Contacts of the helix formed by residues 143 - 157 (chain A) in PDB entry 2IHD
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 PHE 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.2 15.9 - + + -
89A CYS* 3.6 26.9 - - + -
92A PHE* 3.8 32.5 - + + -
105A ALA* 3.4 40.4 - - - -
108A ILE* 3.8 22.9 - - + -
109A PHE* 3.8 14.6 - - + -
113A VAL* 4.4 3.6 - - + -
131A THR* 3.7 26.0 - - + -
140A LEU 4.9 1.4 + - - -
141A THR 3.2 0.6 - - - -
142A CYS* 1.3 86.9 - - + +
144A ASP* 1.3 57.0 + - - +
145A GLN 3.3 2.7 - - - -
146A ALA* 3.2 6.7 + - - -
147A GLN* 2.7 36.7 + - - +
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Residues in contact with ASP 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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93A LYS* 4.3 16.5 + - - +
140A LEU 4.2 5.2 - - - +
141A THR* 3.1 45.3 + - - +
142A CYS 3.5 0.2 - - - -
143A PHE* 1.3 76.7 - - - +
145A GLN* 1.3 57.1 + - - +
147A GLN* 3.8 10.0 - - - +
148A GLY* 2.9 26.7 + - - -
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Residues in contact with GLN 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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126A GLN* 4.6 2.2 + - - +
127A THR* 3.0 41.2 + - + +
130A ALA* 3.8 21.8 - - + +
131A THR* 5.3 2.9 - - - +
134A ASN* 5.7 7.6 + - - +
142A CYS 5.1 1.4 + - - +
143A PHE 3.3 0.4 - - - -
144A ASP* 1.3 77.1 - - - +
146A ALA* 1.3 63.4 + - - +
148A GLY* 3.2 3.0 + - - -
149A LYS* 3.0 36.9 + - - +
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Residues in contact with ALA 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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85A PHE* 3.8 22.0 - - + -
113A VAL* 5.1 1.3 - - + -
123A ILE* 3.8 18.9 - - + +
127A THR* 3.6 11.3 - - - +
131A THR* 3.7 24.7 + - + +
143A PHE* 3.2 8.6 + - - +
145A GLN* 1.3 79.8 - - - +
147A GLN* 1.3 60.8 - - - +
149A LYS* 3.2 4.7 + - - +
150A VAL* 3.1 26.7 + - - +
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Residues in contact with GLN 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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1A CL 4.0 6.5 - - + -
85A PHE* 3.9 4.4 - - - -
86A TRP* 3.2 52.2 + - + +
89A CYS* 3.5 24.6 - - + +
90A GLU* 2.8 24.6 + - - -
93A LYS* 3.1 23.0 + - - +
143A PHE 2.7 20.8 + - - +
144A ASP* 3.8 9.7 - - - +
146A ALA* 1.3 72.5 - - - +
148A GLY* 1.3 57.0 + - - +
150A VAL* 3.1 10.4 - - - +
151A HIS* 2.9 30.5 + - - +
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Residues in contact with GLY 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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1A CL 4.3 13.1 - - - +
144A ASP 2.9 16.0 + - - -
145A GLN 3.2 4.9 + - - -
147A GLN* 1.3 77.6 - - - +
149A LYS* 1.3 61.6 + - - +
151A HIS* 3.4 3.6 + - - +
152A SER* 3.1 23.2 + - - -
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Residues in contact with LYS 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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123A ILE* 3.9 17.3 - - + -
124A ASP* 3.7 12.9 + - - +
127A THR* 3.6 30.3 - - + +
145A GLN* 3.0 28.2 + - - +
146A ALA 3.2 6.5 + - - +
148A GLY* 1.3 78.2 - - - +
150A VAL* 1.3 57.4 + - - +
152A SER* 3.3 8.2 + - - -
153A LEU* 3.0 31.3 + - + +
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Residues in contact with VAL 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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82A ASN* 4.0 24.0 - - + +
85A PHE* 3.6 34.3 - - + -
86A TRP* 4.1 12.1 - - + -
121A VAL* 4.0 15.9 - - + -
123A ILE* 3.6 23.8 - - + -
146A ALA 3.1 4.4 + - - +
147A GLN* 3.1 17.9 - - - +
149A LYS* 1.3 71.9 - - - +
151A HIS* 1.3 65.2 + - - +
153A LEU* 3.4 10.3 + - + +
154A MET* 3.1 28.9 + - - +
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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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1A CL 3.9 13.7 - - + -
57A PHE* 3.7 25.1 - + - -
58A ASP* 2.7 37.5 + - - -
61A LEU* 4.2 0.9 - - + -
86A TRP* 3.6 27.6 - + - +
147A GLN 2.9 18.0 + - - +
148A GLY* 3.5 6.0 + - - +
150A VAL* 1.3 78.9 - - - +
152A SER* 1.3 57.4 + - - +
154A MET* 3.4 11.3 + - - +
155A GLU* 2.9 54.6 + - - +
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLY 3.1 13.5 + - - -
149A LYS* 3.5 12.6 - - - -
151A HIS* 1.3 77.8 + - - +
153A LEU* 1.3 65.5 + - - +
155A GLU* 4.5 6.3 - - - +
156A LYS* 2.7 68.4 + - - +
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Residues in contact with LEU 153 (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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82A ASN* 4.5 24.2 - - - +
122A ASN* 3.8 28.9 - - + +
123A ILE* 4.9 2.9 - - + -
149A LYS* 3.0 20.5 + - + +
150A VAL* 3.4 16.4 + - + +
152A SER* 1.3 76.1 - - - +
154A MET* 1.3 56.9 + - - +
156A LYS* 5.1 0.9 - - - -
157A ASP* 3.0 51.5 + - - +
158A SER* 3.8 1.7 + - - -
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Residues in contact with MET 154 (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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57A PHE* 3.5 28.3 - - + -
70A PHE* 4.0 20.0 - - + -
74A LEU* 4.2 3.8 - - + -
82A ASN* 3.8 20.2 - - + +
83A LEU* 3.7 36.3 - - + -
86A TRP* 3.8 34.1 - - + -
150A VAL 3.1 20.2 + - - +
151A HIS* 3.7 5.2 - - - +
153A LEU* 1.3 78.2 - - - +
155A GLU* 1.3 63.0 + - - +
158A SER* 3.3 12.3 + - - +
159A TYR* 2.8 32.3 + - - +
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Residues in contact with GLU 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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56A SER* 5.3 3.5 - - - -
57A PHE* 3.7 35.1 + - + +
58A ASP* 4.9 4.7 + - - +
151A HIS* 2.9 43.2 + - - +
152A SER* 4.0 6.6 - - - +
154A MET* 1.3 72.7 - - - +
156A LYS* 1.3 62.5 + - + +
159A TYR* 3.8 11.0 - - + +
160A PRO* 3.2 20.1 - - - +
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Residues in contact with LYS 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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152A SER* 2.7 39.3 + - - +
153A LEU* 5.1 0.4 - - - -
155A GLU* 1.3 84.2 - - + +
157A ASP* 1.3 72.8 + - - +
160A PRO* 3.6 14.1 - - - +
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Residues in contact with ASP 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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153A LEU* 3.0 34.1 + - - +
156A LYS* 1.3 90.9 - - - +
158A SER* 1.3 65.1 + - - +
159A TYR 3.5 0.4 - - - -
160A PRO* 3.4 10.0 - - - +
161A ARG* 3.5 43.8 + - - +
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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