Contacts of the helix formed by residues 106 - 121 (chain B) in PDB entry 5D0Y
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 GLN 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B PRO* 3.0 36.7 + - + +
105B ILE* 1.3 77.0 - - - +
107B ILE* 1.3 65.3 + - + +
108B TRP* 3.4 33.8 + - + +
109B ARG* 3.8 28.0 + - + +
110B VAL* 3.1 28.8 + - - +
161B TRP* 6.5 0.4 - - - -
164B LEU* 5.3 0.6 - - - +
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Residues in contact with ILE 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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106B GLN* 1.3 74.1 - - + +
108B TRP* 1.3 84.2 + - + +
109B ARG 3.3 0.2 - - - -
110B VAL* 3.4 8.2 + - + +
111B ILE* 3.0 42.8 + - + +
161B TRP* 4.3 35.7 - - + -
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Residues in contact with TRP 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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99B PHE* 4.7 10.3 - + - -
106B GLN* 3.4 37.3 + - - +
107B ILE* 1.3 91.6 - - + +
109B ARG* 1.3 104.0 + - + +
111B ILE* 3.9 6.2 - - - +
112B ALA* 2.9 39.7 + - + +
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Residues in contact with ARG 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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98B PHE 5.4 0.6 + - - -
99B PHE* 3.4 30.1 + - + +
100B LEU* 4.9 13.5 - - + +
103B LYS* 3.2 49.2 - - - +
104B PRO* 4.5 10.0 + - - +
106B GLN* 3.8 31.0 + - + +
107B ILE 3.3 0.4 - - - -
108B TRP* 1.3 119.9 - - + +
110B VAL* 1.3 55.5 + - - +
112B ALA* 3.8 2.6 - - - +
113B SER* 2.7 38.8 + - - -
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Residues in contact with VAL 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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100B LEU* 4.6 10.3 - - + -
105B ILE* 6.3 0.2 - - + -
106B GLN 3.1 18.2 - - - +
107B ILE* 3.4 10.7 + - + +
108B TRP 3.3 0.4 - - - -
109B ARG* 1.3 75.4 - - - +
111B ILE* 1.3 64.2 + - + +
113B SER* 3.1 16.5 + - - -
114B VAL* 3.1 14.2 + - - +
157B MET* 3.3 39.0 - - + +
160B VAL* 3.5 25.4 - - + -
161B TRP* 4.5 14.8 - - + +
164B LEU* 4.9 6.5 - - + -
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Residues in contact with ILE 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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111A ILE* 4.5 7.2 - - + -
115A ILE* 3.9 35.9 - - + -
107B ILE* 3.0 32.4 + - + +
108B TRP* 4.0 5.2 - - - +
110B VAL* 1.3 76.6 - - + +
112B ALA* 1.3 65.4 + - - +
115B ILE* 3.0 47.6 + - + +
157B MET* 3.8 26.1 - - + +
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Residues in contact with ALA 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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99B PHE* 3.6 22.9 - - + -
108B TRP* 2.9 33.8 + - + +
109B ARG 3.8 1.6 - - - +
111B ILE* 1.3 80.1 - - - +
113B SER* 1.3 64.5 + - - +
115B ILE* 3.5 5.5 - - - +
116B CYS* 2.9 32.4 + - - -
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Residues in contact with SER 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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95B ILE* 5.0 0.2 - - - -
96B TYR* 3.8 25.2 - - - -
99B PHE* 3.7 33.1 - - - -
100B LEU* 3.9 7.2 - - - +
109B ARG 2.7 23.8 + - - -
110B VAL* 3.1 11.3 + - - -
112B ALA* 1.3 71.6 - - - +
114B VAL* 1.3 72.0 + - - +
116B CYS* 2.9 14.0 + - - +
117B VAL* 2.9 19.1 + - - +
160B VAL* 5.1 0.7 - - - +
