Contacts of the helix formed by residues 187 - 202 (chain A) in PDB entry 5KAL
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 THR 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ASN* 4.2 2.5 - - - -
179A ALA* 3.9 20.9 - - + +
185A SER 5.8 0.2 - - - +
186A ILE* 1.3 79.0 - - - +
188A SER* 1.3 66.0 + - - +
189A TYR* 3.6 14.8 + - - +
190A GLY* 3.1 23.4 + - - -
191A PHE* 3.2 14.2 + - - -
305A VAL* 4.6 8.0 + - + +
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Residues in contact with SER 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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169A LYS* 3.9 29.0 - - - +
173A LYS* 4.0 9.0 + - - -
178A ASN* 3.0 24.7 + - - +
187A THR* 1.3 74.2 - - - +
189A TYR* 1.3 62.8 + - - +
191A PHE* 3.1 9.9 + - - +
192A ASN* 2.9 29.0 + - - +
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Residues in contact with TYR 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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147A ASN* 3.2 43.5 + - + +
151A LEU* 4.3 16.2 - - + -
187A THR* 3.2 9.8 + - - +
188A SER* 1.3 77.6 - - - +
190A GLY* 1.3 63.2 + - - +
192A ASN* 3.2 10.5 + - - +
193A LEU* 3.0 51.3 + - + +
297A ASP* 3.1 26.7 + - - -
298A PRO* 3.4 17.0 - - - +
305A VAL* 4.5 14.1 - - + -
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Residues in contact with GLY 190 (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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186A ILE* 4.1 9.4 - - - -
187A THR* 3.1 13.1 + - - -
189A TYR* 1.3 79.2 - - - +
191A PHE* 1.3 56.6 + - - +
193A LEU* 3.1 15.7 + - - +
194A MET* 2.9 37.7 + - - +
295A ILE* 4.5 4.9 - - - +
305A VAL* 4.2 11.9 - - - -
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Residues in contact with PHE 191 (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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168A ILE* 3.9 28.7 - - + -
169A LYS* 5.6 5.8 - - + +
171A TRP* 4.6 10.3 - + - -
172A SER* 3.6 33.9 - - - +
177A LEU* 4.2 18.8 - - + -
178A ASN* 4.6 3.4 - - - -
186A ILE* 3.6 36.8 - - + -
187A THR 3.2 23.0 + - - -
188A SER* 3.1 10.3 + - - +
190A GLY* 1.3 72.5 - - - +
192A ASN* 1.3 66.5 + - - +
194A MET* 3.2 25.3 + - + +
195A VAL* 2.9 28.9 + - - +
244A PHE* 6.0 2.2 - + - -
317A LEU* 5.2 7.2 - - + -
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Residues in contact with ASN 192 (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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54A SER* 5.9 3.8 - - - +
57A VAL* 4.0 26.2 - - - +
58A TYR* 3.7 9.7 + - - -
151A LEU* 4.2 20.7 - - + +
155A PHE* 4.3 7.9 - - + -
165A SER* 2.7 28.2 + - - -
169A LYS* 5.7 4.0 - - - +
188A SER* 2.9 17.2 + - - +
189A TYR* 3.4 12.2 - - - +
191A PHE* 1.3 75.5 - - - +
193A LEU* 1.3 63.3 + - - +
195A VAL* 3.2 6.1 + - - +
196A VAL* 3.0 29.5 + - - +
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Residues in contact with LEU 193 (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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147A ASN* 6.2 0.4 - - + -
151A LEU* 4.5 8.5 - - + -
189A TYR* 3.0 60.6 + - + +
190A GLY* 3.1 10.7 + - - +
192A ASN* 1.3 74.8 - - - +
194A MET* 1.3 62.9 + - - +
196A VAL* 3.4 4.9 + - - +
197A TYR* 2.9 24.7 + - - +
259A ILE* 4.3 4.2 - - + +
261A LEU* 3.8 31.5 - - + +
295A ILE* 3.8 28.7 - - + -
296A GLU 4.6 7.0 - - - +
298A PRO* 4.6 11.2 - - + -
305A VAL* 4.3 6.5 - - + -
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Residues in contact with MET 194 (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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186A ILE* 3.6 43.5 - - + -
190A GLY 2.9 19.1 + - - +
191A PHE* 3.2 30.9 + - + +
193A LEU* 1.3 77.4 - - - +
195A VAL* 1.3 63.0 + - - +
197A TYR* 3.2 2.6 + - - +
198A TYR* 2.9 24.4 + - - +
244A PHE* 4.9 6.3 - - + -
248A PHE* 3.7 23.4 - - + -
259A ILE* 4.0 24.7 - - + -
293A TRP* 3.9 22.7 - - - +
295A ILE* 3.9 11.0 - - + -
317A LEU* 5.8 2.7 - - - -
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Residues in contact with VAL 195 (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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155A PHE* 4.6 8.1 - - + -
