Contacts of the helix formed by residues 185 - 194 (chain P) in PDB entry 1HI0
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 LYS 185 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180P LEU* 2.9 37.4 + - + +
181P MET 4.2 0.2 + - - -
183P GLN* 3.2 39.7 + - + +
184P GLY* 1.3 74.1 - - - +
186P PHE* 1.3 64.3 + - - +
187P ASP 3.4 2.7 - - - -
188P ASP* 3.3 21.4 + - + +
189P ALA* 3.1 20.8 + - - +
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Residues in contact with PHE 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181P MET* 3.5 50.3 - - + -
184P GLY* 3.3 23.4 + - - -
185P LYS* 1.3 73.1 - - - +
187P ASP* 1.3 60.8 + - - +
189P ALA* 3.0 7.0 + - - +
190P TYR* 2.8 29.0 + - - +
195P MET 4.6 2.0 - - - +
196P GLY* 5.8 0.3 - - - -
355P LYS* 4.1 15.7 - - - -
358P GLU* 5.8 0.2 - - - -
359P THR* 3.8 15.7 - - + -
382P PRO 4.0 10.8 - - - +
383P SER 3.3 25.2 + - - +
384P ASN* 4.3 13.5 - - - -
385P PRO* 3.5 26.9 - - + -
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Residues in contact with ASP 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P LYS 3.4 0.8 - - - -
186P PHE* 1.3 74.0 - - - +
188P ASP* 1.3 70.0 + - - +
190P TYR* 3.2 7.6 + - - +
191P GLN* 2.8 43.1 + - - +
382P PRO* 4.3 4.9 - - - +
383P SER* 3.2 42.6 + - - -
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Residues in contact with ASP 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P LEU* 4.1 18.7 - - + +
185P LYS* 3.3 31.9 + - + +
186P PHE 3.2 0.4 - - - -
187P ASP* 1.3 79.3 - - - +
189P ALA* 1.3 65.6 + - - +
191P GLN* 4.2 13.2 + - - +
192P LEU* 2.8 36.5 + - + +
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Residues in contact with ALA 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177P ALA* 4.0 14.4 - - + +
180P LEU* 4.0 12.1 - - + +
181P MET* 3.9 27.1 - - + -
185P LYS 3.1 10.7 + - - +
186P PHE* 3.0 9.5 + - + +
188P ASP* 1.3 79.6 - - - +
190P TYR* 1.3 57.4 + - - +
193P HIS* 2.9 34.8 + - - +
194P GLN 3.6 0.9 + - - -
195P MET* 3.7 12.2 + - - +
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Residues in contact with TYR 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P MET* 2.6 42.5 + - + -
17P LEU* 3.2 16.0 - - + -
153P ILE* 3.4 10.3 - - + +
154P PRO* 3.3 21.4 - - + +
186P PHE 2.8 16.0 + - - +
187P ASP* 3.6 11.7 - - - +
189P ALA* 1.3 73.6 - - - +
191P GLN* 1.3 70.5 + - + +
194P GLN* 2.6 49.7 + - + +
195P MET 3.7 10.7 + - - +
196P GLY* 3.7 9.0 - - - -
197P GLY* 3.6 34.1 - - - +
276P PRO* 5.7 0.2 - - + -
382P PRO* 6.3 1.6 - - + -
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Residues in contact with GLN 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P MET* 4.5 25.8 - - + +
187P ASP* 2.8 36.1 + - - +
188P ASP* 3.9 15.5 + - - +
190P TYR* 1.3 87.3 - - + +
192P LEU* 1.3 67.0 + - + +
194P GLN* 3.3 12.3 + - - -
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Residues in contact with LEU 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P ARG* 5.3 4.0 + - - -
176P GLU* 4.2 9.6 - - - +
180P LEU* 4.4 11.4 - - + -
188P ASP* 2.8 28.0 + - + +
191P GLN* 1.3 81.0 - - + +
193P HIS* 1.3 93.4 + - + +
194P GLN* 3.8 6.2 + - - -
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Residues in contact with HIS 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P ARG* 4.7 11.2 + - + +
170P ALA* 6.0 0.2 - - - -
173P LYS* 3.3 40.6 - - + +
176P GLU* 3.1 30.8 + - - +
177P ALA* 4.0 24.2 - - + -
180P LEU* 4.3 6.0 - - + +
189P ALA 2.9 14.5 + - - +
192P LEU* 1.3 105.1 + - + +
194P GLN* 1.3 80.8 + - - +
195P MET* 3.0 20.7 + - + +
278P ALA* 3.2 14.4 - - - +
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Residues in contact with GLN 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154P PRO* 3.6 37.1 - - + +
155P TYR* 3.5 28.8 + - + +
169P ARG* 5.8 4.0 - - - +
190P TYR* 2.6 35.6 + - + +
191P GLN 3.3 21.6 + - - -
192P LEU 3.8 4.3 + - - +
193P HIS* 1.3 81.7 - - - +
195P MET* 1.3 57.8 + - - +
196P GLY 3.6 4.2 + - - -
276P PRO* 4.3 12.0 - - - +
278P ALA* 3.2 19.4 - - + +
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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