Contacts of the strand formed by residues 189 - 199 (chain A) in PDB entry 5E2I
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 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LYS 4.6 0.9 - - - +
108A SER* 4.3 3.9 + - - -
109A THR 3.7 7.4 - - - -
111A VAL* 3.7 14.4 - - - -
142A VAL* 3.9 9.8 - - - +
184A ILE* 3.0 16.0 + - - -
185A GLN* 3.2 21.7 - - - +
187A PHE 3.3 3.0 + - - -
188A GLY* 1.3 81.3 - - - +
190A ASP* 1.3 60.4 + - - -
191A PRO* 3.5 4.1 - - - +
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Residues in contact with ASP 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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108A SER* 3.4 30.5 + - - +
109A THR 2.8 22.8 + - - +
111A VAL* 3.5 7.9 - - - +
189A GLY* 1.3 71.4 - - - -
191A PRO* 1.3 63.3 - - - +
192A LYS* 2.9 35.7 + - - +
193A THR* 2.7 50.0 + - - +
194A VAL* 3.9 0.2 - - - +
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Residues in contact with PRO 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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108A SER* 5.1 1.6 - - - +
180A VAL 5.0 0.2 - - - +
181A HIS* 3.6 44.6 + - + +
184A ILE* 3.8 20.4 - - + -
185A GLN* 4.5 18.4 - - + +
189A GLY 3.5 9.8 - - - +
190A ASP* 1.3 88.6 - - - +
192A LYS* 1.3 61.1 + - + +
193A THR 3.3 1.3 - - - -
194A VAL* 3.3 19.7 - - + +
218A LEU 5.3 2.4 - - - +
219A PHE* 5.6 1.9 - - - -
220A ARG 5.9 0.2 + - - -
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Residues in contact with LYS 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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108A SER* 4.6 5.1 + - - -
181A HIS* 6.4 0.7 - - + -
190A ASP* 2.9 31.4 + - - +
191A PRO* 1.3 83.7 - - + +
193A THR* 1.3 60.4 + - - +
194A VAL 3.7 1.6 - - - -
220A ARG* 3.1 35.8 + - - +
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Residues in contact with THR 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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109A THR 5.6 0.2 - - - -
110A THR* 3.7 18.2 - - - +
111A VAL 3.1 23.6 + - - +
190A ASP* 2.7 36.6 + - - -
192A LYS* 1.3 82.3 + - - +
194A VAL* 1.3 57.5 + - - +
195A THR 4.0 0.2 + - - -
220A ARG* 4.2 14.0 + - + +
221A ARG* 4.0 8.5 - - - +
477A ALA 3.5 22.9 - - - +
478A LYS 4.0 12.3 - - - +
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Residues in contact with VAL 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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111A VAL* 3.5 16.6 - - + +
113A VAL* 3.7 28.9 - - + -
177A LEU* 5.3 1.3 - - + -
180A VAL* 4.2 16.2 - - + -
181A HIS* 5.8 1.1 - - - +
190A ASP 3.9 4.5 - - - +
191A PRO* 3.3 31.2 + - + +
192A LYS 3.7 2.0 - - - -
193A THR* 1.3 77.2 - - - +
195A THR* 1.3 64.5 + - - +
196A ILE* 4.5 2.2 - - + -
218A LEU 4.5 7.2 - - - +
219A PHE* 3.7 20.5 - - + +
220A ARG* 2.8 30.6 + - - +
221A ARG 3.3 6.6 + - - +
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Residues in contact with THR 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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111A VAL 2.9 11.2 + - - -
112A MET* 3.2 7.9 - - + +
113A VAL 2.8 25.2 + - - -
193A THR 4.0 0.2 + - - -
194A VAL* 1.3 73.1 - - - +
196A ILE* 1.3 74.6 + - - +
197A PHE* 3.9 2.3 + - + -
221A ARG* 3.2 33.6 - - + +
222A ALA* 4.3 0.4 - - - +
223A ILE* 4.1 28.7 - - + -
476A PHE* 4.7 1.1 - - + -
477A ALA* 3.2 33.4 + - + +
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Residues in contact with ILE 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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113A VAL* 3.4 12.1 - - + +
115A ILE* 4.4 8.3 - - + -
177A LEU* 3.5 31.2 - - + -
194A VAL* 4.1 2.6 - - + -
195A THR* 1.3 76.4 - - - +
197A PHE* 1.3 59.8 + - - +
206A VAL* 3.9 33.0 - - + -
209A HIS* 4.1 15.0 - - + -
219A PHE* 3.8 48.0 - - + -
221A ARG 3.1 11.4 + - - +
222A ALA* 3.3 1.7 - - + -
223A ILE 3.0 23.2 + - - +
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Residues in contact with PHE 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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112A MET* 3.9 30.5 - - + -
113A VAL 2.9 23.4 + - - +
114A TRP* 3.3 55.3 - + + -
115A ILE* 2.8 24.7 + - - +
135A LEU* 4.5 3.6 - - + -
143A LEU* 4.1 14.1 - - + -
195A THR* 4.2 3.4 - - + -
196A ILE* 1.3 78.7 - - - +
198A GLY* 1.3 56.6 + - - +
206A VAL* 3.8 5.8 - - - +
223A ILE* 3.2 28.9 - - + -
225A GLN* 3.7 11.2 - - - -
447A VAL* 4.0 20.0 - - + -
448A PHE* 3.9 13.9 - + - -
473A TRP* 4.0 9.2 - + - -
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Residues in contact with GLY 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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114A TRP* 3.6 10.9 - - - -
115A ILE 3.2 16.2 - - - -
197A PHE* 1.3 77.4 - - - +
199A GLU* 1.3 57.8 + - - -
202A GLY 3.7 8.3 - - - -
203A GLY* 3.3 11.8 - - - -
206A VAL* 3.7 2.8 - - - +
223A ILE 3.3 5.5 + - - -
225A GLN* 2.9 28.1 + - - +
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Residues in contact with GLU 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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114A TRP* 3.6 12.9 - - + -
115A ILE 3.8 3.2 + - - -
117A GLY* 3.3 10.9 - - - +
198A GLY* 1.3 73.4 - - - -
200A SER* 1.3 72.1 + - - +
201A ALA 3.1 1.0 + - - -
202A GLY* 2.7 24.3 + - - -
203A GLY 3.4 1.8 - - - +
225A GLN* 3.1 9.9 - - + +
226A SER* 4.0 6.8 - - - -
440A HIS* 3.6 14.0 + - - -
441A GLY* 3.3 25.5 + - - -
443A GLU* 3.1 25.2 - - - +
444A ILE* 3.7 25.1 - - + +
603A PEG 3.2 32.4 - - - +
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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