Contacts of the helix formed by residues 107 - 115 (chain B) in PDB entry 5Y7G
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 GLU 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B THR 4.3 0.6 - - - +
106B LEU* 1.3 75.4 - - - +
108B LEU* 1.3 68.8 + - - +
109B ALA* 3.3 7.4 - - + +
110B GLN* 3.0 35.1 + - + +
111B LEU* 3.2 11.1 + - - +
147B PRO 3.8 15.2 - - - +
149B ALA* 3.4 27.7 + - + +
155B TRP* 4.6 0.2 - - - -
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Residues in contact with LEU 108 (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 GLU* 1.3 73.2 - - - +
109B ALA* 1.3 63.6 + - - +
111B LEU* 3.1 15.5 + - + +
112B PHE* 3.2 22.1 + - + -
124B PHE* 3.5 32.8 - - + -
139B LEU* 3.7 14.8 - - + -
142B LEU* 3.3 40.8 - - + +
143B GLN* 3.5 23.3 - - - +
146B PHE* 3.5 19.5 + - + +
147B PRO 5.0 1.4 + - - +
148B GLU 4.4 3.6 + - - -
155B TRP* 4.0 16.4 - - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 3.3 5.1 - - + +
108B LEU* 1.3 78.8 - - - +
110B GLN* 1.3 63.7 + - + +
112B PHE* 3.3 11.1 + - - +
113B GLY* 3.3 8.7 + - - -
139B LEU* 4.1 26.7 - - + -
143B GLN* 4.2 12.3 + - - +
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Residues in contact with GLN 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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72B THR* 5.8 2.6 - - - +
73B LEU* 3.9 19.4 - - + +
105B THR 3.7 6.0 + - - +
106B LEU* 3.2 23.8 - - + +
107B GLU* 3.0 42.8 + - + +
109B ALA* 1.3 78.4 - - + +
111B LEU* 1.3 58.2 + - - +
113B GLY* 3.0 17.1 + - - +
114B LEU* 3.1 18.4 + - - +
165B GLU* 5.8 1.6 + - - -
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Residues in contact with LEU 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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106B LEU* 4.3 23.0 - - + +
107B GLU 3.2 8.1 + - - +
108B LEU* 3.1 10.9 + - + +
110B GLN* 1.3 78.9 - - - +
112B PHE* 1.3 57.4 + - - +
114B LEU* 3.3 8.2 + - + +
115B LEU* 3.2 48.0 + - + +
120B LEU* 3.8 9.4 - - + +
123B LEU* 3.8 18.6 - - + -
124B PHE* 4.1 11.4 - - + -
152B LEU* 5.6 3.6 - - + -
155B TRP* 3.5 47.6 - - + -
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Residues in contact with PHE 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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108B LEU* 3.2 24.1 + - + -
109B ALA* 3.6 9.4 - - - +
110B GLN 3.2 0.6 - - - -
111B LEU* 1.3 73.2 - - - +
113B GLY* 1.3 61.3 + - - +
115B LEU 3.9 0.6 - - - +
120B LEU* 3.5 43.1 - - + -
124B PHE* 4.2 2.2 - + - -
135B LYS* 3.4 62.2 + - + -
138B LEU* 4.1 7.6 - - + -
139B LEU* 3.4 42.6 - - + -
142B LEU* 3.7 27.8 - - + -
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Residues in contact with GLY 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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109B ALA 3.3 6.3 + - - -
110B GLN* 3.0 9.0 + - - -
112B PHE* 1.3 80.6 - - - +
114B LEU* 1.3 64.9 + - - +
115B LEU 3.2 3.9 + - - +
135B LYS* 5.3 0.7 + - - -
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Residues in contact with LEU 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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73B LEU* 4.1 33.4 - - + +
74B PHE* 4.1 2.2 - - - +
75B ARG* 3.4 50.0 + - + +
78B LYS* 4.8 7.1 + - - -
106B LEU* 3.5 35.4 - - + -
110B GLN 3.1 16.4 + - - +
111B LEU* 3.3 9.1 + - + +
113B GLY* 1.3 78.8 - - - +
115B LEU* 1.3 67.1 + - + +
163B VAL* 3.9 17.0 - - + -
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Residues in contact with LEU 115 (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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75B ARG* 3.1 28.3 - - + +
111B LEU* 3.2 28.9 + - + +
112B PHE 3.9 4.0 - - - +
113B GLY 4.0 2.8 - - - +
114B LEU* 1.3 89.8 - - + +
116B LYS* 1.3 66.9 + - - +
119B GLU* 3.8 22.2 - - + +
120B LEU* 3.7 25.1 - - + +
123B LEU* 5.4 6.3 - - + -
135B LYS* 2.9 24.1 + - - -
156B GLN* 5.7 5.4 - - - +
159B PHE* 4.3 17.0 - - + -
163B VAL* 6.1 2.0 - - + -
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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