Contacts of the helix formed by residues 136 - 150 (chain D) in PDB entry 3IRR
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 GLY 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D SER* 1.3 54.7 + - - -
138D HIS* 3.2 3.6 - - - -
139D MET* 3.2 14.8 + - - +
140D GLU* 2.8 43.6 + - - +
175D VAL* 4.6 12.1 - - - +
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY* 1.3 70.6 - - - -
138D HIS* 1.3 58.2 + - - +
140D GLU* 3.5 17.7 + - - +
141D GLN* 2.8 51.4 + - - +
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Residues in contact with HIS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY* 5.0 0.9 - - - -
137D SER* 1.3 80.8 - - - +
139D MET* 1.3 60.1 + - - +
141D GLN* 3.4 11.7 + - - +
142D ARG* 3.0 35.5 + - - +
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Residues in contact with MET 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY* 3.2 17.7 + - - +
138D HIS* 1.3 75.4 - - - +
140D GLU* 1.3 64.3 + - - +
142D ARG* 3.4 26.6 + - - +
143D ILE* 3.1 41.4 + - + +
165D LEU* 4.3 9.4 - - - +
167D THR* 3.6 24.7 - - + +
171D GLU* 4.1 19.1 - - + +
172D ILE* 4.2 19.3 - - + -
175D VAL* 3.7 23.1 - - + -
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY 2.8 32.5 + - - +
137D SER* 3.5 18.1 + - - +
139D MET* 1.3 75.1 - - - +
141D GLN* 1.3 61.0 + - + +
143D ILE* 3.5 2.4 + - - +
144D LEU* 3.1 32.3 + - + +
175D VAL* 3.5 24.2 - - + +
178D SER* 4.0 12.0 + - - -
179D LEU* 3.8 21.3 - - + +
182D LYS* 2.9 32.6 + - - +
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Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D SER* 2.8 36.3 + - - +
138D HIS* 3.8 13.1 - - - +
140D GLU* 1.3 71.1 - - + +
142D ARG* 1.3 61.2 + - + +
144D LEU* 3.4 10.3 + - + +
145D LYS* 3.0 43.8 + - + +
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Residues in contact with ARG 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D HIS* 3.0 24.5 + - - +
139D MET* 3.7 29.4 - - - +
140D GLU 3.4 0.2 - - - -
141D GLN* 1.3 79.6 - - + +
143D ILE* 1.3 61.1 + - - +
145D LYS* 3.5 12.8 + - + +
146D PHE* 3.1 22.9 + - - +
164D LYS 4.9 0.4 + - - -
165D LEU* 3.4 56.9 + - + +
167D THR* 5.1 0.4 + - - -
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D MET* 3.1 22.8 + - + +
140D GLU 3.9 4.3 - - - +
142D ARG* 1.3 72.8 - - - +
144D LEU* 1.3 66.6 + - - +
146D PHE* 3.4 6.9 + - - +
147D LEU* 3.2 32.6 + - + +
161D LEU* 4.1 11.9 - - + -
165D LEU* 4.1 19.5 - - + -
172D ILE* 4.5 15.3 - - + +
175D VAL* 3.6 34.3 - - + -
176D LEU* 4.0 29.6 - - + -
179D LEU* 4.2 11.2 - - + -
185D LEU* 4.6 0.2 - - + -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLU* 3.1 27.1 + - + +
141D GLN* 3.7 9.4 - - + +
143D ILE* 1.3 73.4 - - - +
145D LYS* 1.3 66.1 + - - +
147D LEU* 3.3 5.0 + - - +
148D GLU* 2.9 41.9 + - - +
179D LEU* 4.4 22.0 - - + -
184D LYS* 4.5 19.7 - - + +
185D LEU* 4.3 23.3 - - + -
197D ILE* 4.6 7.1 - - + +
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Residues in contact with LYS 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLN* 3.0 30.6 + - + +
142D ARG* 3.5 10.3 - - + +
144D LEU* 1.3 75.0 - - - +
146D PHE* 1.3 65.9 + - - +
148D GLU* 2.9 16.4 + - - +
149D GLU* 2.8 39.4 + - - +
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Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ARG 3.1 10.2 + - - +
143D ILE* 3.6 11.2 - - - +
144D LEU 3.4 0.2 - - - -
145D LYS* 1.3 79.7 - - - +
147D LEU* 1.3 65.4 + - + +
149D GLU* 3.4 11.5 + - - +
150D LEU* 3.0 57.0 + - + +
156D THR* 4.6 4.5 - - + -
160D ASP* 5.0 0.2 - - - -
161D LEU* 3.7 31.2 - - + -
164D LYS* 3.3 52.7 - - + -
165D LEU* 5.3 12.8 - - + -
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 3.2 24.4 + - + +
144D LEU* 3.8 3.4 - - - +
146D PHE* 1.3 79.1 - - + +
148D GLU* 1.3 65.2 + - - +
150D LEU* 3.3 24.7 + - + +
151D GLY 3.3 14.0 - - - +
154D LYS 5.2 4.1 - - - +
155D ALA 5.2 0.2 - - - -
156D THR* 3.5 31.6 - - + -
161D LEU* 5.3 2.5 - - + -
185D LEU* 3.6 38.4 - - + -
195D TRP* 3.8 15.0 - - + +
196D LYS* 4.4 12.3 - - - +
197D ILE* 3.8 18.1 - - + +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 2.9 38.3 + - + +
145D LYS* 2.9 15.3 + - - +
147D LEU* 1.3 78.3 - - - +
149D GLU* 1.3 61.4 + - + +
150D LEU 3.3 0.5 + - - -
151D GLY* 3.4 9.4 + - - -
152D GLU* 3.6 14.7 - - - +
197D ILE* 3.4 23.0 - - + +
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Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LYS* 2.8 32.4 + - - +
146D PHE* 3.8 10.7 - - - +
148D GLU* 1.3 72.2 - - + +
150D LEU* 1.3 58.1 + - - +
151D GLY* 2.9 12.6 + - - -
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D PHE* 3.0 39.0 + - + +
147D LEU* 3.4 21.1 - - + +
148D GLU 3.1 1.2 - - - -
149D GLU* 1.3 75.6 - - - +
151D GLY* 1.3 60.1 + - - +
154D LYS* 3.6 27.0 - - + +
155D ALA* 4.1 24.7 - - - +
156D THR* 4.1 17.5 - - - -
164D LYS* 5.5 2.9 - - - +
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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