Contacts of the helix formed by residues 174 - 182 (chain A) in PDB entry 5HKE
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PHE* 3.7 20.8 - - + -
83A ASN* 3.5 20.5 - - - +
153A GLU* 3.5 12.1 - - - +
155A THR* 3.7 7.7 - - + +
162A TYR* 5.2 4.5 - - - +
173A PRO* 1.3 80.3 - - - +
175A PHE* 1.3 67.0 + - - +
176A ASN 3.3 2.7 - - - +
177A TYR* 2.9 34.8 + - + +
178A GLN 3.1 6.4 + - - -
402A PO4 2.5 42.4 + - - -
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Residues in contact with PHE 175 (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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151A VAL* 3.9 7.6 - - + -
153A GLU* 2.9 24.3 + - - +
162A TYR* 3.7 34.5 - + + -
163A ASP 3.8 20.6 - - - -
164A ASN* 3.5 29.4 - - - -
165A PRO* 4.3 2.0 - - + -
168A ILE 3.7 20.0 - - - -
169A LEU* 3.7 19.1 - - + -
173A PRO 4.4 1.8 - - - -
174A GLU* 1.3 73.2 - - - +
176A ASN* 1.3 67.3 - - - +
178A GLN* 3.1 5.5 + - + +
179A MET* 3.0 47.5 + - + +
225A PHE* 3.9 18.6 - + - -
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Residues in contact with ASN 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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162A TYR* 3.6 36.1 + - - +
174A GLU* 3.3 2.0 + - + +
175A PHE* 1.3 81.6 - - - +
177A TYR* 1.3 65.6 + - + +
179A MET* 3.5 6.7 + - - +
180A TYR* 2.9 30.1 + - - +
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Residues in contact with TYR 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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173A PRO* 3.6 26.2 - - + -
174A GLU* 2.9 33.7 + - + +
176A ASN* 1.3 83.9 - - + +
178A GLN* 1.3 64.9 + - - +
180A TYR* 3.9 5.8 - - - +
181A ASN* 3.0 24.9 + - - +
222A GLU* 4.2 2.6 - - - +
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LEU* 6.0 1.1 - - + -
170A THR* 3.4 12.9 + - - -
171A ASN 3.2 14.8 + - - +
172A ASN 3.2 28.3 + - - -
173A PRO* 3.4 21.7 - - - +
174A GLU 3.1 3.6 + - - +
175A PHE* 3.1 12.6 + - + +
177A TYR* 1.3 74.2 - - - +
179A MET* 1.3 63.4 + - - +
181A ASN* 3.4 18.2 + - - +
182A LEU* 3.5 10.9 + - - +
221A PRO 4.3 2.0 + - - -
222A GLU* 3.3 18.7 - - - +
225A PHE* 3.4 52.3 - - + +
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Residues in contact with MET 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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165A PRO* 3.8 25.6 - - + -
166A ILE* 3.6 31.2 - - + -
175A PHE* 3.0 52.2 + - + +
176A ASN* 3.9 7.0 - - - +
178A GLN* 1.3 73.7 - - - +
180A TYR* 1.3 66.5 + - - +
182A LEU* 3.2 36.3 + - + +
183A ASN* 4.1 5.8 + - - +
225A PHE* 4.0 5.6 - - - -
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Residues in contact with TYR 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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176A ASN 2.9 18.3 + - - +
177A TYR* 3.9 6.5 - - - +
179A MET* 1.3 77.0 - - - +
181A ASN* 1.3 60.1 + - - +
183A ASN* 3.0 51.9 + - + +
184A LYS 4.5 0.3 + - - -
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Residues in contact with ASN 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 TYR 3.0 18.4 + - - +
178A GLN* 3.5 8.8 + - - +
179A MET 3.2 0.4 - - - -
180A TYR* 1.3 81.2 - - - +
182A LEU* 1.3 60.9 + - - +
183A ASN 3.2 0.7 + - - -
184A LYS* 3.3 29.6 + - - +
185A TYR* 3.4 17.6 + - - -
222A GLU* 3.5 35.5 + - - +
225A PHE* 6.3 0.2 - - - -
226A VAL* 3.5 28.5 - - - +
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Residues in contact with LEU 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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166A ILE* 3.9 29.2 - - + -
178A GLN 3.8 6.5 - - - +
179A MET* 3.2 28.1 + - + +
181A ASN* 1.3 76.4 - - - +
183A ASN* 1.3 66.2 - - - +
185A TYR* 2.9 27.5 + - + +
186A ARG* 4.0 1.0 + - - -
225A PHE* 4.2 7.2 - - + -
226A VAL* 4.0 35.9 - - + -
229A THR* 4.1 21.8 - - + +
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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