Contacts of the strand formed by residues 105 - 109 (chain A) in PDB entry 1IN7
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 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA 4.5 4.5 - - - +
71A ILE* 4.1 12.1 - - + -
72A ALA* 3.7 36.8 - - + +
75A LEU* 4.2 8.7 - - + -
77A THR* 4.1 4.5 - - - +
78A ASN 2.8 9.2 + - - +
79A ILE* 3.3 20.1 - - + -
80A HIS* 2.8 36.2 + - - -
100A LEU* 5.1 0.2 - - - -
104A ASP* 1.3 76.7 - - - +
106A LEU* 1.3 58.1 + - - +
107A PHE* 4.1 6.1 - - + +
152A THR* 3.4 10.1 - - - -
154A VAL* 3.7 26.0 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A HIS* 3.9 14.4 - - + +
82A THR* 4.2 14.1 - - + -
93A MET* 5.0 4.3 - - - -
96A ILE* 3.6 29.8 - - + -
97A LEU* 4.1 12.3 - - + -
100A LEU* 4.4 8.3 - - + -
104A ASP 4.0 1.0 + - - -
105A VAL* 1.3 72.6 - - - +
107A PHE* 1.3 57.2 + - - +
108A ILE* 4.0 12.8 - - + -
122A LEU* 3.8 24.2 - - + -
151A PHE* 3.7 35.0 - - + -
152A THR 2.9 8.7 + - - +
153A LEU* 3.4 6.2 - - + +
154A VAL 3.0 23.8 + - - +
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Residues in contact with PHE 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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56A LEU* 5.0 0.4 - - + -
64A LYS 4.7 1.6 - - - -
65A THR* 3.8 42.0 - - + -
68A ALA* 3.4 24.5 - - + -
69A HIS* 5.3 1.1 - - - -
79A ILE* 3.9 20.2 - - + -
80A HIS 2.9 15.3 + - - +
81A VAL* 4.2 23.6 - - + -
82A THR* 3.0 29.1 + - - +
105A VAL* 3.7 4.2 + - + -
106A LEU* 1.3 70.6 - - - +
108A ILE* 1.3 60.8 + - - +
109A ASP* 4.0 19.3 - - + -
154A VAL* 3.3 21.5 - - + -
156A ALA* 3.4 35.4 - - + -
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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
----------------------------------------------------------
82A THR* 3.4 16.8 - - + -
83A SER 4.2 3.4 - - - -
84A GLY 3.9 11.9 - - - +
87A LEU* 4.6 4.5 - - + -
93A MET* 4.5 8.1 - - + -
106A LEU* 4.0 18.2 - - + -
107A PHE* 1.3 76.1 - - - +
109A ASP* 1.3 65.3 + - - +
111A ILE* 3.5 33.2 - - + +
114A LEU* 4.3 10.8 - - + -
122A LEU* 3.7 30.3 - - + -
153A LEU* 3.8 13.7 - - + -
154A VAL 3.0 9.8 + - - +
155A GLY* 3.5 1.9 - - - -
156A ALA 3.0 23.5 + - - -
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Residues in contact with ASP 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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64A LYS* 5.0 5.0 - - - -
65A THR* 4.7 6.4 + - - -
81A VAL* 6.2 0.4 - - + -
82A THR 2.9 14.5 + - - +
83A SER* 3.1 9.9 - - - -
84A GLY 3.0 18.9 + - - -
107A PHE* 4.0 20.1 - - + -
108A ILE* 1.3 69.8 - - - +
110A GLU* 1.3 93.2 + - - +
111A ILE 3.1 1.9 + - - -
156A ALA* 3.4 22.3 - - - +
600A ADP 5.1 2.3 + - - -
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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