Contacts of the helix formed by residues 169 - 181 (chain N) in PDB entry 1S72
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 169 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143N ARG* 3.3 48.1 + - + +
144N GLY* 4.2 11.0 - - - +
145N ALA* 4.3 7.0 - - + +
148N ALA* 4.0 24.5 - - + -
167N ASP 4.2 4.0 - - - +
168N LEU* 1.3 86.2 - - - +
170N GLU* 1.3 78.0 + - - +
171N HIS 3.3 0.7 - - - -
172N PHE* 3.1 18.4 - - + +
173N ASP* 2.9 16.1 - - - +
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Residues in contact with GLU 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143N ARG* 3.8 13.0 + - - +
168N LEU* 3.2 31.6 - - + +
169N PRO* 1.3 94.7 - - - +
171N HIS* 1.3 63.5 + - - +
172N PHE 3.0 2.0 - - - -
173N ASP* 3.1 15.3 + - - +
174N GLU* 3.0 31.8 + - + +
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Residues in contact with HIS 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N GLY 2.8 22.3 + - - -
71N TRP* 3.8 18.0 - + + -
72N GLU* 3.3 42.8 + - + -
73N ALA* 4.7 0.2 - - - +
163N PHE* 3.2 23.3 - + + -
168N LEU* 3.6 30.0 + - + +
170N GLU* 1.3 79.2 - - - +
172N PHE* 1.3 61.3 + - - +
174N GLU* 3.4 23.7 + - + +
175N LEU* 3.1 21.3 + - + +
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Residues in contact with PHE 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71N TRP* 4.0 10.0 - - + -
79N PRO* 3.7 25.1 - - + -
82N TYR* 3.8 21.5 - + - -
83N LEU* 3.8 31.4 - - + -
139N TRP* 3.8 24.9 - + - -
142N THR* 4.0 15.0 - - + -
143N ARG* 3.4 49.6 - - + +
168N LEU 3.9 2.1 + - - +
169N PRO* 3.1 12.9 + - + +
171N HIS* 1.3 79.4 - - - +
173N ASP* 1.3 68.8 + - - +
175N LEU* 3.2 4.5 + - - +
176N ARG* 2.9 25.9 + - - +
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Residues in contact with ASP 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139N TRP* 5.1 5.4 + - - -
143N ARG* 2.5 39.9 + - - +
169N PRO 2.9 10.7 - - - +
170N GLU* 3.1 12.2 + - - +
172N PHE* 1.3 83.6 - - - +
174N GLU* 1.3 60.9 - - + +
176N ARG* 3.3 5.6 + - - +
177N GLU* 2.8 34.3 + - - +
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Residues in contact with GLU 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N LEU* 5.7 1.7 - - - +
170N GLU* 3.0 17.9 + - + +
171N HIS* 3.4 29.9 - - + +
173N ASP* 1.3 76.4 - - + +
175N LEU* 1.3 52.8 + - - +
177N GLU* 3.3 9.0 - - - +
178N THR* 2.7 37.4 + - - +
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Residues in contact with LEU 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N LEU* 3.9 18.8 - - + -
69N TYR* 3.6 40.4 - - + +
70N GLY 4.6 5.6 - - - +
71N TRP* 3.2 36.6 - - + -
83N LEU* 3.4 19.5 - - + -
171N HIS* 3.1 12.2 + - + +
172N PHE 3.6 7.4 - - - +
173N ASP 3.1 0.2 - - - -
174N GLU* 1.3 75.9 - - - +
176N ARG* 1.3 68.0 + - - +
177N GLU 3.1 1.3 - - - -
178N THR* 2.9 11.1 + - - +
179N LEU* 2.8 34.3 + - + +
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Residues in contact with ARG 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N TYR* 2.6 36.1 + - + -
83N LEU* 3.9 18.1 - - + +
86N LEU* 4.3 10.5 - - + +
124N ASP* 4.0 13.8 + - - +
139N TRP* 3.0 39.1 - - - -
172N PHE* 2.9 19.8 + - + +
173N ASP* 3.8 7.2 - - - +
175N LEU* 1.3 76.5 - - - +
177N GLU* 1.3 65.9 + - - +
179N LEU* 3.2 7.6 + - - +
180N LEU* 3.0 46.4 + - + +
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Residues in contact with GLU 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173N ASP 2.8 19.4 + - - +
174N GLU* 3.3 9.4 - - - +
176N ARG* 1.3 80.2 - - - +
178N THR* 1.3 65.0 + - - +
180N LEU* 3.3 13.4 + - - +
181N ASP* 3.5 10.4 + - - +
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Residues in contact with THR 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N TYR* 4.4 18.8 + - + +
174N GLU 2.7 21.2 + - - -
175N LEU* 2.9 17.4 + - + +
177N GLU* 1.3 78.1 - - - +
179N LEU* 1.3 65.9 + - - +
180N LEU 2.9 1.9 + - - -
181N ASP* 3.0 23.1 + - + +
184N ILE* 4.1 15.9 - - + +
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Residues in contact with LEU 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N LEU* 4.9 2.5 - - + -
69N TYR* 4.2 19.5 - - + -
83N LEU* 3.9 44.4 - - + +
86N LEU* 4.0 20.4 - - + -
87N LEU* 4.3 18.2 - - + +
90N LEU* 3.3 24.4 - - + +
175N LEU* 2.8 27.3 + - + +
176N ARG 3.7 4.9 - - - +
178N THR* 1.3 72.7 - - - +
180N LEU* 1.3 60.5 + - - +
181N ASP 3.4 7.6 - - - +
184N ILE* 3.0 40.4 - - + +
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Residues in contact with LEU 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N LEU* 4.0 32.8 - - + -
90N LEU* 4.8 9.0 - - + -
124N ASP* 5.0 9.0 - - + +
176N ARG* 3.0 44.6 + - + +
177N GLU* 3.8 10.1 - - - +
178N THR 2.9 0.8 + - - -
179N LEU* 1.3 75.8 - - - +
181N ASP* 1.3 67.7 + - - +
182N GLY* 3.6 1.0 + - - -
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Residues in contact with ASP 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N GLU 3.5 7.3 + - - +
178N THR* 3.0 16.8 + - + +
179N LEU 3.4 8.5 - - - +
180N LEU* 1.3 82.1 - - - +
182N GLY* 1.3 81.8 + - - +
183N ASP* 3.2 28.6 + - - +
184N ILE* 3.6 12.7 - - - +
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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