Contacts of the helix formed by residues 198 - 208 (chain F) in PDB entry 1U1C
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 GLU 198 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F GLY* 3.9 2.3 - - - -
67F THR* 4.0 2.9 - - - +
68F GLY 3.5 12.0 - - - +
69F ILE* 3.4 6.8 - - - +
70F GLY 2.8 25.6 + - - +
71F GLY* 4.7 3.1 - - - +
74F THR* 3.2 29.2 - - + +
91F ARG* 2.9 39.7 + - - +
158F SER* 3.6 1.0 + - - -
196F GLU* 3.0 1.8 + - - -
197F MET* 1.3 96.7 + - - +
199F SER* 1.3 66.6 + - - +
200F ALA 3.5 2.2 - - - -
201F THR* 3.5 8.7 + - - -
202F LEU* 3.2 20.3 + - - +
3052F PO4 2.8 25.4 + - - -
5051F BAU 5.1 0.3 - - - +
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Residues in contact with SER 199 (chain F).
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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91F ARG* 4.0 4.0 - - - +
113F SER* 2.7 25.5 + - - -
156F THR* 4.1 3.5 - - - +
158F SER* 3.4 2.1 + - - -
196F GLU* 2.6 32.4 + - - -
198F GLU* 1.3 74.9 - - - +
200F ALA* 1.3 60.5 + - - +
202F LEU* 3.2 6.0 + - - -
203F LEU* 2.8 41.5 + - - +
215F MET* 3.8 27.6 - - - -
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Residues in contact with ALA 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F SER* 4.0 10.1 - - - -
114F VAL 4.1 0.9 - - - +
115F ARG* 4.0 20.6 - - + -
117F ASP* 3.5 25.8 - - + +
120F SER* 4.2 0.4 - - - -
130F ALA* 3.8 3.3 - - - +
158F SER* 3.1 26.5 + - - +
199F SER* 1.3 76.6 + - - +
201F THR* 1.3 61.0 + - - +
204F THR* 2.6 32.8 + - - -
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Residues in contact with THR 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLY* 3.2 44.6 - - - +
74F THR* 4.5 2.5 - - - -
75F SER* 4.2 12.8 - - - +
117F ASP* 2.5 25.2 + - - +
119F ALA* 3.4 17.2 - - + +
120F SER* 4.1 7.2 - - - +
123F PHE* 5.0 1.3 - - + -
198F GLU 3.5 7.2 + - - -
199F SER 3.3 0.2 - - - -
200F ALA* 1.3 75.9 - - - +
202F LEU* 1.3 65.2 + - - +
204F THR* 4.0 0.7 - - - -
205F MET* 3.0 35.4 + - - +
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Residues in contact with LEU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F VAL* 4.6 7.4 - - + -
74F THR* 4.3 10.7 - - + +
78F VAL* 3.7 25.4 - - + -
89F PHE* 3.9 23.6 - - + +
91F ARG* 3.7 36.1 - - + +
198F GLU 3.2 14.4 + - - +
199F SER* 3.8 3.6 - - - +
201F THR* 1.3 79.1 - - - +
203F LEU* 1.3 74.8 + - + +
205F MET* 3.5 7.6 - - - +
206F CYS* 3.0 36.0 + - - +
213F ALA* 4.2 7.4 - - + -
214F GLY 4.0 12.3 - - - +
215F MET* 5.3 0.9 - - + -
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F THR* 4.2 15.3 - - + -
112F ALA* 4.4 0.2 - - - -
113F SER* 3.7 20.9 - - - +
130F ALA* 3.4 31.4 - - + +
131F VAL 3.8 4.5 - - - +
132F ALA* 3.9 31.9 - - + +
199F SER* 2.8 27.2 + - - +
202F LEU* 1.3 82.6 - - + +
204F THR* 1.3 56.5 + - - +
206F CYS* 3.9 0.7 - - - +
207F ALA* 2.9 34.8 + - - +
213F ALA* 3.9 23.8 - - + +
215F MET* 4.3 10.8 - - + -
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Residues in contact with THR 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ARG* 3.7 16.1 - - - +
120F SER* 3.6 33.1 - - - +
123F PHE* 4.9 0.2 - - + -
124F ALA* 3.9 21.8 - - + +
128F PHE* 4.3 7.9 - - + +
129F PRO 4.8 1.1 - - - -
130F ALA* 3.2 21.6 - - - +
200F ALA 2.6 24.3 + - - -
201F THR 4.0 0.9 - - - -
203F LEU* 1.3 77.2 - - - +
205F MET* 1.3 52.1 + - - +
207F ALA* 4.0 2.3 - - - +
208F SER* 2.7 39.7 + - - -
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Residues in contact with MET 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F THR 4.8 0.2 - - - -
75F SER* 3.6 39.9 - - - +
78F VAL* 3.7 34.8 - - + -
79F GLU* 4.0 10.3 - - + +
123F PHE* 3.6 45.0 - - + +
201F THR* 3.0 26.6 + - - +
202F LEU* 3.5 7.2 - - - +
204F THR* 1.3 76.3 - - - +
206F CYS* 1.3 60.1 + - - +
208F SER* 3.8 4.9 - - - -
209F GLN* 2.7 44.5 + - - +
211F LEU* 4.6 0.6 - - - +
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Residues in contact with CYS 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F VAL* 4.1 11.4 - - - -
89F PHE* 3.8 26.2 - - - -
202F LEU* 3.0 30.4 + - - +
203F LEU 4.1 0.9 - - - +
205F MET* 1.3 77.2 - - - +
207F ALA* 1.3 64.2 + - - +
208F SER 3.2 0.4 - - - -
209F GLN 3.3 0.5 + - - -
210F GLY* 3.2 5.4 + - - -
211F LEU* 2.9 52.3 + - + +
212F ARG 4.6 0.2 - - - -
213F ALA* 3.6 25.4 - - + -
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Residues in contact with ALA 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL* 5.1 6.0 - - + +
190B MET 3.2 12.6 - - - +
191B GLY* 5.1 1.2 - - - -
128F PHE* 3.9 21.4 - - + -
129F PRO 4.8 0.9 - - - +
131F VAL* 3.7 26.9 - - + +
203F LEU 2.9 20.2 + - - +
206F CYS* 1.3 76.0 - - - +
208F SER* 1.3 57.8 + - - +
209F GLN 3.4 0.4 + - - -
210F GLY* 4.4 4.5 + - - -
211F LEU 4.0 3.6 + - - -
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Residues in contact with SER 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ALA 3.7 3.6 - - - +
190B MET* 3.3 38.8 - - - -
175E ARG* 3.2 31.3 + - - -
123F PHE* 4.0 6.4 - - - +
124F ALA* 4.3 7.8 - - - +
128F PHE* 4.0 13.2 - - - -
204F THR 2.7 22.3 + - - -
205F MET* 3.7 8.3 + - - -
207F ALA* 1.3 77.3 - - - +
209F GLN* 1.3 57.8 + - - +
210F GLY 3.8 0.7 - - - -
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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