Contacts of the helix formed by residues 168 - 179 (chain I) in PDB entry 5DSV
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 168 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35I THR* 3.2 24.5 + - - +
166I GLY 3.5 2.9 - - - -
167I LYS* 1.3 75.9 - - - +
169I ARG* 1.3 62.5 + - - +
170I GLN* 3.7 4.0 - - + +
171I ALA* 3.6 30.7 - - + +
172I ALA* 3.5 7.6 - - - +
200I VAL* 3.7 16.4 - - + +
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Residues in contact with ARG 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I MET* 5.2 8.9 + - - +
30I VAL* 3.4 33.9 - - - +
31I GLU* 4.0 20.4 + - - +
134I SER* 4.0 10.9 + - - -
150I MET* 5.7 4.0 - - - +
152I ASP* 5.4 6.7 - - - +
163I CYS* 6.0 1.1 - - - -
164I ALA* 3.5 28.0 + - - +
165I ILE* 4.1 12.9 - - - +
166I GLY 2.9 22.2 + - - +
167I LYS 3.9 0.4 + - - -
168I ALA* 1.3 70.6 - - - +
170I GLN* 1.3 67.7 + - + +
172I ALA* 3.4 3.3 + - - +
173I LYS* 3.1 48.7 + - - +
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Residues in contact with GLN 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I ALA* 3.1 4.5 - - + +
169I ARG* 1.3 80.8 - - + +
171I ALA* 1.3 68.5 + - - +
173I LYS* 3.3 23.1 + - - +
174I THR* 3.0 27.0 + - + +
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Residues in contact with ALA 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ALA* 3.6 20.2 - - + +
170I GLN* 1.3 80.1 - - - +
172I ALA* 1.3 60.0 + - - +
174I THR* 2.9 19.6 + - - -
175I GLU* 3.3 18.0 + - + +
200I VAL* 3.9 16.4 - - + -
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Residues in contact with ALA 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I THR* 4.2 3.6 - - + -
37I ILE* 4.1 13.5 - - + -
164I ALA* 3.8 16.2 - - + -
168I ALA 3.5 18.9 + - - +
169I ARG 3.4 0.6 + - - -
170I GLN 3.3 0.8 - - - -
171I ALA* 1.3 79.6 - - - +
173I LYS* 1.3 60.0 + - - +
175I GLU* 3.5 3.9 + - - +
176I ILE* 3.1 30.8 + - - +
196I ILE* 4.0 10.1 - - + +
200I VAL* 3.8 19.0 - - + +
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Residues in contact with LYS 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I TYR* 5.0 9.6 + - + -
163I CYS* 4.1 20.1 - - + -
164I ALA* 3.9 18.4 - - + +
169I ARG* 3.1 42.1 + - - +
170I GLN* 3.9 15.9 - - - +
171I ALA 3.2 0.6 - - - -
172I ALA* 1.3 75.0 - - - +
174I THR* 1.3 64.7 + - - +
175I GLU 3.1 0.2 - - - -
176I ILE* 3.0 4.7 + - - -
177I GLU* 3.0 25.9 + - - +
54J LEU 5.7 0.6 + - - -
55J SER* 4.8 14.6 - - - +
57J LEU* 3.4 32.2 - - + +
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Residues in contact with THR 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170I GLN* 3.0 22.6 + - + +
171I ALA* 2.9 18.5 + - - -
173I LYS* 1.3 76.0 - - - +
175I GLU* 1.3 60.2 + - - +
177I GLU* 3.3 33.9 + - - +
178I LYS* 3.6 16.7 + - - +
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Residues in contact with GLU 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I ALA* 3.3 17.9 + - + +
172I ALA* 3.5 8.7 - - - +
173I LYS 3.1 0.4 - - - -
174I THR* 1.3 75.4 + - - +
176I ILE* 1.3 63.5 + - - +
178I LYS* 3.2 51.9 + - - +
179I LEU* 4.0 4.7 + - - +
196I ILE* 3.7 32.2 - - + +
199I ILE* 3.5 40.6 - - + +
200I VAL* 4.7 1.1 - - + -
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Residues in contact with ILE 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I ILE* 4.2 17.3 - - + -
38I GLY 4.9 2.0 - - - +
39I ILE* 3.7 30.3 - - + -
162I GLY* 4.5 7.9 - - - -
163I CYS* 4.0 29.8 - - - +
164I ALA* 4.3 2.5 - - + -
172I ALA 3.1 21.1 + - - +
173I LYS* 3.0 11.0 + - + +
175I GLU* 1.3 73.7 - - - +
177I GLU* 1.3 65.8 + - - +
178I LYS 3.1 1.8 - - - -
179I LEU* 3.0 21.6 + - - +
181I MET* 3.8 9.4 - - + +
196I ILE* 3.9 19.1 - - + -
57J LEU* 3.7 16.2 - - + -
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Residues in contact with GLU 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I LYS* 3.0 14.2 + - - +
174I THR* 3.3 38.6 + - - +
176I ILE* 1.3 77.2 - - - +
178I LYS* 1.3 61.0 + - - +
179I LEU 3.5 6.2 + - - +
180I GLN* 5.2 1.6 + - - -
181I MET* 4.5 5.1 - - - +
55J SER* 4.5 2.9 + - - -
56J LYS* 3.3 36.5 + - + +
57J LEU* 3.6 24.7 - - + +
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Residues in contact with LYS 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I THR* 3.8 14.4 - - - +
175I GLU* 3.2 49.8 + - - +
176I ILE 3.1 0.2 - - - -
177I GLU* 1.3 79.7 - - + +
179I LEU* 1.3 67.9 + - + +
180I GLN* 3.8 13.0 + - - +
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Residues in contact with LEU 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I ILE* 4.1 20.0 - - + -
175I GLU 4.0 9.9 - - - +
176I ILE* 3.0 10.9 + - - +
177I GLU 3.5 3.1 - - - +
178I LYS* 1.3 85.6 - - + +
180I GLN* 1.3 64.4 + - - +
181I MET* 3.4 28.2 - - + +
184I MET* 4.6 9.4 - - - -
189I ILE* 5.4 2.5 - - + -
192I GLU* 3.4 50.3 - - + +
196I ILE* 3.7 23.6 - - + -
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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