Contacts of the strand formed by residues 104 - 110 (chain A) in PDB entry 2EZ9
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 VAL 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ALA 5.2 1.3 - - - +
66A ALA* 4.0 16.2 - - + +
67A ALA* 3.8 26.2 - - + +
76A ILE* 3.9 4.7 - - - +
77A GLY 3.3 10.1 - - - +
79A CYS* 4.3 2.5 - - - -
94A LEU* 4.1 23.6 - - + -
97A ALA* 3.6 28.7 - - + -
102A VAL* 3.4 2.6 + - + +
103A PRO* 1.3 80.8 - - - +
105A LEU* 1.3 71.9 + - - +
106A ALA 4.4 0.2 - - - +
157A ALA* 4.0 2.1 - - - +
162A GLY 3.1 6.9 + - - +
163A VAL* 3.4 6.7 - - + +
164A ALA 2.9 26.7 + - - +
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Residues in contact with LEU 105 (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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21A LEU* 3.7 30.1 - - + -
76A ILE* 3.8 16.0 - - + +
77A GLY 2.8 11.1 + - - +
78A VAL* 3.4 14.8 - - + -
79A CYS 3.0 25.8 + - - +
104A VAL* 1.3 75.1 - - - +
106A ALA* 1.3 60.9 + - - +
107A LEU* 3.9 28.5 - - + -
150A ILE* 4.2 7.0 - - + +
153A ALA* 3.7 30.5 - - + -
154A ILE* 4.0 14.4 - - + -
164A ALA* 3.4 12.6 - - + +
166A VAL* 4.5 3.8 - - + -
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Residues in contact with ALA 106 (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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79A CYS* 3.3 13.0 - - - -
90A LEU* 4.3 8.5 - - + -
94A LEU* 3.9 36.6 - - + -
104A VAL 4.1 0.4 - - - -
105A LEU* 1.3 73.5 - - - +
107A LEU* 1.3 65.2 + - - +
108A ILE* 4.5 2.9 - - + -
163A VAL* 4.9 0.4 - - + -
164A ALA 2.9 11.1 + - - +
165A VAL* 3.3 11.8 - - + +
166A VAL 3.1 24.4 + - - -
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Residues in contact with LEU 107 (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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17A VAL* 5.1 9.6 - - + -
18A ILE* 6.1 0.4 - - + -
21A LEU* 5.3 8.1 - - + -
29A LEU* 5.6 5.4 - - + -
37A ILE* 4.5 5.8 - - + -
40A ILE* 4.7 22.2 - - + -
78A VAL* 5.1 7.4 - - + -
79A CYS 3.0 10.3 + - - +
80A PHE* 3.1 18.4 - - + +
81A GLY 3.0 24.4 + - - +
105A LEU* 3.9 26.9 - - + -
106A ALA* 1.3 78.9 - - - +
108A ILE* 1.3 63.1 + - - +
150A ILE* 3.8 26.7 - - + -
166A VAL* 3.5 7.9 - - + +
168A ILE* 4.2 19.7 - - + -
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Residues in contact with ILE 108 (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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37A ILE* 4.4 2.9 - - - -
81A GLY 3.4 6.1 - - - +
82A SER 4.5 1.3 - - - +
87A GLY* 4.2 6.5 - - - -
90A LEU* 3.5 32.3 - - + -
106A ALA* 4.5 4.3 - - + -
107A LEU* 1.3 76.1 - - - +
109A GLY* 1.3 67.3 + - - +
126A GLU* 3.5 28.9 - - - +
130A TYR* 3.7 35.4 - - + +
165A VAL* 3.5 28.7 - - + -
166A VAL 3.0 6.5 + - - +
167A GLN* 3.4 11.8 - - + -
168A ILE* 2.8 30.2 + - - +
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Residues in contact with GLY 109 (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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36A SER* 3.4 18.2 - - - -
37A ILE* 3.9 12.2 - - - +
81A GLY 2.9 15.8 + - - -
83A ALA* 3.2 24.9 - - - +
108A ILE* 1.3 74.8 - - - +
110A GLN* 1.3 51.8 + - - -
126A GLU* 2.6 25.6 - - - +
168A ILE* 4.2 2.9 - - - -
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Residues in contact with GLN 110 (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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36A SER* 3.4 11.5 + - - +
83A ALA* 4.0 4.0 - - - +
108A ILE 4.6 0.2 - - - +
109A GLY* 1.3 73.5 - - - -
111A PHE* 1.3 94.7 + - - +
116A MET* 3.8 33.6 - - + +
122A GLN 4.9 0.2 - - - +
123A GLU* 4.1 9.3 + - - +
124A MET 2.9 29.3 + - - +
125A ASN* 4.8 0.4 - - - +
126A GLU* 3.3 26.8 + - - +
139A THR* 5.3 3.9 - - + +
167A GLN* 4.8 4.4 - - + +
168A ILE 3.2 23.1 + - - +
169A PRO* 4.4 2.7 - - + -
170A VAL* 2.9 24.4 + - - +
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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