Contacts of the helix formed by residues 159 - 169 (chain D) in PDB entry 1IES
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 ALA 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D VAL* 3.2 39.0 + - + +
158D GLN* 1.3 72.6 - - - +
160D GLY* 1.4 55.7 + - - +
163D GLU* 2.9 30.7 + - - +
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Residues in contact with GLY 160 (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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158D GLN* 3.6 1.4 - - - +
159D ALA* 1.4 72.7 - - - +
161D LEU* 1.3 64.4 + - - +
163D GLU* 3.5 8.6 + - - +
164D TYR* 3.1 23.7 + - - +
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Residues in contact with LEU 161 (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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158D GLN* 3.4 26.1 + - + +
160D GLY* 1.3 74.7 - - - +
162D GLY* 1.3 62.2 + - - +
164D TYR* 3.2 9.5 + - + +
165D LEU* 2.9 49.1 + - + +
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Residues in contact with GLY 162 (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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151D ILE* 6.2 0.7 - - - -
154D LEU* 3.7 38.6 - - - +
155D VAL* 4.5 2.5 - - - -
158D GLN 2.7 21.8 + - - -
159D ALA 3.8 1.1 - - - -
161D LEU* 1.3 72.8 - - - +
163D GLU* 1.3 61.1 + - - +
165D LEU* 3.9 1.7 - - - -
166D PHE* 3.1 25.3 + - - +
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Residues in contact with GLU 163 (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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37D PHE* 4.7 0.2 - - - -
44D LEU* 3.3 23.3 - - + +
91D THR* 3.9 19.3 - - - +
92D THR* 2.8 48.9 + - - +
93D LEU 5.6 0.4 - - - +
151D ILE* 5.4 2.5 - - + -
155D VAL* 4.1 14.2 - - + +
159D ALA 2.9 22.6 + - - +
160D GLY* 3.9 6.2 - - - +
161D LEU 3.4 0.2 - - - -
162D GLY* 1.3 71.9 - - - +
164D TYR* 1.3 62.5 + - - +
166D PHE* 3.6 5.4 + - - +
167D GLU* 3.3 24.1 + - - +
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Residues in contact with TYR 164 (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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44D LEU* 4.8 10.3 - - + +
160D GLY 3.1 15.8 + - - +
161D LEU* 3.6 9.2 - - + +
163D GLU* 1.3 79.0 - - - +
165D LEU* 1.3 73.8 + - + +
167D GLU* 3.4 8.2 + - - +
168D ARG* 2.8 64.3 + - + +
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Residues in contact with LEU 165 (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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154D LEU* 4.9 16.2 - - + -
161D LEU* 2.9 44.1 + - + +
162D GLY* 4.0 3.6 - - - +
164D TYR* 1.3 90.7 - - + +
166D PHE* 1.3 55.7 + - - +
168D ARG* 4.0 4.7 - - + -
169D LEU* 2.6 60.9 + - + +
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Residues in contact with PHE 166 (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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92D THR* 4.3 12.3 - - + -
96D MET* 4.6 3.4 - - + -
147D HIS* 3.7 35.2 - + + -
150D ASN* 4.0 13.7 - - + -
151D ILE* 3.7 39.3 - - + -
154D LEU* 3.7 21.4 - - + +
162D GLY 3.1 18.0 + - - +
163D GLU* 3.9 5.8 - - - +
165D LEU* 1.3 73.5 - - - +
167D GLU* 1.3 60.7 + - + +
170D THR* 2.8 58.5 + - + +
171D LEU* 3.0 35.8 + - + -
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Residues in contact with GLU 167 (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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43D ALA 5.3 0.5 - - - +
44D LEU* 4.0 22.0 - - + +
45D GLU* 3.5 9.8 + - - +
46D GLY* 2.7 38.3 + - - +
47D VAL* 4.0 17.0 - - + +
163D GLU 3.3 15.9 + - - +
164D TYR* 3.6 5.3 - - - +
166D PHE* 1.3 80.8 - - + +
168D ARG* 1.3 94.6 + - - +
171D LEU* 3.4 11.4 - - - -
172D LYS* 2.6 37.6 + - - +
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Residues in contact with ARG 168 (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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45D GLU* 4.2 11.5 + - - +
164D TYR* 2.8 55.8 + - + +
165D LEU* 3.6 9.2 - - + +
167D GLU* 1.3 121.8 + - - +
169D LEU* 1.3 60.5 + - + +
172D LYS* 3.0 50.3 + - - +
173D HIS* 2.5 37.1 + - + +
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Residues in contact with LEU 169 (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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165D LEU* 2.6 44.6 + - + +
168D ARG* 1.3 80.4 - - + +
170D THR* 1.3 60.8 + - - +
173D HIS* 3.4 33.8 - - + +
174D ASP* 4.8 0.7 - - - +
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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