Contacts of the strand formed by residues 122 - 127 (chain A) in PDB entry 2ERY
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 MET 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.1 24.0 - - + +
91A LEU* 3.8 25.6 - - + -
108A GLN* 3.9 17.3 - - + -
111A ILE* 3.4 39.3 - - + -
112A LEU* 3.8 26.0 - - + -
120A PHE* 3.1 15.6 + - + +
121A PRO* 1.3 80.2 - - - +
123A ILE* 1.3 71.9 + - - +
151A VAL* 3.9 28.4 - - + +
152A THR 4.5 2.3 + - - -
171A LEU* 4.1 1.9 - - - +
174A VAL* 4.2 8.9 - - - +
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Residues in contact with ILE 123 (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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89A PHE 2.9 7.7 + - - -
90A LEU* 3.6 11.5 - - + -
91A LEU* 2.9 30.2 + - - +
122A MET* 1.3 81.7 - - - +
124A LEU* 1.3 67.2 + - - +
125A ILE* 3.8 13.5 + - + +
151A VAL* 4.7 0.7 - - - -
152A THR* 3.2 33.9 - - + +
154A MET* 4.6 6.1 - - + +
167A ALA* 3.8 5.6 - - - +
170A GLU* 3.4 24.2 - - + +
171A LEU* 3.1 45.5 - - + +
174A VAL* 4.3 8.5 - - + -
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Residues in contact with LEU 124 (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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91A LEU* 3.4 21.1 - - + +
93A PHE* 3.7 21.8 - - + -
104A ILE* 3.7 27.6 - - + -
123A ILE* 1.3 70.9 - - - +
125A ILE* 1.3 61.0 + - - +
142A GLY 3.6 23.1 - - - +
145A LEU* 4.0 15.7 - - + -
146A ALA* 3.8 16.4 - - + +
149A LEU* 5.1 0.9 - - + -
151A VAL* 3.9 14.8 - - + +
152A THR 2.9 15.0 + - - +
153A TYR* 3.3 17.9 - - + -
154A MET 2.9 26.3 + - - -
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Residues in contact with ILE 125 (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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30A LEU* 4.2 18.6 - - + -
90A LEU* 4.1 28.7 - - + -
91A LEU 2.9 12.8 + - - +
92A VAL* 3.4 7.0 - - + -
93A PHE* 3.0 33.2 + - - +
123A ILE* 4.0 14.8 - - + +
124A LEU* 1.3 80.8 - - - +
126A GLY* 1.3 63.1 + - - +
127A ASN* 4.2 1.8 - - + +
154A MET* 3.2 23.1 - - + +
156A ALA* 3.9 26.5 - - + -
167A ALA* 3.8 22.9 - - + -
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Residues in contact with GLY 126 (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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93A PHE* 3.6 26.5 - - - -
95A VAL* 3.8 8.7 - - - +
125A ILE* 1.3 69.4 - - - +
127A ASN* 1.3 63.2 + - - -
129A ALA* 4.4 0.9 - - - +
153A TYR* 3.7 14.2 - - - -
154A MET 3.0 11.1 + - - -
155A GLU* 3.4 8.0 - - - +
156A ALA 3.0 24.7 + - - +
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Residues in contact with ASN 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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1A GDP 3.1 25.7 + - - -
25A VAL 2.9 24.7 + - - +
26A GLY* 3.6 7.5 - - - -
30A LEU* 3.6 20.3 - - + +
92A VAL* 4.0 10.8 - - + -
93A PHE 2.8 17.1 + - - +
94A SER* 3.6 0.2 - - - -
95A VAL* 2.9 27.9 + - - +
125A ILE* 3.5 3.3 + - + -
126A GLY* 1.3 73.1 - - - +
128A LYS* 1.3 77.5 + - - +
129A ALA 3.3 1.3 - - - -
156A ALA 3.4 5.7 - - - +
157A SER* 3.4 5.4 - - - -
158A ALA 3.3 20.6 + - - -
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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