Contacts of the helix formed by residues 139 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A HIS* 2.9 42.7 + + - +
95A LEU* 3.7 44.4 - - + -
96A MSE 3.8 37.2 - - + -
99A ASN* 3.1 15.5 - - + +
131A LEU* 4.2 7.6 - - + -
135A GLU* 3.1 29.4 + - + +
136A LYS* 3.5 3.4 - - - +
138A LYS* 1.3 101.7 + - + +
140A LEU* 1.3 63.3 + - - +
142A VAL* 3.3 15.1 + - + -
143A SER* 3.0 23.7 + - - +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN* 3.2 3.7 + - - +
136A LYS 4.0 4.0 - - - -
137A GLU* 3.3 26.2 - - + +
138A LYS 3.4 3.9 + - - +
139A TYR* 1.3 75.3 - - - +
141A ASN* 1.3 65.1 + - - +
143A SER* 3.4 3.0 + - - -
144A ARG* 2.8 30.0 + - - +
1171A GOL 3.5 21.7 + - - +
103B GLU* 3.6 53.7 - - + +
104B ASP* 5.2 0.7 - - + -
141B ASN* 5.7 1.8 - - - +
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN* 2.8 47.5 + - - +
100A SER* 5.0 0.4 - - - +
102A LEU* 3.9 15.5 - - + +
103A GLU* 3.4 27.1 + - - +
140A LEU* 1.3 77.5 - - - +
142A VAL* 1.3 61.3 + - - +
144A ARG* 3.8 23.9 + - - +
145A TRP* 3.0 31.0 + - - +
103B GLU 4.9 2.8 - - - +
140B LEU* 5.4 3.2 - - - +
141B ASN* 4.5 11.3 - - - +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 3.6 29.6 - - + +
98A LEU* 4.0 22.0 - - + +
99A ASN* 3.3 36.5 + - + +
102A LEU* 4.0 6.7 - - + -
124A LEU* 4.9 0.4 - - + -
128A ILE* 4.3 15.9 - - + -
131A LEU* 6.2 0.2 - - + -
139A TYR* 3.3 13.9 + - + +
141A ASN* 1.3 75.5 - - - +
143A SER* 1.3 60.3 + - - +
145A TRP* 3.3 11.8 + - + +
146A PHE* 2.8 34.8 + - + +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE* 5.9 1.5 - - - +
131A LEU* 5.4 2.4 - - - +
136A LYS* 2.8 38.9 + - - +
139A TYR* 3.0 12.8 + - - +
140A LEU 3.7 4.0 - - - -
142A VAL* 1.3 76.4 - - - +
144A ARG* 1.3 56.7 + - - +
146A PHE* 4.4 1.1 - - - -
147A CYS* 2.9 32.6 + - - +
164A PHE* 3.5 31.1 - - - -
1171A GOL 3.8 10.1 - - - -
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.0 24.5 + - - +
103A GLU 4.0 4.4 + - - -
105A LYS 2.8 20.4 + - - -
106A VAL* 3.8 16.0 + - - +
140A LEU 2.8 19.4 + - - +
141A ASN* 3.8 26.1 + - - +
143A SER* 1.3 76.8 - - - +
145A TRP* 1.3 71.6 + - - +
147A CYS* 3.9 4.1 - - - +
148A HIS* 3.1 22.9 + - - +
1171A GOL 5.5 0.4 + - - -
103B GLU 4.0 7.6 + - - +
104B ASP* 3.5 35.4 - - - +
105B LYS 3.6 17.9 - - - +
106B VAL* 3.8 15.1 - - - +
141B ASN* 5.6 0.2 + - - -
144B ARG* 3.4 30.8 - - - +
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Residues in contact with TRP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.9 0.7 - - + -
102A LEU* 3.7 29.6 - - + -
106A VAL 3.4 21.8 - - - -
108A LEU* 4.3 7.1 - - + +
117A ASP* 3.0 44.4 + - - -
120A LEU* 3.7 26.2 - - + -
121A TYR* 3.6 25.1 - - + -
124A LEU* 4.1 15.9 - - + -
141A ASN 3.0 17.2 + - - +
142A VAL* 3.7 11.2 - - + -
144A ARG* 1.3 86.4 - - - +
146A PHE* 1.3 98.7 + + + +
148A HIS* 3.1 8.2 + - - +
