Contacts of the helix formed by residues 138 - 152 (chain A) in PDB entry 1IW1
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 SER 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU 2.7 21.4 + - - -
135A GLY 3.0 2.9 + - - -
136A ASP 3.1 0.4 - - - -
137A LEU* 1.3 76.9 - - - +
139A GLY* 1.3 67.9 + - - -
140A GLY 3.1 0.2 - - - -
141A GLN* 3.1 21.8 + - - +
142A VAL* 4.0 4.9 + - - +
173A LYS* 2.8 23.7 + - - +
901A HEM 3.3 53.0 - - - +
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Residues in contact with GLY 139 (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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135A GLY 3.0 4.9 + - - -
138A SER* 1.3 78.1 - - - +
140A GLY* 1.3 63.4 + - - +
142A VAL* 3.0 18.2 + - - +
143A ILE* 3.0 18.8 + - - +
901A HEM 3.5 46.1 + - - +
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Residues in contact with GLY 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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135A GLY 2.9 11.9 + - - -
136A ASP* 3.4 15.3 - - - -
138A SER 3.1 0.4 - - - -
139A GLY* 1.3 77.2 - - - +
141A GLN* 1.3 55.5 + - - +
143A ILE* 3.2 9.3 + - - +
144A ALA 2.9 24.8 + - - -
161A TYR* 3.2 31.7 - - - -
901A HEM 5.8 0.4 - - - +
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Residues in contact with GLN 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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136A ASP 2.9 22.2 + - - +
137A LEU* 3.8 18.3 - - - +
138A SER 3.1 14.1 + - - +
140A GLY* 1.3 78.1 - - - +
142A VAL* 1.3 63.1 + - + +
144A ALA* 3.6 6.6 + - - +
145A ARG* 3.2 21.5 + - - +
161A TYR* 3.0 30.6 + - - +
162A HIS* 5.9 1.6 - - - -
163A PHE* 4.5 3.2 - - - -
169A LEU* 4.0 20.3 - - + +
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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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33A LEU* 4.9 4.5 - - + -
138A SER 4.5 7.2 - - - +
139A GLY* 3.0 10.2 + - - +
141A GLN* 1.3 76.5 - - + +
143A ILE* 1.3 65.9 + - - +
145A ARG* 3.2 6.2 + - - +
146A MET* 2.9 38.7 + - + +
901A HEM 3.6 33.7 - - + -
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Residues in contact with ILE 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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29A MET* 4.1 26.9 - - + -
32A LEU* 5.1 2.5 - - + -
33A LEU* 3.9 30.3 - - + -
42A PHE* 4.4 5.6 - - + -
45A LEU* 5.7 1.6 - - + -
139A GLY 3.0 17.2 + - - +
140A GLY* 3.5 15.7 - - - +
142A VAL* 1.3 75.7 - - - +
144A ALA* 1.3 64.3 + - - +
146A MET* 3.1 3.1 + - - +
147A MET* 2.9 40.6 + - + +
161A TYR* 3.4 27.6 - - + +
208A PHE* 6.1 0.4 - - + -
901A HEM 4.6 13.0 - - + -
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Residues in contact with ALA 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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140A GLY 2.9 15.8 + - - +
141A GLN* 3.8 7.2 - - - +
143A ILE* 1.3 75.0 - - - +
145A ARG* 1.3 64.0 + - - +
147A MET 3.2 9.1 + - - +
148A GLN* 3.2 21.4 + - - +
158A LEU* 3.6 19.9 - - + +
161A TYR* 3.8 32.9 - - + -
162A HIS* 5.2 5.4 - - + +
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Residues in contact with ARG 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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141A GLN 3.2 12.3 + - - +
142A VAL* 3.2 8.7 + - - +
144A ALA* 1.3 79.7 - - - +
146A MET* 1.3 72.2 + - + +
148A GLN* 3.3 34.1 + - - +
149A ARG* 2.9 46.5 + - - +
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Residues in contact with MET 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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33A LEU* 3.7 29.6 - - + +
142A VAL* 2.9 31.1 + - + +
143A ILE 3.1 3.8 + - - +
145A ARG* 1.3 88.4 - - + +
147A MET* 1.3 75.2 + - + +
149A ARG* 3.7 38.6 - - - +
150A HIS* 2.9 56.1 + - + +
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Residues in contact with MET 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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32A LEU* 3.9 21.8 - - + +
33A LEU* 4.0 7.6 - - + -
42A PHE* 3.6 48.7 - - + -
143A ILE* 2.9 25.2 + - + +
144A ALA 3.2 6.0 + - - +
146A MET* 1.3 90.7 - - + +
148A GLN* 1.3 63.6 + - - +
151A TYR* 3.3 41.1 + - + +
152A GLY 3.1 6.6 + - - -
153A VAL* 3.1 33.5 + - + +
158A LEU* 4.2 9.0 - - + -
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Residues in contact with GLN 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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144A ALA* 3.2 9.8 + - - +
145A ARG* 3.5 39.6 + - - +
147A MET* 1.3 77.2 - - - +
149A ARG* 1.3 60.3 + - - +
152A GLY* 3.0 24.1 + - - -
153A VAL 3.6 16.2 - - - +
155A PRO* 3.6 34.4 - - - +
158A LEU* 3.5 24.0 - - + +
162A HIS* 4.9 5.0 + - - -
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Residues in contact with ARG 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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145A ARG* 2.9 37.0 + - - +
146A MET* 3.7 30.3 - - + +
147A MET 3.4 0.2 - - - -
148A GLN* 1.3 80.9 - - - +
150A HIS* 1.3 74.0 + - + +
152A GLY 4.5 0.5 + - - -
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Residues in contact with HIS 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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32A LEU 4.6 1.3 - - - -
33A LEU 3.0 29.5 + - - -
34A LYS* 3.5 18.1 - - - -
35A GLY* 3.6 23.6 - - - -
146A MET* 2.9 39.6 + - + +
149A ARG* 1.3 88.0 + - + +
151A TYR* 1.3 73.9 + - + +
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Residues in contact with TYR 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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32A LEU* 2.7 38.5 + - + -
35A GLY* 3.2 24.5 - - - -
37A LEU* 3.0 38.1 + - - -
38A GLY* 3.5 23.3 - - - -
39A VAL* 4.4 9.7 - - + +
147A MET* 3.3 43.8 + - + +
150A HIS* 1.3 87.3 - - + +
152A GLY* 1.3 60.6 + - - +
153A VAL* 3.3 9.4 + - + -
909A SO4 3.0 27.6 + - - -
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Residues in contact with GLY 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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147A MET 3.1 0.4 + - - -
148A GLN* 3.0 19.2 + - - -
149A ARG 4.5 0.6 + - - -
150A HIS 3.7 1.0 - - - -
151A TYR* 1.3 78.1 - - - +
153A VAL* 1.3 66.6 + - - +
154A ASP* 3.4 3.1 + - - -
909A SO4 3.0 21.5 + - - -
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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