Contacts of the strand formed by residues 103 - 108 (chain A) in PDB entry 1UIR
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 LYS 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS 3.1 5.8 + - - +
80A ARG* 3.4 14.1 - - + +
81A VAL 2.9 24.8 + - - +
101A VAL* 3.7 5.0 - - - +
102A GLU* 1.3 83.8 - - + +
104A ALA* 1.3 62.8 + - - +
105A VAL* 3.6 25.5 - - + +
133A ARG 3.4 9.2 - - - +
135A VAL* 4.1 17.7 - - + -
150A GLU* 3.2 35.6 + - - +
152A TYR* 6.2 0.7 - - + -
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Residues in contact with ALA 104 (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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81A VAL* 3.3 7.4 - - + +
83A ILE* 5.2 2.9 - - + -
92A LEU* 3.7 26.4 - - + +
95A VAL* 4.2 17.9 - - + -
96A LEU* 4.1 13.9 - - + -
101A VAL* 4.3 1.8 - - + -
103A LYS* 1.3 74.5 - - - +
105A VAL* 1.3 63.6 + - - +
106A MET 3.9 0.5 + - - -
133A ARG 2.8 13.6 + - - +
134A ALA* 3.4 3.6 - - - +
135A VAL 2.9 24.1 + - - -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL 2.9 9.9 + - - +
82A LEU* 3.3 19.1 - - + +
83A ILE* 2.7 33.7 + - - +
103A LYS* 3.6 33.9 - - + +
104A ALA* 1.3 73.0 - - - +
106A MET* 1.3 56.9 + - - +
107A VAL* 4.1 5.8 - - + -
135A VAL* 3.4 18.6 - - + +
137A VAL* 4.1 17.7 - - + -
144A TYR* 3.9 18.6 - - - +
150A GLU* 4.8 0.2 - - - +
152A TYR* 4.2 18.4 - - + +
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Residues in contact with MET 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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83A ILE* 3.4 18.2 - - + +
85A GLY 3.8 13.5 - - - +
86A GLY 3.1 28.5 - - - +
87A GLY* 3.5 17.5 - - - +
89A GLY* 4.9 0.2 - - - -
92A LEU* 4.5 24.2 - - + -
104A ALA 3.9 1.2 + - - +
105A VAL* 1.3 73.2 - - - +
107A VAL* 1.3 60.2 + - - +
108A ASP* 4.6 3.6 - - + -
114A VAL* 4.6 5.4 - - + -
129A PHE* 3.7 36.1 - - + -
135A VAL 2.8 12.7 + - - +
136A LEU* 3.6 16.4 - - + +
137A VAL* 2.8 33.3 + - - +
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Residues in contact with VAL 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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82A LEU* 3.8 23.6 - - + -
83A ILE 2.8 12.2 + - - +
84A VAL* 3.7 8.5 - - + +
85A GLY 3.0 23.6 + - - -
105A VAL* 4.1 9.2 - - + -
106A MET* 1.3 76.2 - - - +
108A ASP* 1.3 61.8 + - - +
137A VAL* 3.2 14.4 - - + +
139A ASP 3.6 20.2 - - - +
141A ALA* 4.1 21.2 - - - +
144A TYR* 3.9 32.3 - - + -
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Residues in contact with ASP 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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85A GLY* 3.7 27.0 - - - +
87A GLY* 4.2 10.3 + - - -
106A MET* 4.1 7.8 - - + -
107A VAL* 1.3 75.2 - - - +
109A ILE* 1.3 65.5 + - - +
110A ASP* 3.0 36.9 + - - +
113A LEU* 5.3 4.5 - - - +
114A VAL* 3.9 18.0 - - + +
136A LEU* 5.2 0.6 - - + +
137A VAL 2.9 7.1 + - - -
138A ILE* 3.0 16.4 - - + +
139A ASP 2.9 21.3 + - - -
159A LEU* 5.9 0.3 - - - +
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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