Contacts of the helix formed by residues 139 - 152 (chain B) in PDB entry 2UZ8
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 TYR 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B HIS* 2.6 48.0 + + - +
95B LEU* 3.8 40.6 - - + -
96B MSE 3.7 33.2 - - + -
99B ASN* 3.0 19.5 - - + +
131B LEU* 4.4 10.8 - - + -
135B GLU* 3.0 27.4 + - + +
136B LYS* 3.3 3.6 - - - +
138B LYS* 1.3 96.6 - - + +
140B LEU* 1.3 64.5 + - - +
141B ASN 3.1 0.2 + - - -
142B VAL* 3.3 14.0 + - + -
143B SER* 2.9 23.3 + - - +
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Residues in contact with LEU 140 (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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103A GLU* 3.7 63.4 - - + +
104A ASP* 4.7 0.7 - - + -
141A ASN* 5.4 3.1 - - - +
99B ASN* 3.3 2.9 + - - +
136B LYS 3.9 6.5 - - - -
137B GLU* 3.6 15.7 + - + +
138B LYS 3.4 5.8 + - - +
139B TYR* 1.3 75.3 - - - +
141B ASN* 1.3 71.7 + - - +
143B SER* 3.4 2.3 + - - -
144B ARG* 2.9 30.1 + - - +
1171B GOL 3.5 21.7 + - - +
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Residues in contact with ASN 141 (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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103A GLU 4.9 2.4 - - - +
140A LEU* 5.7 1.9 - - - +
141A ASN* 4.5 12.1 - - - +
144A ARG* 5.6 0.2 + - - -
99B ASN* 2.8 45.0 + - - +
100B SER* 5.1 0.2 - - - +
102B LEU* 3.9 10.8 - - + +
103B GLU* 3.5 25.6 + - - +
140B LEU* 1.3 85.2 - - - +
142B VAL* 1.3 62.3 + - - +
144B ARG* 3.4 27.3 + - - +
145B TRP* 3.0 29.8 + - - +
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Residues in contact with VAL 142 (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 LEU* 3.8 21.3 - - + +
98B LEU* 3.9 23.3 - - + -
99B ASN* 3.3 33.8 + - + +
102B LEU* 3.9 7.4 - - + -
124B LEU* 5.0 0.7 - - + -
128B ILE* 4.0 26.5 - - + -
131B LEU* 5.9 1.3 - - + -
139B TYR* 3.7 13.9 - - + +
141B ASN* 1.3 78.2 - - - +
143B SER* 1.4 56.8 + - - +
145B TRP* 3.8 9.1 - - + -
146B PHE* 2.8 29.3 + - + +
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Residues in contact with SER 143 (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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128B ILE* 6.1 0.7 - - - -
131B LEU* 5.5 1.9 - - - +
136B LYS* 2.7 43.8 + - - +
139B TYR* 2.9 11.2 + - - +
140B LEU 3.8 4.0 - - - -
142B VAL* 1.4 76.2 - - - +
144B ARG* 1.3 59.2 + - - +
146B PHE* 3.8 1.2 - - - +
147B CYS* 2.8 33.1 + - - +
164B PHE* 3.5 30.4 - - - -
1171B GOL 4.0 10.5 - - - -
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Residues in contact with ARG 144 (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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103A GLU 3.9 9.4 + - - +
104A ASP* 3.7 32.1 - - - +
105A LYS* 3.7 7.0 - - - +
106A VAL* 3.8 19.5 - - + +
144A ARG* 3.4 36.8 - - - +
102B LEU* 2.8 26.9 + - - +
103B GLU 4.1 2.6 + - - -
105B LYS 2.8 21.0 + - - -
106B VAL* 3.8 16.4 + - - +
140B LEU 2.9 18.6 + - - +
141B ASN* 3.7 26.3 + - - +
143B SER* 1.3 76.5 - - - +
145B TRP* 1.3 67.1 + - - +
147B CYS* 3.5 4.9 + - - +
148B HIS* 3.0 27.7 + - - +
1171B GOL 5.6 0.2 + - - -
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Residues in contact with TRP 145 (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 LEU* 4.8 0.9 - - + -
102B LEU* 3.8 31.2 - - + -
106B VAL 3.4 22.0 - - - -
108B LEU* 4.3 7.3 - - + +
117B ASP* 2.9 45.2 + - - -
