Contacts of the strand formed by residues 212 - 222 (chain E) 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 ARG 212 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87E ARG* 3.0 12.6 + - - +
88E THR* 3.0 30.1 + - - +
89E PHE* 2.8 27.9 + - - +
133E ASP* 3.6 29.2 - - - +
135E GLU* 3.2 33.9 + - - +
136E CYS* 3.8 8.7 - - - -
210E GLY 5.4 2.0 - - - +
211E LEU* 1.3 73.2 - - - +
213E ALA* 1.3 61.2 + - - +
252E LEU* 3.1 51.5 + - - +
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Residues in contact with ALA 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E PHE* 3.2 8.3 - - + +
131E VAL 5.9 0.4 - - - +
132E ALA* 3.5 5.4 - - - +
133E ASP* 2.9 32.4 + - - +
136E CYS* 3.7 5.6 - - - +
202E LEU* 4.3 9.4 - - + +
203E LEU* 3.8 21.1 - - + +
206E CYS* 3.6 29.4 - - + -
211E LEU 3.7 1.8 + - - -
212E ARG* 1.3 75.8 - - - +
214E GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E PHE 2.8 10.3 + - - +
90E LEU* 3.9 3.8 - - - -
91E ARG* 2.9 27.9 + - - +
132E ALA* 4.6 5.4 - - - -
136E CYS* 3.7 17.8 - - - +
137E THR* 5.1 0.4 - - - -
140E LEU* 3.9 13.0 - - - -
202E LEU* 4.1 3.6 - - - +
203E LEU* 4.6 2.7 - - - -
213E ALA* 1.3 73.4 - - - +
215E MET* 1.3 61.1 + - - +
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Residues in contact with MET 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ARG* 3.1 55.9 - - + +
108E LEU 5.8 0.2 - - - +
109E VAL* 3.7 9.7 - - - +
110E THR* 3.2 56.4 + - - +
132E ALA* 5.0 0.4 - - - +
140E LEU* 3.6 5.3 - - - +
156E THR* 5.5 0.4 - - + -
194E ASN* 5.6 0.4 - - - +
196E GLU* 3.7 15.9 - - + +
199E SER* 3.8 15.5 - - - -
202E LEU* 5.3 0.9 - - + -
203E LEU* 4.5 15.4 - - + +
214E GLY* 1.3 75.0 - - - +
216E VAL* 1.3 80.7 + - - +
217E ALA* 3.8 17.7 - - + -
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Residues in contact with VAL 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ARG 2.9 16.3 + - - +
92E ILE* 3.3 20.9 - - + -
93E GLY 3.0 21.8 + - - -
107E VAL* 3.5 25.4 - - + -
108E LEU 3.4 9.4 - - - +
109E VAL* 4.2 12.6 - - + -
140E LEU* 3.7 27.8 - - + -
215E MET* 1.3 79.0 - - - +
217E ALA* 1.3 65.5 + - - +
241E ALA* 4.4 4.7 - - + +
244E ILE* 4.3 9.0 - - + -
245E VAL* 3.9 11.7 - - + -
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Residues in contact with ALA 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 3.3 14.6 - - - +
94E THR 4.4 0.4 - - - -
95E THR* 3.9 26.7 - - + -
106E ASP 4.0 0.2 - - - +
107E VAL* 3.4 7.4 - - - +
108E LEU* 2.8 42.1 + - + +
194E ASN* 4.8 3.6 - - - +
215E MET* 3.8 17.5 - - + -
216E VAL* 1.3 77.6 - - - +
218E GLY* 1.3 59.7 + - - +
219E VAL 4.0 0.2 + - - -
241E ALA* 4.5 1.8 - - - -
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Residues in contact with GLY 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 3.2 8.7 + - - -
94E THR* 3.8 4.9 - - - -
95E THR* 3.3 22.3 + - - -
106E ASP 3.6 6.7 - - - -
107E VAL* 4.6 2.2 - - - -
217E ALA* 1.3 72.1 - - - +
219E VAL* 1.3 63.9 + - - -
220E ILE* 3.5 5.0 + - - +
237E THR* 3.7 17.0 - - - -
238E GLU* 6.2 0.2 - - - -
241E ALA* 4.0 15.8 - - - +
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Residues in contact with VAL 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E THR* 3.8 8.1 - - + +
97E ALA* 3.8 15.0 - - + +
102E ILE* 3.9 14.6 - - + -
103E ASN 3.5 21.1 - - - +
104E VAL* 3.6 7.1 - - + +
105E GLY* 2.7 26.6 + - - +
106E ASP 2.8 21.6 + - - +
108E LEU* 3.7 33.2 - - + -
218E GLY* 1.3 69.6 - - - -
220E ILE* 1.3 59.1 + - - +
221E VAL 3.3 27.1 - - - +
222E ASN* 4.8 0.4 - - - +
237E THR* 3.3 7.5 - - - +
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Residues in contact with ILE 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E THR* 4.1 26.9 - - + -
95E THR 3.3 13.3 + - - +
104E VAL* 3.7 19.3 - - - +
218E GLY 3.5 4.9 + - - +
219E VAL* 1.3 77.7 - - - +
221E VAL* 1.3 61.2 + - - +
229E PRO* 3.4 21.3 - - + +
234E MET* 3.8 48.9 - - + +
237E THR* 4.1 20.2 - - + +
238E GLU* 5.5 1.8 - - + +
5041E BAU 3.7 33.2 - - + -
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Residues in contact with VAL 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E THR 3.8 1.0 + - - -
96E GLY* 3.3 15.8 - - - -
97E ALA 2.9 23.9 + - - -
104E VAL* 4.1 5.6 - - + -
168E ARG* 4.7 0.7 - - - +
219E VAL* 3.3 10.4 - - - +
220E ILE* 1.3 84.0 - - - +
222E ASN* 1.3 68.1 + - - +
223E ARG* 4.7 4.3 - - - -
226E GLN* 4.1 6.1 - - + +
227E GLU* 3.5 45.3 - - - +
228E ILE 4.8 0.4 - - - -
229E PRO* 3.9 13.0 - - + -
5041E BAU 3.8 29.2 - - + +
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Residues in contact with ASN 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA* 3.5 17.4 - - + +
99E GLN 3.1 15.1 + - - +
102E ILE 2.5 31.1 + - - +
103E ASN* 4.7 0.4 - - - +
104E VAL* 4.0 12.3 - - + +
219E VAL* 5.2 0.7 - - + -
221E VAL* 1.3 77.1 - - - +
223E ARG* 1.3 56.4 + - - +
224E THR* 2.5 32.3 + - - +
225E GLN* 3.1 27.5 + - + +
226E GLN* 2.8 38.5 + - - +
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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