Contacts of the helix formed by residues 106 - 118 (chain B) in PDB entry 4YVF
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 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B ILE* 4.2 4.0 - - - -
104B GLY 4.9 2.5 - - - +
105B GLU* 1.3 78.4 - - - +
107B ASP* 1.3 60.6 + - - +
108B GLU* 3.2 10.8 + - - +
109B GLU* 2.8 47.2 + - + +
110B TYR* 2.8 28.6 + - - +
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Residues in contact with ASP 107 (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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81B ILE* 4.8 12.8 - - - +
106B THR* 1.3 76.7 - - - +
108B GLU* 1.3 66.3 + - + +
110B TYR* 3.5 8.1 + - - +
111B LEU* 3.2 22.9 + - - +
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Residues in contact with GLU 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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106B THR* 3.2 8.3 + - - +
107B ASP* 1.3 79.0 - - + +
109B GLU* 1.3 60.1 + - + +
111B LEU* 3.5 8.9 + - - +
112B TRP* 2.9 28.2 + - - +
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Residues in contact with GLU 109 (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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8B LYS* 5.7 0.9 + - - -
102B TRP* 3.5 34.8 + - + -
104B GLY 4.1 1.7 - - - +
105B GLU* 3.3 11.7 - - + -
106B THR* 2.8 53.8 + - + +
108B GLU* 1.3 75.9 - - + +
110B TYR* 1.3 55.6 + - - +
112B TRP* 3.0 9.1 + - + +
113B CYS* 2.7 41.6 + - - -
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Residues in contact with TYR 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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53B CYS* 3.7 5.4 - - - -
78B SER 3.1 22.2 - - - -
79B CYS* 3.0 35.4 + - - -
80B ASN* 3.4 4.7 - - - -
81B ILE* 3.6 22.2 - - + -
105B GLU* 3.4 21.5 + - - -
106B THR 2.8 17.6 + - - +
107B ASP* 3.6 7.9 - - - +
109B GLU* 1.3 75.4 - - - +
111B LEU* 1.3 69.4 + - + +
113B CYS* 3.1 14.4 + - + +
114B ILE* 3.3 34.4 + - + +
134B ASP* 2.5 33.4 + - - -
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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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107B ASP 3.2 14.1 + - - +
108B GLU* 3.7 7.6 - - - +
110B TYR* 1.3 86.7 - - + +
112B TRP* 1.3 63.2 + - - +
114B ILE* 3.3 11.4 + - + +
115B GLU* 3.1 36.7 + - - +
138B LEU* 3.5 32.5 - - + -
142B LYS* 5.1 10.3 - - + +
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Residues in contact with TRP 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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5B LEU* 4.2 18.2 - - + -
8B LYS* 3.4 36.8 - - + -
100B TYR* 4.0 17.5 - + - -
102B TRP* 4.4 4.5 - + - -
108B GLU 2.9 19.5 + - - +
109B GLU* 3.0 10.5 + - + +
111B LEU* 1.3 76.9 - - - +
113B CYS* 1.3 80.4 + - - +
115B GLU* 3.3 14.2 + - - -
116B GLN* 3.0 73.8 + - + +
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Residues in contact with CYS 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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77B SER* 3.7 6.8 - - - -
78B SER 5.5 0.7 - - - +
100B TYR* 3.2 34.7 - - - +
102B TRP* 3.6 31.4 - - - -
105B GLU* 3.7 15.0 - - - +
109B GLU 2.7 24.6 + - - -
110B TYR* 3.1 9.8 + - + +
112B TRP* 1.3 81.4 - - - +
114B ILE* 1.3 65.0 + - - +
116B GLN* 3.2 12.5 + - - +
117B THR* 3.3 15.6 - - - +
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Residues in contact with ILE 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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53B CYS* 3.9 12.1 - - + -
77B SER* 3.6 22.7 - - - +
78B SER 4.7 0.9 - - - +
110B TYR* 3.3 47.7 + - + +
111B LEU* 3.3 9.6 + - + +
113B CYS* 1.3 76.7 - - - +
115B GLU* 1.3 61.4 + - - +
117B THR* 2.6 23.4 + - - +
118B LEU* 3.3 6.2 - - - +
134B ASP* 4.2 12.3 - - + -
135B LEU* 3.5 31.2 - - + +
138B LEU* 3.4 25.4 - - + -
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Residues in contact with GLU 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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4B LYS* 5.2 0.3 + - - -
111B LEU* 3.1 27.3 + - - +
112B TRP* 3.5 20.2 + - - +
113B CYS 3.2 0.2 - - - -
114B ILE* 1.3 77.9 - - - +
116B GLN* 1.3 65.2 + - - +
117B THR 3.0 4.8 + - - -
118B LEU* 3.3 24.3 + - - +
119B TYR* 4.4 8.3 + - - -
138B LEU* 3.9 13.9 - - + -
142B LYS* 2.8 30.0 + - - +
143B TYR* 2.5 29.1 + - - +
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Residues in contact with GLN 116 (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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4B LYS* 2.9 49.1 + - - +
5B LEU 5.5 0.5 + - - -
75B GLN* 3.6 1.7 + - - -
100B TYR* 3.4 36.4 - - + -
112B TRP* 3.0 77.5 + - + +
113B CYS 3.2 2.2 + - - +
115B GLU* 1.3 83.2 + - - +
117B THR* 1.3 59.0 + - - +
118B LEU 3.6 0.2 - - - -
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Residues in contact with THR 117 (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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51B ALA* 3.7 13.6 - - - +
52B GLY 4.9 1.9 + - - +
75B GLN* 2.7 37.7 + - - +
76B TRP 3.2 40.4 - - - +
77B SER* 3.9 5.4 + - - +
100B TYR* 3.9 4.7 - - + -
113B CYS 3.3 15.7 - - - +
114B ILE* 2.6 21.1 + - - +
115B GLU 3.0 0.2 - - - -
116B GLN* 1.3 79.9 - - - +
118B LEU* 1.3 65.5 + - - +
119B TYR 3.3 0.4 - - - -
120B PHE* 3.4 11.6 - - - -
135B LEU* 4.5 2.1 - - - +
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Residues in contact with LEU 118 (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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114B ILE* 3.3 17.0 - - + +
115B GLU* 3.3 17.4 + - - +
117B THR* 1.3 80.0 - - - +
119B TYR* 1.3 69.0 + - + +
120B PHE 4.2 0.2 - - - -
124B PRO* 3.4 4.2 - - - +
125B LEU* 2.9 37.7 + - + +
135B LEU* 3.6 27.4 - - + -
138B LEU* 4.4 4.0 - - + -
139B ILE* 4.2 14.4 - - + -
143B TYR* 3.5 54.3 - - + +
146B LEU* 4.2 9.0 - - + -
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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