Contacts of the helix formed by residues 100 - 113 (chain A) in PDB entry 1D5R
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 LEU 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.9 42.1 - - + +
89A PRO* 4.4 7.2 - - + +
90A PHE* 3.9 18.8 - - + -
96A PRO* 3.8 22.9 - - + -
97A GLN* 3.0 24.0 + - + +
99A GLU* 1.3 77.8 - - - +
101A ILE* 1.3 60.4 + - + +
103A PRO* 3.1 19.4 - - + +
104A PHE* 3.3 12.1 + - - +
134A MET* 4.5 6.1 - - + -
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Residues in contact with ILE 101 (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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96A PRO* 4.1 22.9 - - + -
97A GLN 4.2 0.2 - - - +
98A LEU* 3.2 20.4 + - + +
100A LEU* 1.3 75.6 - - - +
102A LYS* 1.3 68.8 + - - +
104A PHE* 3.0 5.0 + - - +
105A CYS* 3.0 22.3 + - - -
133A VAL* 4.9 5.8 - - + -
134A MET* 4.1 13.5 - - + -
137A ALA* 3.5 30.1 - - + -
174A TYR* 4.0 40.6 - - + +
175A VAL* 5.8 0.2 - - - -
178A TYR* 3.8 23.8 - - + -
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Residues in contact with LYS 102 (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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98A LEU 4.5 2.0 + - - -
99A GLU* 4.5 1.5 + - - -
101A ILE* 1.3 76.8 - - - +
103A PRO* 1.3 73.6 - - + +
105A CYS* 3.0 12.5 + - - +
106A GLU* 2.9 50.3 + - + +
141A HIS* 4.9 6.1 + - - -
178A TYR* 3.8 30.7 + - + +
181A LEU* 6.3 2.2 - - + -
187A ASP* 5.7 9.9 - - - -
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Residues in contact with PRO 103 (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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88A TYR* 3.9 12.0 + - + +
99A GLU 3.1 24.2 - - - +
100A LEU* 3.1 20.9 - - + +
102A LYS* 1.3 89.0 - - + +
104A PHE* 1.3 58.2 + - - +
106A GLU* 3.3 13.8 + - + +
107A ASP* 3.0 24.4 + - - +
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Residues in contact with PHE 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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68A TYR* 3.4 32.1 - + + -
70A LEU* 4.7 5.4 - - + -
88A TYR* 3.7 36.3 - + + -
100A LEU 3.3 12.7 + - - +
101A ILE 3.0 9.0 + - - +
103A PRO* 1.3 77.9 - - - +
105A CYS* 1.3 64.8 + - - +
107A ASP* 3.3 2.9 + - - +
108A LEU* 3.0 54.7 + - + +
122A ILE* 4.1 15.7 - - + -
134A MET* 3.4 60.3 - - + -
135A ILE* 5.5 0.2 - - - -
138A TYR* 4.7 1.1 - - + -
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Residues in contact with CYS 105 (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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101A ILE* 3.0 16.2 + - - +
102A LYS 3.5 7.6 - - - +
104A PHE* 1.3 82.2 - - - +
106A GLU* 1.3 58.6 + - - +
109A ASP* 2.9 31.2 + - - +
137A ALA* 3.7 18.8 - - - -
138A TYR* 3.6 41.9 - - + -
141A HIS* 3.6 28.7 + - + -
178A TYR* 4.0 7.9 - - - +
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Residues in contact with GLU 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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102A LYS* 2.9 50.0 + - + +
103A PRO* 3.8 13.5 - - - +
105A CYS* 1.3 74.9 - - - +
107A ASP* 1.3 57.2 + - - +
109A ASP* 3.6 5.1 - - - +
110A GLN* 2.7 37.1 + - - +
141A HIS* 4.0 17.7 + - + +
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Residues in contact with ASP 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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66A LYS* 2.9 21.9 + - - -
68A TYR* 2.7 31.9 + - + -
86A ALA* 4.4 3.5 - - - +
88A TYR* 2.6 35.6 + - + +
103A PRO 3.0 8.7 + - - +
104A PHE 3.3 8.7 - - - +
106A GLU* 1.3 75.8 - - - +
108A LEU* 1.3 63.9 + - - +
110A GLN* 2.9 23.4 + - - +
111A TRP* 3.1 6.1 + - - +
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Residues in contact with LEU 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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32A ILE* 5.2 5.8 - - + -
68A TYR* 3.4 23.5 + - + +
104A PHE* 3.0 35.7 + - + +
105A CYS 4.0 2.9 - - - +
107A ASP* 1.3 80.1 + - - +
109A ASP* 1.3 57.8 + - - +
110A GLN 3.3 0.2 + - - -
111A TRP* 3.3 3.0 + - + +
112A LEU* 3.0 56.9 + - + +
120A ALA* 4.0 16.4 - - + -
122A ILE* 4.7 9.9 - - + -
135A ILE* 5.7 3.1 - - + -
138A TYR* 3.5 32.8 - - + -
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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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105A CYS 2.9 21.3 + - - +
106A GLU* 3.8 6.7 - - - +
108A LEU* 1.3 75.0 - - - +
110A GLN* 1.3 55.9 + - - +
112A LEU* 4.0 1.0 - - - +
113A SER* 2.7 40.6 + - - -
138A TYR* 3.5 28.8 + - + -
141A HIS* 4.5 15.8 - - - +
142A ARG* 4.1 16.3 + - - +
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Residues in contact with GLN 110 (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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106A GLU 2.7 18.1 + - - +
107A ASP* 3.0 13.9 - - - +
109A ASP* 1.3 73.7 - - - +
111A TRP* 1.3 56.7 + - - +
113A SER* 2.5 24.4 + - - -
115A ASP* 2.7 51.9 - - - +
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Residues in contact with TRP 111 (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 TYR 3.5 30.1 - - - -
66A LYS* 3.5 32.4 - - + +
68A TYR* 4.2 9.9 - - - +
83A CYS* 5.9 0.7 - - + -
84A ARG* 5.7 5.6 - - + -
107A ASP 3.1 7.8 + - - +
108A LEU 3.9 4.9 - - - +
110A GLN* 1.3 81.3 - - + +
112A LEU* 1.3 67.7 + - + +
113A SER 3.4 0.3 + - - -
114A GLU 3.5 0.9 + - - -
115A ASP* 2.7 16.8 - - - +
116A ASP* 3.2 36.3 - - + -
117A ASN* 2.5 69.7 - - + +
118A HIS 4.0 0.2 - - - +
119A VAL 2.9 30.9 + - - +
120A ALA* 4.5 5.4 - - + -
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Residues in contact with LEU 112 (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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31A ASN* 3.6 30.2 - - + +
32A ILE* 3.9 23.1 - - + -
108A LEU* 3.0 42.8 + - + +
109A ASP* 4.4 1.6 - - - +
111A TRP* 1.3 79.5 - - + +
113A SER* 1.3 56.1 + - - +
114A GLU* 2.8 20.7 + - - +
117A ASN 4.2 3.1 - - - +
118A HIS* 3.5 32.1 - - - +
119A VAL* 3.9 3.1 - - - +
120A ALA 4.1 1.8 - - - +
138A TYR* 3.5 22.4 - - + +
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Residues in contact with SER 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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109A ASP* 2.7 22.0 + - - -
110A GLN* 2.5 30.0 + - - -
112A LEU* 1.3 74.0 - - - +
114A GLU* 1.3 71.2 + - - +
115A ASP* 3.0 5.4 + - - +
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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