Contacts of the strand formed by residues 109 - 114 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D VAL* 3.8 26.9 - - + -
104D PHE* 3.9 22.0 - - + -
105D ALA 3.7 15.0 - - - +
106D PRO* 3.3 15.3 + - + +
107D ASP 3.5 2.3 - - - -
108D GLU* 1.3 80.0 - - - +
110D THR* 1.3 69.9 + - - +
111D VAL* 5.6 1.1 - - + -
120D ILE* 5.1 1.6 - - + -
121D THR 3.4 4.0 - - - +
122D GLY* 4.0 16.4 - - - -
138D PHE* 4.3 14.6 - - + -
157D LEU* 3.9 21.3 - - + -
163D LEU* 4.5 23.8 - - + -
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP 5.7 2.2 - - - +
108D GLU 5.2 1.8 - - - -
109D LEU* 1.3 81.9 - - - +
111D VAL* 1.3 64.9 + - - +
112D LYS* 4.3 12.4 - - - +
119D GLU 3.6 1.2 + - - +
120D ILE* 3.4 6.2 - - - +
121D THR* 2.7 53.7 + - - +
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 5.6 1.1 - - + -
110D THR* 1.3 79.6 - - - +
112D LYS* 1.3 70.7 + - - +
113D THR* 5.5 0.4 - - - +
118D VAL* 3.8 26.5 - - + -
119D GLU 3.4 3.6 - - - +
120D ILE* 4.2 19.5 - - + -
153D VAL* 4.9 7.0 - - + -
155D SER* 3.4 36.8 - - - +
163D LEU* 4.3 11.9 - - + -
165D VAL* 4.3 7.0 - - + -
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D THR* 5.0 12.3 - - - +
111D VAL* 1.3 84.7 - - - +
113D THR* 1.3 65.0 + - - +
114D LYS* 5.6 1.1 - - + -
117D VAL 3.8 0.7 - - - +
118D VAL* 3.5 1.7 - - - -
119D GLU* 2.8 52.5 + - + +
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Residues in contact with THR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D VAL* 5.5 0.7 - - - +
112D LYS* 1.3 76.3 - - - +
114D LYS* 1.3 69.9 + - - +
116D GLY 5.1 2.7 - - - +
117D VAL 3.3 11.0 - - - +
118D VAL* 3.8 13.7 - - - +
144D LEU* 3.6 26.7 - - + -
148D VAL 5.9 0.4 - - - +
150D PRO* 3.7 34.4 + - + +
153D VAL* 3.8 18.5 - - - +
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 5.6 1.3 - - + -
113D THR* 1.3 80.0 - - - +
115D ASP* 1.3 95.3 + - - +
116D GLY 3.2 2.2 - - - -
117D VAL* 2.9 25.4 + - - +
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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