Contacts of the strand formed by residues 188 - 193 (chain A) in PDB entry 5JEI
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 TYR 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ILE* 5.2 0.2 - - - -
116A LYS 4.8 4.2 + - - -
119A THR* 5.3 1.4 + - - +
133A ILE* 4.1 2.9 - - - -
134A ALA* 3.2 22.9 - - + -
135A TYR* 3.9 3.1 - - - -
136A GLY* 3.5 16.5 + - - -
169A VAL* 2.7 25.5 + - + -
171A VAL* 4.2 4.7 - - - +
177A GLY* 4.2 1.8 - - - -
180A ARG* 3.5 55.2 - - + +
181A VAL* 3.8 32.3 - - + +
184A SER* 3.7 22.8 - - - +
186A GLY* 3.4 5.9 - - - -
187A LYS* 1.3 80.0 - - - +
189A ALA* 1.3 72.0 + - - +
190A TYR* 3.5 33.8 - + + -
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Residues in contact with ALA 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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113A ILE* 4.5 5.8 - - + -
114A MET 3.5 13.0 - - - +
115A ILE* 4.2 16.2 - - + +
119A THR* 5.4 0.9 - - + -
127A LEU* 4.0 28.0 - - + -
133A ILE* 3.9 6.3 - - + +
134A ALA 2.9 7.9 + - - +
135A TYR* 3.1 27.1 - - + +
136A GLY 3.5 2.4 + - - -
181A VAL* 4.5 0.4 - - - -
188A TYR* 1.3 82.3 - - - +
190A TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 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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113A ILE* 3.7 1.9 - - - -
114A MET* 2.8 47.4 + - + +
136A GLY 3.5 10.8 - - - -
137A THR* 3.6 18.2 - - - -
138A LEU* 3.3 24.6 + - - +
171A VAL* 3.3 33.5 - - + +
174A THR* 4.1 16.8 + - + -
177A GLY* 3.9 19.5 - - - -
178A VAL* 4.4 1.1 - - + -
181A VAL* 3.5 20.4 - - + +
188A TYR* 3.5 16.6 - + + -
189A ALA* 1.3 73.0 - - - +
191A LEU* 1.3 65.1 + - - +
192A LEU* 3.6 40.2 - - + +
301A FWD 4.7 2.2 + - - -
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Residues in contact with LEU 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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111A ILE* 4.5 4.3 - - + -
112A SER 3.3 12.3 - - - +
113A ILE* 3.9 22.0 - - + -
127A LEU* 4.3 6.1 - - + -
135A TYR* 3.8 11.9 - - + -
136A GLY 2.9 18.3 + - - +
137A THR* 3.7 21.2 - - + -
138A LEU 4.4 0.3 + - - -
143A THR* 4.1 5.4 - - - +
147A PHE* 3.8 17.9 - - + -
158A MET* 3.5 33.4 - - + -
162A MET* 3.8 24.2 - - - -
190A TYR* 1.3 74.0 - - - +
192A LEU* 1.3 63.0 + - - +
215A LEU* 4.3 14.6 - - + -
301A FWD 4.4 0.9 - - - +
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Residues in contact with LEU 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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111A ILE* 4.3 3.8 - - - +
112A SER* 2.8 40.7 + - - +
114A MET* 3.6 49.1 - - + -
143A THR* 4.8 3.4 - - - -
174A THR* 4.0 10.1 - - + -
178A VAL* 5.1 0.2 - - + -
190A TYR* 3.6 29.4 - - + +
191A LEU* 1.3 74.6 - - - +
193A GLU* 1.3 68.2 + - - +
196A MET* 3.8 13.5 - - + -
197A ASN* 3.6 28.7 - - + +
301A FWD 3.1 15.7 - - - +
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Residues in contact with GLU 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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91A THR* 2.8 22.4 + - - +
109A LEU* 3.6 21.3 - - + +
110A GLY 3.7 5.2 - - - +
111A ILE* 4.4 4.0 - - + +
142A SER* 3.2 11.3 + - - -
143A THR* 3.9 7.1 + - - +
192A LEU* 1.3 75.4 - - - +
194A SER* 1.3 66.3 + - - +
195A THR* 3.2 3.6 - - - +
196A MET* 3.0 19.9 + - - -
197A ASN 3.0 9.4 + - - -
218A LYS* 4.5 2.1 - - - -
220A TYR* 2.7 33.1 + - - +
301A FWD 2.8 51.2 + - + +
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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