120B LEU* 3.8 25.4 - - + -
121B TYR* 3.6 25.8 - - + -
124B LEU* 4.2 15.9 - - + -
141B ASN 3.0 17.9 + - - +
142B VAL* 3.8 11.0 - - + +
144B ARG* 1.3 84.9 - - - +
146B PHE* 1.3 100.4 + + + +
148B HIS* 3.1 7.2 + - - +
149B ILE* 3.0 39.5 + - + +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 3.4 45.0 - + - -
124B LEU* 4.4 1.6 - - + -
125B HIS* 3.7 24.9 - + - -
128B ILE* 3.6 33.9 - - + -
142B VAL* 2.8 21.6 + - + +
143B SER* 3.8 3.1 - - - +
145B TRP* 1.3 97.2 - + + +
147B CYS* 1.3 57.5 - - - +
149B ILE* 3.3 4.0 + - - +
150B GLN* 2.9 44.6 + - - +
162B VAL* 3.8 16.4 - - + -
164B PHE* 3.6 21.3 - + + -
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Residues in contact with CYS 147 (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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104A ASP 5.7 0.2 - - - +
111A TYR* 4.8 1.6 - - - -
143B SER 2.8 19.4 + - - +
144B ARG* 3.8 4.9 - - - +
146B PHE* 1.3 79.3 - - - +
148B HIS* 1.3 61.4 + - - +
150B GLN* 3.5 4.3 + - - +
151B HIS* 3.1 50.8 + - - -
164B PHE* 3.5 35.4 - - + -
166B LYS* 2.7 34.5 - - - +
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Residues in contact with HIS 148 (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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106A VAL* 3.6 27.6 - - + +
107A TYR* 3.9 26.9 - + - -
111A TYR 5.0 5.9 + - - -
106B VAL* 4.1 9.9 - - + +
107B TYR* 2.9 44.8 + + - -
144B ARG 3.0 14.9 + - - +
145B TRP* 3.1 11.2 + - - +
147B CYS* 1.3 78.8 - - - +
149B ILE* 1.3 65.3 + - + +
151B HIS* 3.3 4.4 + - - +
152B TYR* 3.1 35.0 + + - +
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Residues in contact with ILE 149 (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 TYR* 4.4 2.7 - - + -
113B PHE* 4.3 22.0 - - + -
117B ASP* 4.0 21.8 - - + +
121B TYR* 3.6 34.8 - - + -
145B TRP* 3.0 48.6 + - + +
146B PHE 3.9 3.6 - - - +
148B HIS* 1.3 89.5 - - + +
150B GLN* 1.3 65.5 + - - +
151B HIS 3.1 2.0 - - - -
152B TYR* 2.9 19.5 + - + +
155B ILE* 3.9 20.3 - - + +
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Residues in contact with GLN 150 (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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121B TYR* 3.7 23.0 + - + +
146B PHE* 2.9 32.6 + - + +
147B CYS* 3.8 2.4 - - - +
149B ILE* 1.3 75.8 - - - +
151B HIS* 1.3 89.3 + - + +
152B TYR 4.5 0.5 - - - +
156B ARG* 3.5 34.2 + - - +
160B SER 4.3 2.1 - - - +
161B SER* 3.6 10.3 - - - -
162B VAL* 2.8 44.7 + - - +
164B PHE* 3.9 15.5 - - - -
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Residues in contact with HIS 151 (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 TYR* 4.1 29.2 - + + +
147B CYS* 3.1 41.8 + - - +
148B HIS* 3.7 4.5 - - - +
149B ILE 3.1 0.8 - - - -
150B GLN* 1.3 102.2 + - + +
152B TYR* 1.3 64.4 + - - +
153B PRO* 3.4 6.2 - - - +
156B ARG* 5.7 2.7 + - - -
161B SER* 5.4 6.5 - - - -
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Residues in contact with TYR 152 (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 TYR* 3.7 19.9 + - - -
113B PHE* 3.5 60.9 - + + +
148B HIS* 3.1 28.5 + + - +
149B ILE* 2.9 20.2 + - + +
150B GLN 4.5 1.0 - - - +
151B HIS* 1.3 76.2 - - - +
153B PRO* 1.3 88.8 - - + +
154B GLY 3.2 0.9 + - - -
155B ILE* 3.1 27.6 + - + +
156B ARG 4.5 1.6 + - - -
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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