Contacts of the strand formed by residues 112 - 117 (chain A) in PDB entry 1CXZ
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 ILE 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.5 15.5 - - + +
82A MET* 3.7 46.2 - - + -
103A VAL* 3.8 16.2 - - + -
104A LYS* 4.2 30.1 - - + +
107A CYS 5.9 0.4 - - - +
110A VAL 3.4 14.8 + - - +
111A PRO* 1.3 75.0 - - - +
113A ILE* 1.3 68.0 + - - +
151A ILE* 4.3 9.4 - - + +
152A GLY 5.4 0.8 + - - +
153A ALA* 3.3 19.3 - - + +
154A PHE* 2.6 36.1 + - - +
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Residues in contact with ILE 113 (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 VAL* 3.7 28.0 - - + -
80A ILE 2.9 7.5 + - - -
81A LEU* 3.6 14.4 - - + -
82A MET 3.0 23.4 + - - +
112A ILE* 1.3 80.2 - - - +
114A LEU* 1.3 72.0 + - - +
115A VAL* 3.5 14.9 + - + +
154A PHE* 4.1 9.0 - - + -
155A GLY 3.6 6.7 - - - +
157A MET* 4.2 19.7 - - + -
170A VAL* 5.2 3.8 - - + +
173A MET* 4.0 21.5 - - + -
174A ALA* 3.9 16.4 - - + +
177A ALA* 4.1 13.9 - - + -
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Residues in contact with LEU 114 (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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82A MET* 3.4 20.4 - - + +
84A PHE* 3.7 31.9 - - + -
95A ILE* 3.9 23.8 - - + -
112A ILE* 4.0 2.2 - - - +
113A ILE* 1.3 74.2 - - - +
115A VAL* 1.3 57.8 + - - +
144A GLY 3.3 26.7 - - - +
147A MET* 3.9 16.2 - - + +
148A ALA* 3.5 22.2 - - + +
151A ILE* 4.7 5.8 - - + -
153A ALA* 4.2 7.9 - - + +
155A GLY 3.0 12.9 + - - +
156A TYR* 3.4 9.3 - - + -
157A MET 3.0 24.9 + - - -
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Residues in contact with VAL 115 (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* 4.3 6.5 - - + -
81A LEU* 4.0 16.4 - - + -
82A MET 2.8 11.4 + - - +
83A CYS* 3.5 16.7 - - - +
84A PHE* 3.2 33.2 + - - +
113A ILE* 3.7 24.7 - - + +
114A LEU* 1.3 78.1 - - - +
116A GLY* 1.3 61.9 + - - +
117A ASN* 3.4 23.1 + - - +
157A MET 3.3 7.4 - - - +
159A CYS* 3.9 16.6 - - - -
170A VAL* 4.1 14.8 - - + -
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Residues in contact with GLY 116 (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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84A PHE* 3.6 28.3 - - - -
86A ILE* 3.6 11.5 - - - +
114A LEU 4.2 0.2 + - - -
115A VAL* 1.3 71.5 - - - +
117A ASN* 1.3 62.6 + - - -
156A TYR* 4.2 4.4 - - - -
157A MET 2.8 14.4 + - - -
158A GLU* 3.3 3.6 - - - -
159A CYS 3.0 27.2 + - - +
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Residues in contact with ASN 117 (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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16A CYS 2.9 30.0 + - - +
17A GLY* 3.3 24.0 + - - -
18A LYS* 4.4 0.4 - - - +
21A LEU* 3.7 7.9 - - - +
83A CYS* 3.6 25.1 - - - +
84A PHE 2.9 12.8 + - - +
85A SER* 4.4 0.2 - - - -
86A ILE* 2.8 28.5 + - - +
115A VAL* 3.4 21.2 - - - +
116A GLY* 1.3 71.0 - - - +
118A LYS* 1.3 69.0 + - + +
119A LYS 3.3 1.8 - - - -
159A CYS* 3.5 14.1 - - - -
161A ALA* 6.5 0.7 - - - -
500A GSP 5.8 0.9 - - - +
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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