Contacts of the helix formed by residues 171 - 179 (chain A) in PDB entry 3K8G
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 PRO 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A LEU* 1.4 89.6 - - + +
172A PRO* 1.3 77.2 - - + +
173A ARG 3.4 0.7 - - - -
174A PHE* 3.2 18.0 + - + +
175A GLU* 3.1 19.3 + - - +
190A TYR* 3.6 44.2 - - + -
215A GLU* 3.6 33.2 - - + +
217A TYR* 4.0 0.2 - - - +
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Residues in contact with PRO 172 (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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170A LEU 3.8 1.3 - - - +
171A PRO* 1.3 87.0 - - + +
173A ARG* 1.3 57.3 + - - +
175A GLU* 3.4 9.3 + - + +
176A LYS* 2.9 27.3 + - - +
215A GLU* 5.3 2.5 - - - +
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Residues in contact with ARG 173 (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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171A PRO* 3.4 1.0 - - - +
172A PRO* 1.3 76.6 - - - +
174A PHE* 1.3 61.8 + - - +
176A LYS* 3.3 7.9 + - + +
177A GLU* 2.8 52.6 + - - +
186A THR* 4.1 3.6 + - - +
215A GLU* 4.5 3.5 + - - +
217A TYR* 3.6 49.7 + - + +
228A THR* 4.5 10.9 + - - +
303A MPD 3.1 41.6 + - - +
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Residues in contact with PHE 174 (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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37A LEU* 4.0 11.4 - - + -
47A TYR* 3.6 31.9 - - + -
48A LEU 3.9 17.7 - - - -
49A TYR* 4.1 3.4 - - + -
170A LEU* 3.7 27.6 - - + -
171A PRO* 3.2 19.2 + - + +
173A ARG* 1.3 78.5 - - - +
175A GLU* 1.3 64.3 + - - +
177A GLU* 3.2 3.3 + - - +
178A CYS* 3.0 41.7 + - - -
188A ALA* 3.5 37.0 - - + +
189A LEU 4.0 3.6 - - - -
190A TYR* 3.8 16.8 - - + -
217A TYR* 3.3 18.9 + + - +
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Residues in contact with GLU 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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35A ASP* 5.3 3.8 - - - +
37A LEU* 4.0 16.4 - - - +
168A PRO 4.8 4.2 - - - +
169A GLN* 5.4 0.2 - - - -
170A LEU* 3.5 37.7 + - + +
171A PRO 3.1 18.9 + - - +
172A PRO* 3.5 10.3 - - + +
174A PHE* 1.3 78.2 - - - +
176A LYS* 1.3 62.2 + - - +
178A CYS* 3.3 14.2 + - - +
179A THR* 3.5 14.9 + - - +
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Residues in contact with LYS 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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172A PRO 2.9 15.5 + - - +
173A ARG* 3.6 13.2 - - + +
175A GLU* 1.3 73.2 - - - +
177A GLU* 1.3 67.7 + - - +
179A THR* 3.0 24.3 + - - +
180A SER* 2.8 27.6 + - - +
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Residues in contact with GLU 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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49A TYR* 3.2 31.6 + - + -
173A ARG* 2.8 59.9 + - + +
174A PHE 3.7 3.6 - - - +
176A LYS* 1.3 75.1 - - - +
178A CYS* 1.3 57.9 + - - +
180A SER* 2.9 25.4 + - - -
184A SER* 3.2 27.9 + - - -
186A THR* 3.5 18.6 + - + +
188A ALA* 4.2 17.7 - - + -
217A TYR* 4.3 3.8 - - + -
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Residues in contact with CYS 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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37A LEU* 3.8 17.5 - - + -
49A TYR* 3.8 30.4 + - - -
83A TYR* 3.0 39.6 + - + -
174A PHE* 3.0 45.9 + - - -
175A GLU* 3.5 11.7 - - - +
176A LYS 3.2 0.6 - - - -
177A GLU* 1.3 76.7 - - - +
179A THR* 1.3 62.3 + - + +
180A SER 3.8 0.2 + - - -
181A GLU* 4.7 2.4 - - - +
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Residues in contact with THR 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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175A GLU 3.5 10.3 + - - +
176A LYS* 3.0 23.0 + - - +
178A CYS* 1.3 82.4 - - + +
180A SER* 1.3 58.9 + - - +
181A GLU* 3.4 6.7 + - - +
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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