Contacts of the helix formed by residues 182 - 195 (chain A) in PDB entry 1UMK
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 GLY 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ALA* 3.6 7.7 - - - +
179A GLY 2.9 10.3 + - - -
181A THR* 1.3 78.4 + - - +
183A ILE* 1.3 60.9 + - - +
184A THR 3.2 0.4 - - - -
185A PRO* 3.3 10.7 - - - +
186A MET* 3.6 11.3 - - - +
273A CYS* 3.4 47.4 - - - +
274A GLY* 4.5 1.3 - - - -
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Residues in contact with ILE 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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178A ALA* 3.8 5.6 - - + +
180A GLY 3.2 13.4 + - - +
181A THR* 2.9 4.6 - - - +
182A GLY* 1.3 78.7 - - - +
184A THR* 1.3 64.9 + - + +
186A MET* 3.1 7.7 + - + +
187A LEU* 2.8 29.5 + - + +
205A LEU* 3.6 36.8 - - + -
207A PHE* 3.5 34.8 - - + -
216A LEU* 4.1 12.3 - - + +
217A LEU* 3.9 26.2 - - + -
221A LEU* 3.9 23.1 - - + -
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Residues in contact with THR 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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94A THR* 3.4 23.3 + - - +
95A PRO 4.8 1.7 - - - +
96A ILE* 4.3 11.2 - - + -
108A VAL* 4.8 9.9 - - + +
181A THR* 3.1 9.0 + - - +
183A ILE* 1.3 86.3 - - + +
185A PRO* 1.3 74.7 - - - +
187A LEU* 3.4 5.9 + - - +
188A GLN* 3.1 24.1 + - - +
216A LEU* 5.8 0.4 - - + -
217A LEU* 4.3 13.0 - - + -
1301A FAD 2.8 36.3 + - + +
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Residues in contact with PRO 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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94A THR* 3.6 24.4 - - + +
181A THR 4.0 2.0 - - - +
182A GLY 3.3 14.6 - - - +
184A THR* 1.3 98.7 - - - +
186A MET* 1.3 60.2 + - - +
188A GLN* 3.6 5.3 + - + +
189A VAL* 3.4 25.8 + - - +
273A CYS* 3.8 14.8 - - + -
300A PHE* 3.7 34.2 - - + -
1301A FAD 3.8 19.3 - - + -
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Residues in contact with MET 186 (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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176A MET* 3.7 40.1 - - + +
177A ILE 3.6 10.3 - - - +
178A ALA* 4.0 12.8 - - + -
182A GLY 3.6 11.2 - - - +
183A ILE* 3.1 8.4 + - + +
185A PRO* 1.3 75.2 - - - +
187A LEU* 1.3 61.8 + - - +
189A VAL* 3.1 4.9 + - - +
190A ILE* 2.8 34.5 + - + +
205A LEU* 4.2 9.2 - - + -
271A LEU* 3.6 7.4 - - - +
272A MET 3.5 17.7 - - - +
273A CYS* 3.4 33.4 - - + +
300A PHE* 3.8 23.3 - - + -
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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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96A ILE* 4.6 6.1 - - + -
183A ILE* 2.8 25.0 + - + +
184A THR* 3.4 5.6 + - - +
186A MET* 1.3 72.6 - - - +
188A GLN* 1.3 57.8 + - - +
190A ILE* 4.2 8.5 - - + +
191A ARG* 2.8 69.4 + - - +
217A LEU* 3.8 39.5 - - + -
220A GLU* 4.8 2.9 - - + -
221A LEU* 4.0 18.4 - - + -
224A LEU* 3.7 29.6 - - + -
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Residues in contact with GLN 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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72A LEU* 3.7 20.2 + - - +
73A PRO 4.0 6.5 + - - -
74A VAL* 3.6 15.2 - - + +
75A GLY* 2.7 32.2 + - - -
76A GLN 3.3 20.4 + - - +
94A THR* 3.8 15.4 - - + +
95A PRO* 4.8 8.4 + - - +
97A SER 5.4 5.2 - - - +
98A SER* 6.4 1.8 - - - -
184A THR 3.1 17.8 + - - +
185A PRO* 3.6 7.3 - - - +
187A LEU* 1.3 77.0 - - - +
189A VAL* 1.3 56.8 + - - +
