Contacts of the helix formed by residues 189 - 197 (chain B) in PDB entry 5K58
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 ARG 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.2 25.5 - - - +
160A SER* 3.4 31.9 + - - -
161A GLN* 3.2 55.6 - - - +
96B LEU* 5.6 1.3 - - - -
165B PHE* 3.8 20.3 - - + -
169B MET* 3.7 27.7 - - - +
172B ARG* 5.8 0.4 - - - +
182B PRO 4.6 3.1 - - - -
184B ASP 3.8 11.0 + - - -
185B ASP* 3.2 19.3 + - - +
186B PHE* 2.4 38.4 + - + +
188B ALA* 1.3 72.3 - - - +
190B TRP* 1.3 62.9 + - - +
191B PRO 3.3 1.6 - - - -
192B LEU* 3.1 13.3 + - - +
193B ILE* 3.7 6.8 - - - +
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Residues in contact with TRP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B THR* 3.8 14.9 - - + +
88B LEU* 3.5 43.7 - - + -
89B ARG* 3.5 58.7 - - + +
92B VAL* 4.7 4.3 - - + -
186B PHE* 2.8 36.0 + + + +
187B ASP 4.6 2.2 - - - +
189B ARG* 1.3 72.1 - - - +
191B PRO* 1.4 68.4 - - + +
192B LEU 2.9 4.9 - - - -
193B ILE* 2.8 44.0 + - + -
194B ALA* 3.3 37.9 + - + +
197B LEU* 4.6 0.4 - - + -
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Residues in contact with PRO 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN* 5.1 2.1 - - - +
187B ASP 3.1 23.6 - - - +
188B ALA* 3.6 6.3 - - - +
189B ARG 3.5 6.3 - - - +
190B TRP* 1.4 99.6 - - + +
192B LEU* 1.3 62.2 + - + +
193B ILE 3.3 0.7 - - - -
194B ALA* 4.9 3.4 - - + +
195B ALA* 3.1 24.3 + - - +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A THR* 4.0 21.8 - - + +
157A LEU* 4.3 8.5 - - + +
158A LEU* 3.6 33.2 - - + +
161A GLN* 3.1 42.8 - - + +
196A GLN* 3.4 40.0 - - + +
198A GLN* 5.5 1.6 - - - +
188B ALA 3.2 25.6 - - - +
189B ARG 3.1 4.1 + - - +
190B TRP 2.8 1.4 + - - -
191B PRO* 1.3 82.7 - - + +
193B ILE* 1.3 62.0 + - - +
195B ALA* 3.8 6.7 - - - +
196B GLN* 3.9 8.1 - - - +
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLN* 4.9 4.3 - - - +
88B LEU* 4.3 3.8 - - + -
92B VAL* 4.2 14.4 - - + -
162B ILE* 3.6 37.9 - - + +
165B PHE* 3.8 34.5 - - + -
186B PHE* 4.8 3.8 - - + -
189B ARG 3.7 11.0 - - - +
190B TRP* 2.8 44.6 + - + +
192B LEU* 1.3 78.8 - - - +
194B ALA* 1.3 56.3 + - - +
195B ALA 3.0 4.0 - - - -
196B GLN* 3.0 32.6 + - - +
197B LEU* 3.8 5.1 + - - +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B THR* 4.6 6.3 - - + -
190B TRP* 3.3 38.6 + - + +
191B PRO* 5.1 2.9 - - + +
193B ILE* 1.3 74.0 - - - +
195B ALA* 1.3 53.9 + - - +
196B GLN 2.9 5.4 - - - -
197B LEU* 2.7 48.5 + - + +
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ALA* 3.3 32.2 - - - +
196A GLN* 4.3 2.7 - - - +
198A GLN* 4.3 8.3 - - - +
191B PRO 3.1 23.1 + - - +
192B LEU* 3.8 15.3 - - - +
194B ALA* 1.3 77.1 - - - +
196B GLN* 1.3 58.4 + - - +
197B LEU 5.2 0.4 - - - -
198B GLN* 4.1 11.5 + - - +
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Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.3 42.2 + - + +
193A ILE* 4.2 3.4 - - - +
195A ALA* 4.5 4.3 - - + -
196A GLN* 4.5 9.2 + - - +
153B THR* 4.2 6.9 + - - +
158B LEU* 3.8 23.8 - - + +
161B GLN* 3.8 25.8 - - - +
162B ILE* 3.1 28.9 - - - +
192B LEU 3.9 12.3 - - - +
193B ILE* 3.0 13.7 + - - +
194B ALA 2.9 1.0 - - - -
195B ALA* 1.3 80.5 - - - +
197B LEU* 1.3 59.5 + - - +
198B GLN* 3.1 19.9 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B THR* 3.6 32.8 - - + -
88B LEU* 3.7 33.4 - - + -
140B MET* 5.6 3.4 - - + -
151B TYR* 3.7 23.6 - - + +
158B LEU* 3.6 28.0 - - + -
162B ILE* 5.6 1.6 - - + -
190B TRP* 4.6 2.2 - - + -
193B ILE 4.2 2.9 - - - +
194B ALA* 2.7 32.8 + - + +
196B GLN* 1.3 76.1 - - - +
198B GLN* 1.3 63.6 + - - +
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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