Contacts of the strand formed by residues 109 - 114 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 3.8 28.5 - - + -
104B PHE* 3.9 19.7 - - + -
105B ALA 3.7 15.0 - - - +
106B PRO* 3.4 13.9 + - + +
107B ASP 3.4 2.6 + - - +
108B GLU* 1.3 79.1 - - - +
110B THR* 1.3 71.5 + - - +
111B VAL* 5.9 0.9 - - + -
120B ILE* 5.0 1.3 - - + -
121B THR 3.3 11.0 - - - +
122B GLY* 4.0 10.1 - - - -
138B PHE* 4.2 15.9 - - + -
157B LEU* 4.0 19.7 - - + -
163B LEU* 4.8 21.1 - - + -
130D GLU 4.5 1.7 - - - +
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP 5.9 1.8 - - - +
108B GLU 5.5 1.3 - - - -
109B LEU* 1.3 80.8 - - - +
111B VAL* 1.3 64.7 + - - +
112B LYS* 4.3 10.0 - - - +
119B GLU 3.6 1.4 - - - +
120B ILE* 3.4 5.7 - - - +
121B THR* 3.0 50.3 + - - +
130D GLU* 3.3 41.7 - - + +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 5.7 1.1 - - + -
110B THR* 1.3 79.2 - - - +
112B LYS* 1.3 70.9 + - - +
113B THR* 5.1 0.4 - - - +
118B VAL* 3.9 25.1 - - + -
119B GLU 3.5 3.6 - - - +
120B ILE* 4.2 14.1 - - + -
153B VAL* 4.8 8.1 - - + -
155B SER* 4.0 29.2 - - - +
163B LEU* 4.2 17.7 - - + -
165B VAL* 4.4 15.3 - - + -
128D GLN* 4.1 5.0 - - - +
129D ASP 5.3 1.4 - - - +
130D GLU 5.1 1.7 + - - +
131D HIS 6.1 0.7 - - - -
132D GLY* 5.8 4.0 + - - -
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 5.1 10.5 - - - +
111B VAL* 1.3 83.2 - - - +
113B THR* 1.3 62.8 + - - +
114B LYS* 4.2 2.2 + - + -
117B VAL 3.7 0.9 - - - +
118B VAL* 3.6 1.0 - - - +
119B GLU* 2.8 47.7 + - + +
128D GLN* 3.6 43.4 + - + +
129D ASP* 4.2 21.7 - - - +
130D GLU* 5.3 1.3 - - - -
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 5.1 0.9 - - - +
112B LYS* 1.3 76.0 + - - +
114B LYS* 1.3 67.2 + - - +
116B GLY* 5.1 3.1 - - - +
117B VAL 3.4 9.6 - - - +
118B VAL* 3.8 12.0 - - - +
144B LEU* 3.8 28.3 - - + -
150B PRO* 3.6 35.1 - - + +
153B VAL* 3.7 22.5 - - + +
128D GLN* 2.9 28.9 + - - -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 4.2 2.6 + - + -
113B THR* 1.3 77.6 - - - +
115B ASP* 1.3 104.3 + - - +
116B GLY 3.2 2.0 - - - -
117B VAL* 3.1 24.0 + - - +
150B PRO* 6.0 0.7 - - - -
128D GLN* 5.3 2.5 - - - +
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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