Contacts of the strand formed by residues 106 - 110 (chain B) in PDB entry 2E98
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 ARG 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ASN 3.9 1.8 + - - -
105B VAL* 1.3 73.9 - - - +
107B LEU* 1.3 66.0 + - - +
108B ARG* 4.9 14.1 - - + +
131B THR 3.4 21.5 - - - +
132B ALA* 3.5 29.6 + - - +
134B ASN 4.0 17.7 + - - +
136B GLY 5.4 0.7 - - - +
137B LEU 2.9 7.9 + - - +
138B THR* 3.3 30.0 + - + +
139B LEU 2.7 29.1 + - - +
185B GLU* 4.8 23.0 + - - +
186B LEU* 5.2 5.1 - - - +
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Residues in contact with LEU 107 (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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93B LEU* 3.9 27.8 - - + -
97B VAL* 4.6 8.3 - - + -
100B LEU* 4.6 18.6 - - + -
105B VAL* 3.8 2.2 + - + -
106B ARG* 1.3 75.0 - - - +
108B ARG* 1.3 70.8 - - - +
109B ILE* 4.4 12.3 - - + -
127B SER* 4.1 18.6 - - - +
128B GLU* 3.5 21.8 - - + +
131B THR* 3.0 20.5 + - + +
139B LEU* 3.4 27.6 - - + +
141B ILE* 4.1 22.7 - - + -
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Residues in contact with ARG 108 (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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106B ARG* 4.9 17.7 - - + +
107B LEU* 1.3 83.7 - - - +
109B ILE* 1.3 74.0 + - - +
110B ILE* 4.9 5.0 - - + +
128B GLU* 3.4 41.2 + - - +
138B THR* 4.5 10.5 - - + -
139B LEU 2.9 6.6 + - - +
140B ASN* 3.2 23.9 - - + +
141B ILE* 2.8 25.1 + - - +
185B GLU* 4.6 14.3 + - - +
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Residues in contact with ILE 109 (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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89B PHE* 4.1 21.1 - - + -
93B LEU* 5.2 2.2 - - + -
107B LEU* 4.4 19.5 - - + -
108B ARG* 1.3 87.6 + - - +
110B ILE* 1.3 66.4 + - - +
111B GLY 4.2 1.2 + - - +
113B THR* 3.9 20.4 - - + +
124B ILE* 3.6 32.1 - - + -
128B GLU* 2.9 19.5 + - + +
141B ILE* 3.2 26.9 - - + +
143B ALA* 3.7 25.1 - - + -
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Residues in contact with ILE 110 (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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66B THR* 4.0 24.9 - - + -
108B ARG* 4.1 6.5 - - + +
109B ILE* 1.3 80.2 - - - +
111B GLY* 1.3 59.6 + - - +
140B ASN* 4.5 14.8 - - + +
141B ILE 2.9 10.3 + - - +
142B ALA* 3.3 17.9 - - + +
143B ALA 3.0 23.5 + - - +
145B TYR* 3.6 27.6 - - + +
182B CYS* 4.2 24.5 - - + -
183B MET* 4.2 22.7 - - + +
204B PHE* 4.8 1.3 - - + -
205B LEU* 4.5 6.5 - - + -
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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