Contacts of the strand formed by residues 67 - 71 (chain A) in PDB entry 1EOB
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 LEU 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.9 26.2 - - + +
18A HIS* 5.0 2.9 - - + +
21A LEU* 3.6 44.2 - - + -
22A LEU* 3.9 20.0 - - + -
65A ASP 3.9 0.4 + - - -
66A VAL* 1.3 72.8 - - - +
68A ILE* 1.3 69.6 + - - +
69A GLU* 4.2 7.9 - - + -
94A ARG* 4.0 16.8 - - + -
95A THR 3.5 10.1 - - - +
96A GLY* 4.4 1.1 - - - -
129A ILE 3.9 0.5 - - - +
130A ILE* 3.7 0.9 - - - -
131A PHE* 2.8 56.3 + - + +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.3 5.8 - - + -
66A VAL* 3.4 20.4 - - + +
67A LEU* 1.3 85.8 - - - +
69A GLU* 1.3 69.8 + - - +
94A ARG* 3.2 4.2 - - - +
95A THR* 2.9 38.5 + - + +
97A ALA 5.7 0.4 - - - +
104A TRP* 4.4 26.7 - - + -
106A PHE* 3.4 23.6 - - + -
128A LEU* 3.5 34.5 - - + -
129A ILE 3.5 2.0 - - - +
130A ILE* 3.1 28.5 - - + -
187A ILE* 5.2 0.7 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.2 7.9 - - + +
68A ILE* 1.3 79.3 - - - +
70A ILE* 1.3 64.4 + - - +
92A TRP* 3.1 26.8 + - - +
93A GLY 3.1 8.3 - - - +
94A ARG* 2.7 38.9 + - + -
106A PHE* 4.3 0.2 - - - -
128A LEU* 3.3 4.5 - - - +
129A ILE* 3.0 42.4 + - + +
131A PHE* 4.5 4.9 - - + -
470B TRP* 3.6 6.4 - - + -
473B ARG* 2.9 43.8 + - - -
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Residues in contact with ILE 70 (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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39A LEU* 4.1 12.3 - - + -
51A LEU* 4.7 5.8 - - + -
69A GLU* 1.3 79.7 - - - +
71A TRP* 1.3 60.3 + - - +
72A GLN* 4.0 22.4 - - - +
92A TRP* 3.2 22.1 - - - -
93A GLY 3.0 16.6 + - - +
106A PHE* 3.7 50.9 - - + -
108A THR* 4.7 4.0 - - + -
126A ILE* 3.5 21.5 - - + -
127A SER 3.1 4.3 - - - -
128A LEU* 3.9 21.1 - - + -
470B TRP* 4.6 1.3 - - - -
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Residues in contact with TRP 71 (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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70A ILE* 1.3 73.6 - - - +
72A GLN* 1.3 62.1 + - - +
79A TYR* 3.4 29.7 + + + -
80A PRO* 3.9 23.3 - - + -
81A SER* 4.0 0.7 - - - -
90A LEU 3.6 14.1 - - - -
91A GLY* 3.3 25.4 - - - -
92A TRP* 4.0 3.4 - - + -
126A ILE* 4.4 0.2 - - - -
127A SER* 2.8 38.5 + - - +
344B SER 3.4 17.1 + - - -
347B THR* 2.9 38.8 + - - -
348B ALA 3.4 25.1 - - - -
349B PRO* 3.3 34.5 - - + -
470B TRP* 3.9 35.2 - + + -
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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