161A CYS 5.6 0.2 - - - +
164A LEU* 4.4 17.3 - - + -
165A SER* 4.3 32.5 - - - +
168A ILE* 4.4 17.0 - - + -
191A PHE 2.9 20.7 + - - +
192A ASN* 3.2 8.5 + - - +
194A MET* 1.3 75.9 - - - +
196A VAL* 1.3 63.5 + - + +
198A TYR* 3.3 1.9 + - - +
199A LEU* 2.9 40.2 + - + +
244A PHE* 4.2 21.5 - - + -
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Residues in contact with VAL 196 (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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151A LEU* 3.9 19.5 - - + -
154A TYR* 3.8 37.9 - - + -
155A PHE* 4.4 23.6 - - + -
192A ASN 3.0 19.2 + - - +
193A LEU 3.9 2.9 - - - +
195A VAL* 1.3 76.5 - - - +
197A TYR* 1.3 58.6 + - - +
199A LEU* 3.4 8.4 + - + +
200A LEU* 2.9 34.3 + - + +
205A LEU* 4.5 4.7 - - + -
261A LEU* 3.9 21.5 - - + -
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Residues in contact with TYR 197 (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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193A LEU 2.9 17.4 + - - +
194A MET 3.2 3.6 + - - +
196A VAL* 1.3 77.4 - - - +
198A TYR* 1.3 64.9 + - - +
200A LEU* 2.9 17.5 + - + +
201A GLN* 3.0 53.2 + - + +
247A PHE* 4.1 21.1 - + - -
248A PHE* 4.5 4.9 - + - -
252A PHE* 4.6 12.5 - + - -
257A GLN* 5.0 2.9 + - - +
258A VAL 4.4 12.4 + - - -
259A ILE* 3.6 28.5 - - + -
260A SER 3.4 35.2 - - - -
261A LEU* 4.0 9.8 - - + +
263A ARG 5.9 0.4 - - - -
265A GLY 4.0 6.8 + - - -
266A ILE* 3.8 19.1 - - - +
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Residues in contact with TYR 198 (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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164A LEU* 4.3 10.5 - - + -
194A MET 2.9 16.7 + - - +
195A VAL* 3.7 4.0 - - - +
197A TYR* 1.3 82.2 - - - +
199A LEU* 1.3 97.3 + - + +
200A LEU 3.1 0.9 + - - -
201A GLN* 3.1 12.4 + - - +
202A ARG* 3.3 25.7 + - + +
204A HIS* 5.4 5.7 - - - -
240A GLN* 3.6 12.5 + - + +
243A ASP* 2.8 40.9 + - - +
244A PHE* 3.7 41.1 - + + -
247A PHE* 3.9 30.1 - + + -
248A PHE* 3.9 15.7 - - + -
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Residues in contact with LEU 199 (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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155A PHE* 4.8 7.6 - - + -
161A CYS* 4.1 37.2 - - + -
164A LEU* 4.5 9.0 - - + -
195A VAL* 2.9 37.7 + - + +
196A VAL* 3.8 2.5 - - + +
198A TYR* 1.3 98.2 - - + +
200A LEU* 1.3 61.5 + - - +
202A ARG* 3.5 5.4 + - - +
204A HIS* 3.3 41.0 + - + +
205A LEU* 3.6 32.8 + - + -
240A GLN* 5.6 5.4 - - + -
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Residues in contact with LEU 200 (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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154A TYR* 3.7 33.4 - - + +
196A VAL* 2.9 16.3 + - + +
197A TYR* 2.9 12.3 + - + +
199A LEU* 1.3 75.2 - - - +
201A GLN* 1.3 73.0 + - - +
203A ASN* 3.2 17.2 + - - -
205A LEU* 3.8 27.8 - - + +
206A GLN 4.7 2.7 - - - +
207A PHE* 4.1 30.7 - - + +
260A SER 5.3 1.8 - - - +
261A LEU* 4.3 21.1 - - + -
263A ARG 5.1 5.8 - - - +
264A PRO* 5.6 2.7 - - + -
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Residues in contact with GLN 201 (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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197A TYR* 3.0 52.1 + - + +
198A TYR 3.1 6.5 + - - +
200A LEU* 1.3 82.9 - - - +
202A ARG* 1.3 64.1 + - + +
203A ASN* 3.2 7.8 + - - +
247A PHE* 4.0 23.1 - - + -
263A ARG 5.8 0.4 + - - -
265A GLY* 3.3 33.2 + - - +
266A ILE* 4.1 14.6 - - - +
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Residues in contact with ARG 202 (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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198A TYR* 3.3 30.7 + - + +
199A LEU* 4.1 5.2 - - - +
200A LEU 3.2 1.0 - - - -
201A GLN* 1.3 79.1 + - + +
203A ASN* 1.3 69.9 + - - +
204A HIS* 3.0 33.3 + - + +
243A ASP* 2.9 35.9 + - - +
246A HIS* 4.9 0.4 - - - -
247A PHE* 3.7 23.4 - - - +
251A GLU* 2.7 42.4 + - - -
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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