Contacts of the strand formed by residues 212 - 222 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D ARG* 3.1 11.9 + - + +
88D THR* 3.1 26.1 + - + -
89D PHE* 2.9 27.4 + - - +
133D ASP* 3.4 31.6 - - - +
135D GLU* 3.2 28.1 + - - +
136D CYS* 3.7 9.4 - - - -
210D GLY 5.9 0.2 - - - +
211D LEU* 1.3 73.5 - - - +
213D ALA* 1.3 60.6 + - - +
252D LEU* 3.2 53.1 + - - +
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Residues in contact with ALA 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D PHE* 3.2 10.1 - - + +
131D VAL 5.9 0.2 - - - +
132D ALA* 3.6 5.1 - - - +
133D ASP* 2.8 38.3 + - - +
136D CYS* 3.6 6.0 - - - +
202D LEU* 4.3 7.6 - - + +
203D LEU* 3.9 19.1 - - + +
206D CYS* 3.7 30.1 - - + -
211D LEU 3.7 1.2 + - - -
212D ARG* 1.3 76.2 - - - +
214D GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D PHE 2.9 9.0 + - - +
90D LEU* 4.0 3.3 - - - +
91D ARG* 2.9 27.4 + - - +
132D ALA* 4.6 4.5 - - - -
136D CYS* 3.7 18.4 - - - +
137D THR* 5.0 0.4 - - - -
140D LEU* 3.9 14.1 - - - -
202D LEU* 4.0 4.2 - - - +
203D LEU* 4.6 2.0 - - - -
213D ALA* 1.3 74.7 - - - +
215D MET* 1.3 62.3 + - - +
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Residues in contact with MET 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ARG* 3.1 45.1 - - + +
109D VAL* 3.7 9.0 - - - +
110D THR* 3.2 58.0 + - - +
132D ALA* 5.0 0.6 - - - +
137D THR* 5.8 0.2 + - - -
140D LEU* 3.6 5.1 - - - +
156D THR* 5.6 0.4 - - + -
194D ASN* 5.6 0.2 - - - +
196D GLU* 3.5 28.3 - - + +
199D SER* 3.9 15.3 - - - -
202D LEU* 5.1 0.7 - - + -
203D LEU* 4.5 14.3 - - + +
214D GLY* 1.3 74.7 - - - +
216D VAL* 1.3 78.2 + - - +
217D ALA* 3.8 17.5 - - + -
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ARG 3.0 18.2 + - - +
92D ILE* 4.2 11.7 - - + -
93D GLY 3.0 21.8 + - - -
107D VAL* 3.6 26.7 - - + -
108D LEU 3.4 9.9 - - - +
109D VAL* 4.4 8.7 - - + -
140D LEU* 3.7 23.1 - - + -
215D MET* 1.3 78.4 - - - +
217D ALA* 1.3 65.3 + - - +
241D ALA* 4.5 5.6 - - + +
244D ILE* 4.0 15.3 - - + -
245D VAL* 4.1 17.7 - - + -
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Residues in contact with ALA 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ILE* 6.0 0.2 - - - -
93D GLY 3.3 12.1 - - - +
94D THR 4.5 0.2 - - - -
95D THR* 3.8 27.1 - - + -
106D ASP 4.0 0.2 - - - +
107D VAL* 3.4 8.2 - - - +
108D LEU* 2.8 37.8 + - + +
110D THR* 5.9 0.9 - - - +
194D ASN* 4.7 4.5 - - - +
215D MET* 3.8 17.7 - - + -
216D VAL* 1.3 78.6 - - - +
218D GLY* 1.3 59.7 + - - +
219D VAL 4.1 0.3 + - - -
241D ALA* 4.8 3.4 - - - -
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Residues in contact with GLY 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D GLY 3.1 11.0 + - - -
94D THR* 3.7 5.0 - - - -
95D THR* 3.0 23.3 + - - -
106D ASP 3.7 4.9 - - - -
107D VAL* 4.8 1.3 - - - -
217D ALA* 1.3 73.9 - - - +
219D VAL* 1.3 63.2 + - - -
220D ILE* 3.4 3.8 + - - +
237D THR* 4.1 14.4 - - - -
241D ALA* 4.4 14.9 - - - +
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Residues in contact with VAL 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D THR* 3.7 8.7 - - + -
97D ALA* 3.8 15.0 - - + +
102D ILE* 3.8 13.5 - - + +
103D ASN 3.7 19.5 - - - +
104D VAL* 3.5 8.9 - - + +
105D GLY 2.7 26.5 + - - -
106D ASP 2.9 24.2 + - - +
108D LEU* 3.8 33.0 - - + -
218D GLY* 1.3 69.4 - - - -
220D ILE* 1.3 59.1 + - - +
221D VAL 3.5 24.7 - - - +
222D ASN* 5.1 0.2 - - - -
237D THR* 3.3 8.4 - - - +
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Residues in contact with ILE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D THR* 4.2 24.7 - - + -
95D THR 3.3 11.9 + - - +
104D VAL* 3.4 20.7 - - - +
218D GLY 4.4 6.1 - - - +
219D VAL* 1.3 76.2 - - - +
221D VAL* 1.3 69.3 + - + +
234D MET* 4.0 43.5 - - + +
237D THR* 4.0 18.8 - - + -
238D GLU 5.9 0.2 - - - +
5031D BAU 3.7 34.8 - - + -
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Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D THR 3.8 1.4 + - - -
96D GLY* 3.3 9.6 - - - -
97D ALA 2.8 31.2 + - - -
104D VAL* 4.1 3.6 - - - -
168D ARG* 4.7 0.7 - - - +
219D VAL* 3.5 8.1 - - - +
220D ILE* 1.3 89.0 - - + +
222D ASN* 1.3 65.5 + - - +
223D ARG* 4.3 16.6 - - - +
5031D BAU 3.8 37.7 - - + -
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Residues in contact with ASN 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ALA* 3.4 14.3 - - + +
99D GLN 2.8 19.6 + - - +
102D ILE 2.6 29.6 + - - +
104D VAL* 3.9 10.8 - - + +
219D VAL* 5.2 0.7 - - + -
221D VAL* 1.3 77.7 - - - +
223D ARG* 1.3 63.7 + - - +
224D THR* 2.6 31.6 + - - +
225D GLN* 3.2 49.7 + - + +
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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