Contacts of the helix formed by residues 181 - 189 (chain A) in PDB entry 5T0I
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A TYR* 5.8 0.4 - - - -
179A GLY 3.3 6.7 + - - +
180A CYS* 1.3 71.6 - - - +
182A GLU* 1.3 72.0 + - + +
183A GLN* 3.2 5.0 + - - -
184A ILE* 3.2 6.3 + - - +
185A GLU* 2.8 38.1 + - + +
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Residues in contact with GLU 182 (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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181A LYS* 1.3 89.3 - - + +
183A GLN* 1.3 74.1 + - - +
185A GLU* 4.1 6.3 - - - -
186A LYS* 3.1 37.1 + - + +
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Residues in contact with GLN 183 (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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180A CYS* 3.4 16.5 - - + +
181A LYS 3.4 18.5 + - - -
182A GLU* 1.3 84.8 + - - +
184A ILE* 1.3 62.3 + - - +
185A GLU 3.2 0.2 + - - -
186A LYS* 4.2 1.9 - - - +
187A LEU* 3.3 26.8 + - + +
224A LEU* 6.5 0.4 - - + -
341A ILE* 4.3 24.3 - - + +
342A GLU 5.1 2.5 - - - +
343A PHE* 5.9 2.7 - - + -
344A SER* 3.1 38.2 - - - +
347A ASP* 5.8 2.6 + - - -
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Residues in contact with ILE 184 (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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174A TYR* 3.7 27.8 - - + +
177A VAL* 4.5 9.4 - - + -
180A CYS* 3.2 25.7 + - + +
181A LYS* 3.2 5.8 + - - +
183A GLN* 1.3 79.3 - - - +
185A GLU* 1.3 61.1 + - - +
187A LEU* 3.6 22.7 - - + +
188A ARG* 3.1 28.4 + - - +
224A LEU* 3.6 30.1 - - + -
227A ARG* 3.3 37.9 - - - +
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Residues in contact with GLU 185 (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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174A TYR* 5.4 2.8 + - - -
181A LYS* 2.8 26.6 + - + +
182A GLU* 3.8 6.7 - - - +
183A GLN 3.1 0.6 - - - -
184A ILE* 1.3 80.1 - - + +
186A LYS* 1.3 63.2 + - + +
188A ARG* 2.7 56.8 + - - +
189A GLU* 3.1 23.2 + - - +
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Residues in contact with LYS 186 (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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182A GLU* 3.1 24.7 + - + +
183A GLN* 4.3 1.8 - - - +
185A GLU* 1.3 80.6 - - + +
187A LEU* 1.3 58.2 - - - +
189A GLU* 3.3 37.6 + - - +
190A VAL* 3.8 9.2 + - - +
339A ARG* 3.3 57.3 + - - +
341A ILE* 5.9 2.7 - - + -
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Residues in contact with LEU 187 (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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183A GLN* 3.3 22.9 + - + +
184A ILE* 3.6 35.2 - - + +
186A LYS* 1.3 75.6 - - - +
188A ARG* 1.3 60.9 + - - +
189A GLU 3.5 0.2 - - - -
190A VAL* 3.1 25.9 - - + +
191A VAL* 3.2 11.8 - - + +
212A VAL* 5.8 3.8 - - + -
214A LEU* 4.4 15.9 - - + -
224A LEU* 4.4 17.0 - - + +
227A ARG* 3.7 14.8 - - - +
318A LEU* 6.5 0.4 - - + -
339A ARG* 5.2 7.2 - - + +
341A ILE* 3.8 24.5 - - + -
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Residues in contact with ARG 188 (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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174A TYR* 4.8 20.0 + - - -
184A ILE 3.1 17.9 + - - +
185A GLU* 2.7 44.7 + - - +
187A LEU* 1.3 75.6 - - - +
189A GLU* 1.3 57.7 + - - +
190A VAL 3.2 5.3 + - - -
191A VAL* 4.4 1.8 - - - -
192A GLU* 2.9 61.5 + - + +
193A THR* 3.3 10.7 + - - +
227A ARG* 3.8 20.0 - - - +
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Residues in contact with GLU 189 (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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185A GLU* 3.1 19.4 + - - +
186A LYS* 3.3 51.6 + - - +
188A ARG* 1.3 75.3 - - - +
190A VAL* 1.3 59.1 + - - +
191A VAL 3.3 0.4 - - - -
193A THR* 3.3 21.8 - - + +
194A PRO* 3.1 20.7 - - - +
201A PHE* 3.7 16.1 - - + -
316A LYS* 4.6 0.5 + - - -
339A ARG* 4.9 3.1 + - - -
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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