Contacts of the strand formed by residues 126 - 131 (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 ILE 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.8 2.2 - - + -
51A LEU* 4.1 20.9 - - + -
70A ILE* 3.5 35.0 - - + -
71A TRP 3.9 8.3 - - - +
72A GLN* 3.5 30.1 - - + +
108A THR* 4.5 9.2 - - + -
111A PRO* 4.1 9.0 - - + -
125A HIS* 1.3 82.9 - - - +
127A SER* 1.3 65.9 + - - +
128A LEU 3.7 0.5 + - - -
142A ARG* 3.4 3.5 - - - -
143A VAL* 2.9 38.6 + - + +
145A PHE* 3.9 26.2 - - + -
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Residues in contact with SER 127 (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* 3.1 6.1 - - - +
71A TRP* 2.8 46.6 + - - +
79A TYR* 5.0 0.9 + - - -
125A HIS* 4.3 8.1 + - - -
126A ILE* 1.3 72.8 - - - +
128A LEU* 1.3 59.8 + - - +
141A THR 3.8 6.5 - - - -
142A ARG* 4.4 9.2 + - - +
344B SER* 4.2 19.8 + - - -
345B GLU* 4.5 3.1 + - - -
470B TRP* 3.8 27.2 + - - -
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Residues in contact with LEU 128 (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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51A LEU* 4.8 1.6 - - + -
68A ILE* 3.5 23.1 - - + -
69A GLU 3.3 4.7 - - - +
70A ILE* 3.9 12.1 - - + -
104A TRP* 4.2 20.6 - - + -
126A ILE 3.7 0.2 + - - -
127A SER* 1.3 75.9 - - - +
129A ILE* 1.3 65.1 + - - +
130A ILE* 3.2 34.3 - - + -
139A LEU 3.7 0.3 - - - +
140A HIS* 3.6 5.0 + - - +
141A THR* 3.0 48.6 + - + +
143A VAL* 3.9 26.0 - - + -
185A PHE* 4.3 2.2 - - + -
187A ILE* 4.1 8.7 - - + -
470B TRP* 5.0 2.8 + - - -
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Residues in contact with ILE 129 (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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67A LEU 3.9 0.5 - - - +
68A ILE* 3.5 9.9 - - - +
69A GLU* 3.0 44.8 + - + +
128A LEU* 1.3 77.8 - - - +
130A ILE* 1.3 65.2 + - - +
131A PHE* 3.3 43.2 - - + -
138A GLY* 4.0 9.6 - - - -
139A LEU 3.2 15.5 - - - +
140A HIS* 3.5 31.2 - - + +
470B TRP* 3.8 16.8 - - + -
473B ARG* 3.8 13.7 - - + +
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Residues in contact with ILE 130 (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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55A VAL* 4.5 11.2 - - + -
66A VAL* 3.3 27.1 - - + -
67A LEU 3.7 1.6 - - - -
68A ILE* 3.1 25.4 - - + -
128A LEU* 3.2 23.8 - - + -
129A ILE* 1.3 72.9 - - - +
131A PHE* 1.3 61.4 + - - +
135A ILE* 3.9 21.7 - - + +
138A GLY* 3.2 8.1 - - - -
139A LEU* 2.9 45.7 + - + +
141A THR* 5.3 0.4 - - + -
187A ILE* 3.5 22.9 - - + -
189A ILE* 5.2 2.2 - - + -
197A PHE* 4.8 10.3 - - + -
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Residues in contact with PHE 131 (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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13A GLY* 5.3 5.4 - - - -
17A VAL* 5.2 6.9 - - + +
65A ASP 4.5 0.2 - - - +
66A VAL* 3.4 1.4 - - - +
67A LEU* 2.8 54.7 + - + +
69A GLU* 4.5 2.2 - - - -
129A ILE* 3.3 41.7 - - + -
130A ILE* 1.3 74.9 - - - +
132A ALA* 1.3 67.7 + - - +
135A ILE* 4.4 3.4 - - + -
138A GLY* 3.6 27.4 - - - -
473B ARG* 3.8 28.5 - - + -
474B LEU* 5.5 0.9 - - - -
475B ILE* 3.5 52.3 - - + -
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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