Contacts of the strand formed by residues 54 - 61 (chain A) in PDB entry 3IE7
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 ASN 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1A LEU* 3.0 8.0 - - - +
2A ILE* 3.0 14.6 - - + +
4A THR* 5.7 0.7 - - + -
44A SER* 3.5 27.2 + - - +
47A LEU* 3.5 36.5 - - + +
48A SER* 3.1 24.7 + - - +
52A ILE 3.0 21.3 + - - +
53A LYS* 1.3 79.8 - - - +
55A GLU* 1.3 64.1 + - - +
56A ALA 4.8 0.2 + - - -
77A ILE* 4.9 1.4 - - - +
78A ASN* 3.9 24.9 + - - +
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Residues in contact with GLU 55 (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 LEU* 4.0 8.9 - - + +
2A ILE 2.9 6.5 + - - -
3A TYR* 3.2 35.2 - - + -
4A THR* 3.1 23.2 + - - +
44A SER* 4.5 2.7 - - - -
54A ASN* 1.3 75.1 - - - +
56A ALA* 1.3 66.1 + - - +
57A LEU* 3.8 4.5 + - + +
78A ASN* 3.5 9.3 - - + +
79A HIS* 4.0 19.5 + - - +
80A ASP* 4.0 10.3 - - - +
128A LYS* 2.8 34.1 + - - -
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Residues in contact with ALA 56 (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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4A THR* 3.4 9.6 - - - +
41A LEU* 3.7 25.8 - - + -
44A SER* 3.6 15.8 + - - +
55A GLU* 1.3 71.9 - - - +
57A LEU* 1.3 64.0 + - - +
77A ILE* 4.0 6.1 - - + -
78A ASN 2.9 17.6 + - - +
79A HIS* 3.3 3.5 - - + +
80A ASP 3.0 26.9 + - - -
81A PHE* 3.9 8.9 - - + -
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Residues in contact with LEU 57 (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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3A TYR* 4.0 28.3 - - + -
4A THR 2.8 15.3 + - - +
5A ILE* 4.2 14.6 - - + -
6A THR* 2.9 23.8 + - - -
55A GLU* 3.8 22.0 - - - +
56A ALA* 1.3 81.3 - - - +
58A GLY* 1.3 59.2 + - - +
80A ASP* 3.8 18.4 - - + +
81A PHE* 3.7 10.8 - - - -
121A LEU* 4.5 7.4 - - + -
124A GLN* 4.0 11.2 - - - +
125A ILE* 4.4 23.1 - - + -
128A LYS* 4.1 15.5 - - + -
129A VAL* 5.1 4.7 - - + -
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Residues in contact with GLY 58 (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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5A ILE* 5.0 2.0 - - - -
6A THR 3.2 16.2 - - - -
57A LEU* 1.3 78.0 - - - +
59A ILE* 1.3 70.9 + - - -
80A ASP 4.9 0.6 + - - -
81A PHE* 3.2 12.6 - - - +
82A LEU* 2.8 29.6 + - - +
121A LEU* 4.3 9.5 - - - +
124A GLN* 5.1 0.4 + - - -
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Residues in contact with ILE 59 (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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6A THR 3.6 4.4 + - - -
7A LEU* 4.0 22.5 - - + +
9A PRO* 3.2 23.1 - - - +
58A GLY* 1.3 82.2 - - - +
60A ALA* 1.3 63.0 + - - +
81A PHE* 3.6 1.0 - - - -
82A LEU* 3.5 22.2 - - + +
84A GLU* 4.1 13.0 - - + -
111A PHE* 3.5 27.4 - - + -
113A VAL* 4.2 27.8 - - + -
117A ASN* 4.1 17.3 - - + +
118A LYS* 6.0 0.7 - - - -
121A LEU* 3.9 26.5 - - + -
145A TYR* 5.5 2.7 - - + -
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Residues in contact with ALA 60 (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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9A PRO* 4.2 3.8 - - + -
59A ILE* 1.3 73.5 - - - +
61A GLY* 1.3 62.3 - - - +
65A LEU* 4.1 14.4 - - + -
68A LEU* 3.6 23.8 - - + -
81A PHE* 4.1 14.5 - - + -
82A LEU 3.0 9.4 + - - +
83A VAL* 3.4 5.2 - - - +
84A GLU 2.9 24.6 + - - -
89A THR* 3.5 12.3 - - - +
111A PHE* 3.6 5.8 - - - -
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Residues in contact with GLY 61 (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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60A ALA* 1.3 73.4 - - - +
62A SER* 1.3 64.8 + - - -
63A ASP 3.4 0.6 + - - -
64A ASN* 3.7 5.7 - - - +
65A LEU* 3.6 22.7 + - - +
83A VAL* 4.3 0.9 - - - -
87A THR* 3.4 26.9 - - - -
89A THR* 2.9 19.8 + - - -
111A PHE* 3.4 9.3 - - - -
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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