149A ILE* 2.9 39.7 + - + +
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.4 41.4 - + - -
124A LEU* 4.4 1.1 - - + -
125A HIS* 3.8 32.5 - + - -
128A ILE* 3.6 34.5 - - + -
142A VAL* 2.8 24.3 + - + +
143A SER* 3.9 2.9 - - - +
145A TRP* 1.3 95.6 - + + +
147A CYS* 1.3 58.6 + - - +
149A ILE* 3.3 3.8 + - - +
150A GLN* 2.9 38.5 + - - +
162A VAL* 3.6 22.7 - - + -
164A PHE* 3.5 21.1 - + + -
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Residues in contact with CYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER 2.9 19.6 + - - +
144A ARG* 3.9 5.4 - - - +
146A PHE* 1.3 78.0 - - - +
148A HIS* 1.3 60.3 + - - +
150A GLN* 3.5 4.2 + - - +
151A HIS* 3.0 51.3 + - - -
164A PHE* 3.5 34.5 - - + -
166A LYS* 2.7 35.4 - - - +
104B ASP 5.6 0.2 - - - +
111B TYR* 4.6 1.8 - - - -
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Residues in contact with HIS 148 (chain A).
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* 4.0 15.0 - - + +
107A TYR* 2.8 45.4 + + - -
144A ARG 3.1 14.0 + - - +
145A TRP* 3.1 11.1 + - - +
147A CYS* 1.3 74.8 - - - +
149A ILE* 1.3 71.0 + - + +
151A HIS* 3.4 4.9 + - - +
152A TYR* 3.1 31.0 + + - +
106B VAL* 3.7 24.7 - - + +
107B TYR* 3.9 27.0 - + - -
111B TYR 5.0 5.3 + - - -
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 4.2 4.9 - - + -
113A PHE* 3.8 34.1 - - + -
117A ASP* 4.0 15.0 - - + +
118A ILE* 4.8 0.2 - - - -
121A TYR* 3.5 36.1 - - + -
145A TRP* 2.9 44.2 + - + +
146A PHE* 4.0 4.0 - - - +
148A HIS* 1.3 95.8 - - + +
150A GLN* 1.3 62.9 + - - +
152A TYR* 3.0 17.3 + - + +
155A ILE* 3.9 20.3 - - + +
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Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.5 28.0 + - + +
146A PHE* 2.9 25.5 + - - +
147A CYS* 3.6 9.2 - - - +
149A ILE* 1.3 76.8 - - - +
151A HIS* 1.3 86.7 + - + +
152A TYR 4.6 0.7 - - - +
156A ARG* 3.4 29.6 + - - +
160A SER 4.2 2.6 - - - +
161A SER* 3.6 14.1 - - - -
162A VAL* 2.8 45.2 + - - +
164A PHE* 3.7 17.3 - - - -
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Residues in contact with HIS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A CYS* 3.0 40.9 + - - +
148A HIS* 3.8 4.0 - - - +
149A ILE 3.1 0.4 - - - -
150A GLN* 1.3 100.1 + - + +
152A TYR* 1.3 65.2 + - - +
153A PRO* 3.5 5.7 - - - +
156A ARG* 5.9 2.8 + - - -
161A SER* 5.0 8.5 - - - -
111B TYR* 4.1 29.9 - + + +
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 3.7 23.1 + + - -
113A PHE* 3.5 60.2 - + + +
148A HIS* 3.1 24.4 + + - +
149A ILE* 3.0 18.6 + - + +
150A GLN 4.6 1.9 - - - +
151A HIS* 1.3 77.9 - - - +
153A PRO* 1.4 86.9 - - + +
154A GLY 3.1 3.1 + - - -
155A ILE* 3.2 25.2 + - + +
156A ARG 4.6 0.2 + - - -
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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