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Residues in contact with VAL 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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96B TYR* 4.0 15.9 - - + +
110B VAL* 3.1 19.0 + - + +
113B SER* 1.3 83.8 + - - +
115B ILE* 1.3 56.8 + - - +
117B VAL* 3.9 0.6 - - - +
118B THR* 2.6 46.0 + - - +
153B PRO* 3.6 30.3 - - + +
156B HIS* 3.6 14.6 - - + +
157B MET* 3.7 20.2 - - + +
160B VAL* 4.0 27.1 - - + -
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Residues in contact with ILE 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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111A ILE* 3.9 33.0 - - + -
115A ILE* 5.6 1.3 - - + -
154A TRP* 4.0 27.6 - - + -
111B ILE* 3.0 39.1 + - + +
112B ALA* 3.5 6.5 - - - +
114B VAL* 1.3 77.7 - - - +
116B CYS* 1.3 65.1 + - - +
118B THR* 4.2 3.2 - - - -
119B VAL* 3.1 33.8 + - + +
153B PRO* 5.9 0.7 - - - -
157B MET* 3.8 14.8 - - + -
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Residues in contact with CYS 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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95B ILE* 4.1 7.2 - - + -
99B PHE* 3.5 31.4 - - + -
112B ALA* 2.9 26.4 + - - +
113B SER 2.9 5.1 + - - +
115B ILE* 1.3 80.8 - - - +
117B VAL* 1.3 66.9 + - - +
119B VAL* 3.9 2.9 - - - +
120B ILE* 3.0 41.9 + - + +
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Residues in contact with VAL 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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92B GLU* 4.2 10.5 - - + +
95B ILE* 3.8 28.7 - - + +
96B TYR* 3.4 42.2 - - + +
113B SER 2.9 16.9 + - - +
114B VAL 3.9 3.8 - - - +
116B CYS* 1.3 75.1 - - - +
118B THR* 1.3 65.5 + - - +
121B CYS* 2.9 34.3 + - + +
122B TYR* 3.4 33.7 + - + +
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Residues in contact with THR 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 VAL* 2.6 34.2 + - - +
115B ILE* 4.2 4.9 - - - -
116B CYS 3.2 0.2 - - - -
117B VAL* 1.3 75.8 - - - +
119B VAL* 1.3 59.0 + - + +
122B TYR* 3.3 29.1 - - + +
123B ILE* 2.7 33.9 + - + +
149B GLU* 3.7 36.3 - - + +
152B THR* 5.5 0.9 - - - +
153B PRO* 4.1 12.7 - - + +
156B HIS* 4.7 1.9 + - - -
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Residues in contact with VAL 119 (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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115B ILE* 3.1 26.5 + - + +
116B CYS* 3.9 4.0 - - - +
117B VAL 3.2 0.8 - - - -
118B THR* 1.3 79.6 - - + +
120B ILE* 1.3 63.3 + - + +
123B ILE* 3.3 21.3 - - + +
124B GLY* 2.7 31.0 + - - -
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Residues in contact with ILE 120 (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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91B LEU* 5.2 6.1 - - + -
95B ILE* 4.1 22.0 - - + -
116B CYS* 3.0 25.1 + - + +
119B VAL* 1.3 85.9 - - + +
121B CYS* 1.3 56.2 + - - +
124B GLY* 3.2 6.0 - - - -
125B LEU* 2.8 43.5 + - + +
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Residues in contact with CYS 121 (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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88B THR* 3.9 17.5 - - + -
91B LEU* 3.9 19.3 - - - -
92B GLU* 3.5 36.3 - - + -
95B ILE* 4.3 11.7 - - - -
117B VAL* 2.9 22.6 + - + +
120B ILE* 1.3 73.9 - - - +
122B TYR* 1.3 68.7 + - + +
125B LEU* 3.2 10.2 + - - +
126B ASN* 2.8 32.9 + - - +
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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