Contacts of the helix formed by residues 175 - 182 (chain A) in PDB entry 1IEQ
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 GLU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.5 33.4 - - + +
122A TYR* 5.6 0.9 - - - -
124A VAL* 5.3 0.4 - - + -
125A LYS* 3.4 39.3 + - + +
172A SER 3.5 16.1 + - - +
173A MET 2.9 2.3 - - - -
174A THR* 1.3 76.1 + - - +
176A LEU* 1.3 61.3 + - - +
177A ILE 3.1 0.4 - - - -
178A PRO* 2.9 21.6 - - - +
179A GLY 3.3 8.3 + - - -
244A LYS* 2.8 32.2 + - - +
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Residues in contact with LEU 176 (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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97A VAL 5.8 3.8 - - - +
112A ASN* 5.8 0.7 - - - +
115A LEU* 5.7 2.7 - - + -
124A VAL* 3.5 38.2 - - + +
125A LYS* 4.3 0.4 - - - +
127A ILE* 4.5 9.0 - - + -
128A GLY* 3.6 16.7 - - - +
131A THR* 5.6 1.6 - - - +
145A ALA* 4.3 6.1 - - + -
146A PRO* 3.3 34.5 - - + -
163A TYR* 3.9 7.4 - - - +
173A MET 3.4 12.9 + - - +
174A THR 2.9 0.2 - - - -
175A GLU* 1.3 80.7 - - - +
177A ILE* 1.3 57.3 + - - +
179A GLY* 3.0 2.9 + - - -
180A LEU* 2.8 48.9 + - + +
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Residues in contact with ILE 177 (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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146A PRO* 3.6 29.4 - - + -
148A ILE* 5.9 0.7 - - + -
174A THR* 3.4 15.7 - - + +
176A LEU* 1.3 76.9 - - - +
178A PRO* 1.3 64.7 - - + +
179A GLY 3.1 0.2 + - - -
180A LEU* 3.1 6.1 + - - +
181A GLN* 2.7 54.4 + - + +
203A ALA* 4.4 4.0 - - + -
205A ALA* 5.1 1.3 - - + -
241A ALA* 3.7 35.2 - - + -
244A LYS* 3.8 18.8 - - + +
246A VAL* 3.7 22.4 - - + +
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Residues in contact with PRO 178 (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 LYS* 4.2 11.3 - - - -
129A GLU* 5.0 0.7 - - - +
174A THR 3.3 4.9 - - - +
175A GLU* 2.9 32.8 - - - +
177A ILE* 1.3 92.0 - - + +
179A GLY* 1.3 55.0 + - - +
182A GLY* 2.6 44.2 + - - +
183A ASP* 3.5 24.9 + - - +
184A VAL* 6.3 0.9 - - + -
200A LYS* 4.6 0.9 + - - -
244A LYS* 3.9 31.2 - - + +
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Residues in contact with GLY 179 (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 LYS* 3.4 29.6 - - - +
128A GLY 3.4 7.0 - - - -
129A GLU* 3.3 15.8 - - - -
175A GLU 3.3 4.4 + - - -
176A LEU 3.0 6.2 + - - -
177A ILE 3.0 1.2 - - - -
178A PRO* 1.3 79.8 - - - +
180A LEU* 1.3 58.6 + - - +
200A LYS* 3.0 27.7 + - - +
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Residues in contact with LEU 180 (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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96A ALA 5.6 0.2 - - - +
128A GLY* 3.2 21.8 - - - +
131A THR* 3.8 27.4 - - + -
132A ALA* 3.5 9.5 - - - +
143A ALA* 4.8 9.2 - - + -
145A ALA* 3.9 26.5 - - + +
146A PRO* 4.8 0.4 - - + -
176A LEU* 2.8 40.3 + - + +
177A ILE 3.7 2.7 - - - +
179A GLY* 1.3 77.3 - - - +
181A GLN* 1.3 60.1 + - + +
200A LYS* 3.4 10.2 - - - +
201A VAL* 3.0 42.2 + - + +
203A ALA* 4.2 8.7 - - + -
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Residues in contact with GLN 181 (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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177A ILE* 2.7 25.6 + - - +
178A PRO* 5.1 0.2 - - + -
180A LEU* 1.3 73.5 - - - +
182A GLY* 1.3 62.5 + - - +
194A PHE* 2.9 20.0 + - + +
195A VAL* 3.5 2.3 - - - +
196A ALA 2.9 28.9 + - - -
200A LYS* 3.3 9.5 - - - +
201A VAL 3.2 16.6 - - - +
202A ALA* 3.5 1.0 - - - +
203A ALA* 2.6 37.8 - - + +
244A LYS 4.1 2.3 - - - +
245A GLY 2.7 27.0 - - - +
246A VAL* 3.5 2.3 - - - -
247A SER* 2.7 33.8 + - - +
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Residues in contact with GLY 182 (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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178A PRO* 2.6 31.2 + - - +
180A LEU 3.6 1.4 - - - -
181A GLN* 1.3 79.8 - - - +
183A ASP* 1.3 66.9 + - - +
184A VAL* 3.6 3.1 + - - +
194A PHE* 3.5 10.4 - - - -
196A ALA* 4.4 6.1 - - - -
200A LYS* 3.8 19.4 - - - +
244A LYS 5.3 0.5 - - - +
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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