Contacts of the strand formed by residues 125 - 131 (chain B) in PDB entry 2E7Y
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B TYR* 4.1 13.1 + - - -
19B PRO* 4.8 5.1 - - - +
20B GLU* 2.8 45.0 + - - +
116B PHE* 3.7 4.6 - - - -
117B LEU* 2.9 40.2 + - + +
119B ASN* 5.2 16.6 - - + +
123B PHE* 3.3 0.8 - - - +
124B LYS* 1.3 90.6 - - + +
126B TYR* 1.3 63.1 + - - +
145B ILE* 4.8 7.3 - - + +
146B PHE 2.9 10.8 - - - +
147B GLU* 2.8 39.3 + - + +
149B ARG* 5.1 0.2 - - - +
184B VAL* 3.5 27.0 - - - +
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Residues in contact with TYR 126 (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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114B ARG* 3.6 30.3 + - + -
115B VAL 3.2 16.6 - - - +
116B PHE* 3.5 38.1 - + + -
117B LEU* 4.2 2.7 - - - +
125B ARG* 1.3 76.9 - - - +
127B VAL* 1.3 65.9 + - - +
128B GLN* 3.5 17.5 + - + -
144B HIS 3.8 0.2 - - - +
145B ILE* 3.5 2.5 - - - -
146B PHE* 2.6 82.3 + + + -
148B VAL* 4.0 16.2 - - + -
181B HIS* 2.8 34.4 + + - +
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Residues in contact with VAL 127 (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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22B ILE* 4.0 18.2 - - + -
24B PHE* 4.9 2.5 - - + -
45B PHE* 3.6 44.9 - - + -
113B GLU 3.8 1.9 - - - +
114B ARG* 3.4 5.0 - - - -
115B VAL* 2.9 31.9 + - + +
117B LEU* 4.2 11.4 - - + -
126B TYR* 1.3 77.4 - - - +
128B GLN* 1.3 62.8 + - - +
129B PRO* 4.2 0.8 - - + +
143B TYR* 3.6 32.1 - - + -
144B HIS 3.2 9.6 - - - +
145B ILE* 4.4 9.4 - - + -
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Residues in contact with GLN 128 (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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112B GLY* 3.4 33.0 + - - +
114B ARG* 3.1 33.0 + - + +
126B TYR* 3.5 9.6 + - + -
127B VAL* 1.3 77.1 - - - +
129B PRO* 1.3 66.6 + - - +
130B PHE* 3.9 3.3 + - - -
143B TYR* 3.6 3.8 - - - -
144B HIS* 2.8 38.3 + - + +
146B PHE* 4.1 27.0 - - + -
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Residues in contact with PRO 129 (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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109B LEU* 4.3 13.2 - - + -
110B LYS 3.4 24.7 - - - +
111B GLU* 4.1 0.6 - - - +
112B GLY* 2.7 32.2 + - - +
113B GLU 2.9 27.4 - - - +
127B VAL 4.2 1.3 - - - +
128B GLN* 1.3 83.7 + - + +
130B PHE* 1.3 59.0 + - - +
141B PHE* 3.3 31.2 - - + -
142B GLY 3.3 7.0 - - - +
143B TYR* 3.5 15.7 - - + -
144B HIS* 6.0 0.2 - - - -
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Residues in contact with PHE 130 (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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111B GLU* 3.7 10.1 - - - +
128B GLN 4.0 1.6 - - - -
129B PRO* 1.3 77.6 - - - +
131B ARG* 1.3 72.1 + - - +
132B THR* 4.3 1.8 - - + -
141B PHE* 3.2 7.3 - - - -
142B GLY* 2.7 48.8 + - - -
143B TYR 3.3 26.2 - - - -
144B HIS* 3.4 32.8 - + + -
186B THR* 3.9 7.4 - - + -
187B ILE 3.7 7.6 - - - -
194B LEU* 3.5 37.9 - - + -
198B GLU* 3.7 31.6 - - + +
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Residues in contact with ARG 131 (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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111B GLU* 2.9 50.2 + - - +
130B PHE* 1.3 84.1 - - - +
132B THR* 1.3 70.2 + - - +
139B VAL* 3.4 29.7 - - - +
140B SER 3.7 14.1 - - - +
141B PHE* 4.1 9.7 - - + -
194B LEU* 5.1 2.1 - - - +
198B GLU* 5.3 1.0 - - - +
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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