Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 1IRP
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 GLU 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LYS* 2.8 19.8 + - - -
73A SER* 2.9 31.7 + - - +
75A ASP* 1.3 88.1 + - - +
77A THR* 1.3 74.2 + - - +
78A ARG* 2.7 49.6 + - + +
120A TRP* 3.1 29.4 - - - -
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A CYS* 3.8 29.6 - - + +
71A VAL 2.5 23.0 + - - +
72A LYS* 3.3 17.5 - - - -
73A SER* 4.7 1.1 - - - +
76A GLU* 1.3 85.1 + - - +
78A ARG* 1.3 77.3 + - - +
98A ARG* 3.5 15.7 - - + +
114A SER* 4.4 2.0 - - - +
120A TRP* 3.6 37.1 - - + +
134A LEU* 4.3 1.6 - - - +
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Residues in contact with ARG 78 (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 GLN* 4.7 11.0 - - - +
69A SER 3.7 0.5 - - - +
70A CYS* 3.7 1.1 - - - -
71A VAL* 3.0 35.9 + - + +
73A SER* 5.8 2.2 - - - -
76A GLU* 2.7 51.5 + - + +
77A THR* 1.3 91.5 + - - +
79A LEU* 1.3 72.9 + - - +
80A GLN 3.5 0.7 + - - -
120A TRP* 4.2 3.8 - - - -
132A VAL 4.3 4.9 - - - +
133A SER* 4.3 12.2 - - - +
134A LEU* 3.2 46.3 + - - +
135A THR* 5.6 1.1 - - - +
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Residues in contact with LEU 79 (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 GLN* 3.0 27.2 + - - +
31A LEU* 5.3 4.6 - - + +
68A LEU* 3.8 32.1 - - + -
69A SER 3.4 18.4 - - - +
78A ARG* 1.3 76.8 - - - +
80A GLN* 1.3 62.1 + - - +
81A LEU* 5.5 0.2 - - - +
101A PHE* 3.5 28.0 - - + -
112A PHE* 4.4 19.1 - - + -
132A VAL* 3.8 46.4 - - + +
134A LEU* 3.7 21.4 - - + +
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Residues in contact with GLN 80 (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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29A ASN* 2.9 46.6 + - - +
30A GLN* 4.0 6.7 + - - +
31A LEU* 6.2 0.2 - - - -
67A CYS 3.0 14.0 - - - +
68A LEU* 3.4 6.3 - - - -
69A SER* 3.1 23.0 + - - +
71A VAL* 3.4 38.2 - - + +
78A ARG 3.5 0.2 + - - -
79A LEU* 1.3 75.9 - - - +
81A LEU* 1.3 90.2 + - - +
82A GLU* 3.5 8.1 + - + +
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Residues in contact with LEU 81 (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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26A LEU* 3.7 25.1 - - + -
28A ASN 4.0 19.1 - - - +
29A ASN* 3.3 32.8 - - - +
30A GLN* 4.1 1.8 - - - +
31A LEU* 4.1 15.5 - - + -
62A HIS* 4.3 1.6 - - - +
66A MET* 3.6 29.3 - - + +
67A CYS 3.4 7.4 - - - -
68A LEU* 3.7 17.9 - - + -
80A GLN* 1.3 88.1 + - - +
82A GLU* 1.3 62.3 + - - +
83A ALA 3.9 0.9 + - - -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A MET* 3.6 1.1 - - - -
67A CYS* 2.8 49.8 + - + +
69A SER* 2.3 31.4 + - - +
71A VAL* 4.1 15.7 - - + +
80A GLN* 3.5 12.0 + - + +
81A LEU* 1.3 73.7 - - - +
83A ALA* 1.3 64.0 + - - +
84A VAL* 3.3 3.1 + - + -
99A PHE* 3.4 28.9 - - - -
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Residues in contact with ALA 83 (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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65A LYS 3.7 1.8 - - - +
66A MET* 3.5 25.5 - - + -
81A LEU 3.9 1.8 + - - -
82A GLU* 1.3 70.1 - - - +
84A VAL* 1.3 59.6 + - - +
85A ASN* 3.4 14.1 + - + +
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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