL 3.4 9.9 - - - +
118F VAL* 4.0 9.8 - - + +
144F LEU* 3.7 29.6 - - + -
150F PRO* 3.8 38.0 - - + +
153F VAL* 3.8 22.5 - - + +
128H GLN* 3.0 29.9 + - - -
133H TYR* 4.5 0.2 + - - -
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F LYS* 5.7 2.7 - - + -
113F THR* 1.3 77.1 - - - +
115F ASP* 1.3 85.2 + - - +
116F GLY 3.3 1.6 - - - -
117F VAL* 3.0 24.8 + - - +
150F PRO* 5.8 1.1 - - - -
128H GLN* 5.6 2.2 - - - +
76L ALA* 5.2 13.7 - - - +
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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