Contacts of the helix formed by residues 154 - 164 (chain A) in PDB entry 4UHX
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A MET* 4.3 2.5 - - + -
147A ASN 3.6 19.7 - - - -
148A LEU* 3.5 6.8 - - - +
149A CYS* 2.9 45.3 + - + -
152A THR* 3.1 13.9 + - - -
153A GLY* 1.3 81.9 - - - +
155A ARG* 1.3 61.8 + - - +
156A PRO* 3.3 4.0 - - - -
157A ILE* 2.9 28.0 + - + +
158A ILE* 3.0 21.3 + - + +
1209A ILE* 5.0 4.3 - - + -
1239A PRO* 2.7 32.7 + - + -
1240A ALA* 3.5 26.1 - - - -
1241A ILE* 3.4 31.9 - - + -
1244A MET* 4.2 9.6 - - + -
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Residues in contact with ARG 155 (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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109A CYS 4.6 5.7 + - - -
110A HIS* 5.9 2.8 - - - +
153A GLY 2.9 13.4 + - - +
154A TYR* 1.3 70.1 - - - +
156A PRO* 1.4 82.1 - - + +
158A ILE* 3.3 6.0 + - - +
159A ASP* 2.8 64.0 + - - +
201A LEU* 4.2 11.5 - - - +
202A PHE* 4.7 5.5 - - - -
563A SER* 3.4 32.5 - - - +
565A LEU* 3.3 31.1 - - - +
1198A ALA 5.5 1.4 + - - -
1201A ILE* 4.1 8.9 - - - +
1202A GLY* 5.2 2.6 - - - +
1205A GLU* 2.7 44.8 + - - +
1244A MET* 3.9 17.4 - - + +
1248A LEU* 4.4 9.2 - - + -
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Residues in contact with PRO 156 (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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109A CYS* 3.6 19.5 - - - +
110A HIS* 3.2 27.6 - - + +
111A GLY* 3.5 10.9 - - - -
113A GLN* 6.0 0.7 - - - +
152A THR* 3.6 22.4 - - - +
154A TYR* 3.4 4.5 - - - +
155A ARG* 1.4 124.6 - - + +
157A ILE* 1.3 60.1 + - - +
159A ASP* 3.4 5.5 + - + +
160A ALA* 3.2 16.8 + - - +
1202A GLY* 5.9 2.7 - - - -
1205A GLU* 3.9 4.7 - - - +
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Residues in contact with ILE 157 (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 ILE* 4.0 23.8 - - + -
111A GLY* 3.7 23.1 - - - +
117A CYS* 5.0 1.3 - - - -
121A MET* 3.7 36.3 - - + -
125A ILE* 4.3 6.2 - - + +
144A LEU* 3.7 26.9 - - + -
149A CYS* 4.7 4.0 - - + -
152A THR* 3.8 20.2 - - - +
154A TYR* 2.9 18.7 + - + +
156A PRO* 1.3 75.1 - - - +
158A ILE* 1.3 57.5 + - + +
160A ALA* 3.3 8.0 + - - +
161A CYS* 3.0 25.5 + - - -
1241A ILE* 5.9 1.6 - - + -
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Residues in contact with ILE 158 (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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137A LEU* 4.2 22.4 - - + -
141A THR* 4.6 11.4 - - + -
144A LEU* 5.5 2.5 - - + -
154A TYR* 3.0 16.4 + - + +
155A ARG* 3.7 7.6 - - + +
157A ILE* 1.3 77.2 - - + +
159A ASP* 1.3 60.8 + - - +
161A CYS* 3.3 6.7 + - - +
162A LYS* 3.0 34.2 + - - +
561A HIS* 4.1 24.5 - - + +
1241A ILE* 4.0 30.7 - - + -
1244A MET* 3.3 33.7 - - + -
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Residues in contact with ASP 159 (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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109A CYS* 4.4 2.9 - - + -
155A ARG* 2.8 49.0 + - - +
156A PRO* 3.5 10.1 - - + +
158A ILE* 1.3 77.5 - - - +
160A ALA* 1.3 60.4 + - - +
162A LYS* 3.3 29.1 + - - +
163A THR* 3.4 16.6 + - - +
200A LYS* 4.6 10.8 + - - -
202A PHE* 3.9 27.7 - - + -
563A SER* 4.3 9.2 + - - -
565A LEU* 5.0 1.2 - - - +
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Residues in contact with ALA 160 (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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105A ARG* 3.9 24.5 - - + +
106A ILE* 3.9 19.5 - - + +
109A CYS* 3.8 11.1 - - - -
125A ILE* 5.7 3.6 - - + -
156A PRO 3.2 10.5 + - - +
157A ILE* 3.4 11.2 - - + +
158A ILE 3.3 0.2 - - - -
159A ASP* 1.3 78.8 - - - +
161A CYS* 1.3 59.7 + - - +
163A THR* 2.5 27.0 + - - -
164A PHE* 3.4 12.3 - - + -
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Residues in contact with CYS 161 (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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125A ILE* 3.9 19.3 - - - -
137A LEU* 3.8 13.5 - - + -
140A LEU* 3.2 45.1 - - + +
141A THR* 5.8 1.3 - - + -
144A LEU* 3.7 27.4 - - - -
157A ILE 3.0 20.5 + - - -
158A ILE* 3.5 10.3 - - - +
160A ALA* 1.3 76.2 - - - +
162A LYS* 1.3 62.9 + - - +
164A PHE* 3.2 16.0 + - - +
165A CYS* 3.6 3.1 - - - -
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Residues in contact with LYS 162 (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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137A LEU* 3.4 36.1 - - + -
158A ILE* 3.0 20.8 + - - +
159A ASP* 3.3 23.1 + - - +
161A CYS* 1.3 76.6 - - - +
163A THR* 1.3 62.0 + - - +
165A CYS* 3.1 27.9 + - + +
167A THR* 5.5 1.4 - - - +
204A GLU* 5.2 1.4 - - - +
561A HIS 2.7 26.6 + - - -
562A CYS* 4.4 5.7 - - - +
563A SER* 5.0 4.6 + - - +
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Residues in contact with THR 163 (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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105A ARG* 3.2 37.4 + - - -
109A CYS* 4.7 2.5 - - - -
159A ASP 3.5 15.0 - - - +
160A ALA* 2.5 23.4 + - - +
162A LYS* 1.3 75.1 - - + +
164A PHE* 1.3 59.9 + - - +
165A CYS 4.6 2.4 - - - +
202A PHE* 4.8 2.9 - - + -
204A GLU* 3.7 43.9 - - + +
207A PHE* 4.2 15.0 - - + -
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Residues in contact with PHE 164 (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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101A PRO* 4.1 9.6 - - + -
102A VAL* 3.6 41.3 - - + -
105A ARG* 3.5 39.3 - - + -
125A ILE* 4.5 9.0 - - + -
129A LEU* 3.9 37.2 - - + -
133A PRO 4.6 3.1 - - - +
134A GLU* 5.0 2.9 - - - +
135A PRO* 3.5 16.1 - - - +
140A LEU* 4.4 5.4 - - + -
160A ALA* 3.4 26.2 - - + -
161A CYS* 3.2 12.9 + - - +
162A LYS 3.2 0.8 - - - -
163A THR* 1.3 78.7 + - - +
165A CYS* 1.3 58.9 + - - +
166A LYS 3.8 1.7 + - - -
210A LEU* 4.3 18.8 - - + -
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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