Contacts of the helix formed by residues 179 - 187 (chain A) in PDB entry 1REC
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 ASN 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A PHE* 3.6 24.4 - - - -
175A GLY* 3.0 18.7 + - - +
176A THR 3.9 4.2 - - - +
178A ALA* 1.3 72.6 - - + +
180A LYS* 1.3 60.2 + - - +
181A GLU* 3.2 19.8 + - - +
182A ILE* 2.8 50.0 + - + +
183A LEU 3.3 6.8 + - - -
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Residues in contact with LYS 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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99A ASN* 4.4 10.0 + - - +
176A THR 3.5 10.7 + - - -
177A LEU* 2.7 43.4 + - - +
178A ALA 3.9 4.8 + - - +
179A ASN* 1.3 73.6 + - - +
181A GLU* 1.3 61.5 + - - +
183A LEU* 3.5 27.9 - - + +
184A ARG* 3.0 24.4 + - - +
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Residues in contact with GLU 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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154A LYS* 4.3 6.8 + - - -
158A PHE* 4.1 24.2 - - + -
179A ASN* 3.0 22.7 + - - +
180A LYS* 1.3 78.6 - - - +
182A ILE* 1.3 61.8 + - - +
184A ARG* 3.1 45.6 + - - +
185A LEU* 3.2 28.1 + - - +
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Residues in contact with ILE 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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155A ILE* 5.5 2.5 - - + -
158A PHE* 3.8 37.0 - - + +
159A PHE* 3.7 35.2 - - + -
175A GLY* 3.7 24.2 - - - +
176A THR* 3.8 15.3 - - + -
179A ASN* 2.8 32.6 + - + +
181A GLU* 1.3 73.6 - - - +
183A LEU* 1.3 65.1 + - - +
185A LEU* 3.0 19.8 + - + +
186A ILE* 3.1 16.6 + - + +
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Residues in contact with LEU 183 (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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98A THR* 3.5 34.5 - - + -
99A ASN* 4.1 19.7 - - + +
102A LEU* 3.9 22.9 - - + -
176A THR* 3.5 15.8 + - - +
179A ASN 3.3 1.8 + - - -
180A LYS* 3.3 42.5 + - + +
182A ILE* 1.3 79.0 - - - +
184A ARG* 1.3 62.1 + - - +
186A ILE* 3.5 11.1 + - + +
187A GLN* 3.0 27.1 + - - +
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Residues in contact with ARG 184 (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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142A PRO* 5.2 4.0 - - - +
145A GLU* 2.7 43.8 + - - -
151A ARG* 3.6 15.8 + - - +
154A LYS* 3.9 2.8 - - - +
180A LYS 3.0 16.6 + - - +
181A GLU* 3.1 40.9 + - - +
182A ILE 3.2 0.2 - - - -
183A LEU* 1.3 78.2 - - - +
185A LEU* 1.3 73.1 + - - +
187A GLN* 3.4 31.4 + - - +
196A LYS* 4.9 19.3 - - + -
197A LEU* 6.3 1.2 - - - +
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Residues in contact with LEU 185 (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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109A TYR* 4.6 0.5 + - - -
126A VAL* 5.0 1.9 - - - +
129A ILE* 5.9 0.9 - - - +
145A GLU* 3.8 26.2 - - + +
151A ARG* 3.3 39.2 + - - +
154A LYS* 3.9 20.9 - - + -
155A ILE* 3.5 34.4 - - + +
158A PHE* 3.6 36.3 - - + -
181A GLU 3.2 15.6 + - - +
182A ILE* 3.0 12.1 + - + +
184A ARG* 1.3 84.9 - - - +
186A ILE* 1.3 59.5 + - - +
187A GLN 3.7 1.4 + - - +
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Residues in contact with ILE 186 (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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98A THR* 4.5 0.7 - - + -
102A LEU* 4.9 2.0 - - + -
105A ALA* 4.7 3.6 - - + -
109A TYR* 2.7 37.5 + - + +
155A ILE* 4.1 28.5 - - + -
159A PHE* 4.9 1.1 - - + -
172A PHE* 4.4 24.0 - - + -
176A THR* 4.0 17.9 - - + -
182A ILE* 3.1 19.2 + - + +
183A LEU* 3.6 27.1 - - + +
185A LEU* 1.3 76.0 - - - +
187A GLN* 1.3 71.4 + - - +
188A PHE* 3.1 26.0 + - + +
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Residues in contact with GLN 187 (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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98A THR* 3.1 21.8 + - + +
129A ILE* 3.8 10.2 - - - +
151A ARG* 5.3 2.6 + - - -
183A LEU* 3.0 17.4 + - - +
184A ARG* 3.4 25.9 + - - +
185A LEU 3.3 3.6 - - - +
186A ILE* 1.3 79.0 - - - +
188A PHE* 1.3 61.4 - - - +
189A GLU* 3.3 19.7 - - - +
192A LYS* 3.7 32.8 + - + +
193A VAL* 3.8 18.7 - - + +
196A LYS* 3.8 27.4 - - - +
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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