Contacts of the strand formed by residues 88 - 94 (chain B) in PDB entry 1EEJ
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 HIS 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLU* 3.8 1.4 - - - +
87B LYS* 1.3 87.8 + - + +
89B VAL* 1.3 68.8 + - - +
90B ILE* 5.2 0.4 - - + -
115B GLY 3.1 6.6 + - - +
116B ILE* 4.5 5.8 - - + -
117B THR* 2.9 25.9 + - - -
203B LYS* 4.1 15.7 - - + -
206B LEU* 3.3 61.3 + - + +
207B ASP* 2.8 27.8 + - - -
210B GLN* 3.0 30.4 + - + +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLU* 3.2 40.8 - - + +
88B HIS* 1.3 75.1 - - - +
90B ILE* 1.3 66.6 + - - +
91B THR* 5.4 0.2 - - - +
117B THR* 3.6 7.6 - - + -
119B ARG* 3.6 43.3 - - + +
187B LEU 4.6 0.2 - - - -
188B SER* 3.9 29.7 + - - -
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B HIS* 5.2 0.4 - - + -
89B VAL* 1.3 81.0 - - - +
91B THR* 1.3 62.0 + - - +
92B VAL* 3.8 21.5 - - + -
104B LEU* 6.3 1.1 - - + -
111B TYR* 5.8 1.6 - - + -
116B ILE* 3.8 17.3 - - + -
117B THR 3.0 13.7 + - - +
118B VAL* 3.6 10.7 - - + -
119B ARG* 2.9 27.5 + - - +
185B VAL* 3.8 22.7 - - + -
186B VAL 3.8 3.1 - - - +
187B LEU* 4.3 6.3 - - + -
202B MET* 4.4 20.2 - - + -
206B LEU* 3.9 34.3 - - + -
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.2 9.7 - - + +
78B MET* 4.1 23.3 - - + -
89B VAL* 5.4 0.2 - - - +
90B ILE* 1.3 72.0 - - - +
92B VAL* 1.3 63.2 + - - +
93B PHE* 4.2 2.0 + - + -
119B ARG* 2.8 40.3 + - - +
121B LEU* 4.1 20.2 - - + -
184B ALA 3.7 0.9 - - - +
185B VAL* 3.5 2.3 - - - -
186B VAL* 2.7 56.8 + - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.8 22.2 - - + -
91B THR* 1.3 78.4 - - - +
93B PHE* 1.3 75.1 + - - +
94B THR* 3.4 2.4 + - - +
104B LEU* 4.1 15.3 - - + -
118B VAL* 3.8 19.1 - - + -
119B ARG 2.8 9.7 + - - +
120B TYR* 3.4 24.1 - - + -
121B LEU 3.1 23.8 + - - +
183B PRO* 3.9 19.3 - - + -
184B ALA 3.4 7.9 - - - +
185B VAL* 4.2 11.2 - - + -
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.7 2.7 - - + -
91B THR* 5.1 2.0 - - + -
92B VAL* 1.3 72.9 - - - +
94B THR* 1.3 59.2 + - - +
121B LEU* 3.5 40.4 - - + -
122B ALA 4.5 1.1 - - - -
123B PHE* 3.9 28.0 - + + -
170B HIS 3.4 25.6 - - - -
173B LEU* 4.6 4.3 - - + -
174B GLY* 3.7 14.6 - - - -
177B LEU* 4.0 16.4 - - + -
179B VAL* 3.7 20.9 - - + -
182B THR* 3.8 3.9 - - + +
183B PRO* 3.4 7.4 - - - +
184B ALA* 2.8 42.6 + - + +
186B VAL* 3.6 28.0 - - + -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 4.5 3.4 - - - -
93B PHE* 1.3 75.1 - - - +
95B ASP* 1.3 66.9 + - - +
101B CYS* 3.3 25.6 - - - +
104B LEU* 6.2 0.2 - - - +
120B TYR* 3.5 42.9 - - + -
121B LEU 3.0 12.0 + - - +
122B ALA 3.7 0.3 - - - -
123B PHE 2.8 27.2 + - - +
136B MET* 3.7 6.0 - - - +
140B TRP* 4.2 4.7 - - + -
149B PHE* 3.9 24.5 - - + -
153B MET* 4.6 0.7 - - - +
182B THR* 4.4 0.9 - - - -
183B PRO* 5.3 0.6 - - - +
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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