191A ARG* 3.9 6.3 - - - +
192A ALA* 3.2 27.0 + - - +
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Residues in contact with VAL 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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74A VAL* 4.1 17.7 - - + -
75A GLY* 4.6 5.8 - - - -
148A LEU* 5.2 0.2 - - + -
150A TYR* 4.8 5.4 - - + -
156A PHE* 4.2 25.8 - - + -
176A MET* 3.7 19.5 - - + -
185A PRO 3.4 13.2 + - - +
186A MET 3.1 6.7 + - - +
188A GLN* 1.3 79.7 - - - +
190A ILE* 1.3 64.8 + - - +
192A ALA* 3.1 3.5 + - - +
193A ILE* 3.0 39.4 + - + +
271A LEU* 4.7 6.1 - - + -
300A PHE* 4.5 15.9 - - + -
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Residues in contact with ILE 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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176A MET* 3.7 26.2 - - + -
186A MET* 2.8 29.2 + - + +
187A LEU* 3.7 9.2 - - - +
189A VAL* 1.3 72.6 - - - +
191A ARG* 1.3 58.3 + - - +
193A ILE* 3.2 1.7 + - - +
194A MET* 2.9 48.0 + - + +
203A CYS* 4.4 12.3 - - - -
205A LEU* 4.2 13.7 - - + -
221A LEU* 4.4 4.7 - - + -
224A LEU* 4.0 22.2 - - + -
232A PHE* 3.6 39.3 - - + -
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Residues in contact with ARG 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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96A ILE* 3.1 34.0 + - - +
187A LEU* 2.8 57.2 + - + +
188A GLN* 3.9 5.4 - - - +
190A ILE* 1.3 73.1 - - - +
192A ALA* 1.3 63.0 + - - +
194A MET* 4.0 4.8 - - - +
195A LYS* 3.1 33.1 + - + +
217A LEU* 5.2 1.6 - - - +
220A GLU* 3.5 32.3 - - - +
223A GLU* 5.8 1.0 + - - -
224A LEU* 4.0 18.7 - - + +
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Residues in contact with ALA 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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74A VAL* 3.7 32.5 - - + -
150A TYR* 4.4 10.9 - - + -
188A GLN 3.2 17.3 + - - +
189A VAL 3.1 6.3 + - - +
191A ARG* 1.3 77.0 - - - +
193A ILE* 1.3 62.3 + - - +
195A LYS* 3.6 25.9 - - - +
196A ASP* 3.8 9.5 + - - +
199A ASP* 4.7 0.7 - - - +
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Residues in contact with ILE 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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150A TYR* 3.5 33.2 - - + +
174A VAL* 5.0 2.9 - - + -
189A VAL* 3.0 28.7 + - + +
190A ILE 3.7 5.6 - - - +
192A ALA* 1.3 77.4 - - - +
194A MET* 1.3 74.2 + - + +
196A ASP 3.2 13.0 + - - +
199A ASP* 3.5 22.4 - - - +
201A THR* 3.6 34.5 - - + +
203A CYS* 3.3 27.4 - - - -
231A ARG* 3.0 21.3 + - - +
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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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190A ILE* 2.9 35.5 + - + +
191A ARG 4.1 2.7 - - - +
193A ILE* 1.3 97.8 - - + +
195A LYS* 1.3 60.6 + - - +
196A ASP 3.2 2.2 + - - -
197A PRO* 4.6 1.0 - - - +
203A CYS* 4.0 14.8 - - - -
224A LEU* 4.2 13.2 - - + -
228A HIS* 3.6 53.6 - - + +
231A ARG* 3.0 59.5 + - + +
232A PHE* 4.1 10.3 - - + -
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Residues in contact with LYS 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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98A SER* 3.9 16.6 + - - -
100A ASP* 3.0 33.7 + - - +
191A ARG* 3.1 19.6 + - + +
192A ALA* 3.6 22.9 - - - +
194A MET* 1.3 74.9 - - - +
196A ASP* 1.3 60.1 + - + +
197A PRO* 3.3 11.1 - - - +
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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