Contacts of the helix formed by residues 103 - 117 (chain A) in PDB entry 4XXH
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A SER 3.1 13.8 + - - +
101A GLN* 3.2 4.4 - - - -
102A PHE* 1.3 77.4 - - - +
104A PRO* 1.4 63.8 - - - +
105A GLN* 3.2 15.6 + - - +
106A LEU* 3.2 26.0 + - - +
107A VAL* 3.1 24.1 + - - +
127A PHE* 3.8 3.9 - - - -
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Residues in contact with PRO 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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102A PHE 3.5 8.7 - - - +
103A SER* 1.4 83.3 - - - +
105A GLN* 1.3 77.9 + - - +
107A VAL 3.4 0.3 + - - -
108A ALA* 3.0 25.5 + - - +
127A PHE* 3.9 4.4 - - + -
128A THR 4.6 1.6 - - - +
129A GLY* 3.5 40.6 - - - +
130A ILE* 4.1 13.2 - - + -
134A MET* 3.3 20.9 - - + +
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Residues in contact with GLN 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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103A SER* 3.2 13.7 + - - +
104A PRO* 1.3 94.4 - - - +
106A LEU* 1.3 59.3 + - - +
108A ALA* 3.3 8.9 + - - +
109A GLU* 3.0 33.2 + - - +
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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
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99A GLU 3.8 14.8 - - - +
100A SER* 3.5 20.2 - - - +
101A GLN* 5.1 5.8 - - + -
103A SER* 3.2 22.8 + - - +
105A GLN* 1.3 72.2 - - - +
107A VAL* 1.4 59.6 - - - +
109A GLU* 3.2 25.2 + - - +
110A HIS* 2.9 46.7 + - + +
89B TYR* 3.8 33.7 - - + +
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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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68A ILE* 4.7 4.3 - - + -
100A SER* 3.4 26.2 - - - -
103A SER 3.1 14.0 + - - +
104A PRO 3.6 7.0 - - - +
105A GLN 3.3 0.2 - - - -
106A LEU* 1.4 74.9 - - - +
108A ALA* 1.4 55.6 + - - +
110A HIS* 3.2 8.8 + - - +
111A LEU* 2.9 46.0 + - + +
124A LEU* 4.0 23.6 - - + -
127A PHE* 3.8 15.5 - - + -
130A ILE* 3.8 11.4 - - + -
134A MET* 3.7 15.9 - - + -
135A LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 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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104A PRO 3.0 14.2 + - - +
105A GLN* 3.3 12.5 + - - +
107A VAL* 1.4 73.4 - - - +
109A GLU* 1.3 62.1 + - + +
111A LEU* 3.5 8.0 + - - +
112A GLY* 3.2 18.5 + - - -
134A MET* 4.0 20.4 - - + +
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Residues in contact with GLU 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 GLN* 3.0 20.0 + - - +
106A LEU* 3.2 28.5 + - - +
108A ALA* 1.3 74.6 - - + +
110A HIS* 1.4 67.5 + - + +
112A GLY* 3.3 2.9 + - - -
113A VAL* 3.1 25.7 + - + +
116A ARG* 4.9 1.6 + - - -
89B TYR* 5.5 3.1 - - - -
94B ASP* 4.5 6.4 - - - +
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Residues in contact with HIS 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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68A ILE* 3.9 30.1 - - + -
98A MET* 3.5 28.0 - - + +
99A GLU 2.8 28.2 + - - -
100A SER* 4.7 0.9 - - - -
106A LEU* 2.9 37.7 + - + +
107A VAL* 3.6 9.0 - - - +
109A GLU* 1.4 71.9 - - + +
111A LEU* 1.4 52.8 + - - +
113A VAL* 3.1 5.0 + - - +
114A LEU* 2.9 39.3 + - - +
89B TYR* 3.7 13.9 - + - -
94B ASP* 3.0 36.8 + - - -
95B PRO 5.2 1.8 - - - -
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Residues in contact with LEU 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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68A ILE* 4.2 19.1 - - + -
107A VAL* 2.9 39.0 + - + +
108A ALA* 3.8 7.6 - - - +
110A HIS* 1.4 76.0 - - - +
112A GLY* 1.3 55.0 + - - +
114A LEU* 3.5 2.9 + - + -
115A LYS* 2.9 29.9 + - - +
122A VAL* 4.3 10.1 - - + -
124A LEU* 5.4 0.9 - - + -
134A MET* 3.6 25.4 - - + +
135A LEU* 4.1 14.8 - - + -
138A TRP* 3.4 37.2 + - + +
142A LEU* 4.3 14.4 - - + -
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Residues in contact with GLY 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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108A ALA 3.2 13.9 + - - -
109A GLU* 3.3 3.1 + - - -
110A HIS 3.3 0.4 - - - -
111A LEU* 1.3 72.9 - - - +
113A VAL* 1.4 58.9 + - - +
115A LYS* 3.3 5.9 + - - +
116A ARG* 3.0 56.6 + - - +
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Residues in contact with VAL 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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98A MET* 4.5 9.2 - - + -
109A GLU* 3.1 14.7 + - + +
110A HIS 3.1 9.1 + - - +
112A GLY* 1.4 75.9 - - - +
114A LEU* 1.3 64.1 + - + +
116A ARG* 3.5 4.6 + - - +
117A ARG* 3.1 27.9 + - + +
62B ASP* 3.9 32.7 - - + +
63B LYS 5.7 0.2 - - - +
64B VAL* 3.8 27.6 - - + -
94B ASP* 3.8 26.9 - - + +
96B ILE* 5.7 1.1 - - + -
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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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66A ALA* 3.7 31.0 - - + -
68A ILE* 4.0 17.9 - - + -
96A ILE* 3.9 11.2 - - + -
98A MET* 3.8 27.6 - - + -
110A HIS 2.9 20.8 + - - +
111A LEU* 3.7 7.2 - - + +
113A VAL* 1.3 77.8 - - + +
115A LYS* 1.4 61.1 + - - +
117A ARG* 3.3 2.4 + - + -
118A ASN 3.2 4.5 + - - -
119A ILE* 3.1 46.8 + - + +
122A VAL* 4.0 11.9 - - + -
138A TRP* 3.9 13.2 - - + -
96B ILE* 5.4 0.7 - - + -
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Residues in contact with LYS 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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111A LEU 2.9 17.6 + - - +
112A GLY* 3.5 9.0 - - - +
114A LEU* 1.4 75.2 - - - +
116A ARG* 1.3 60.8 + - + +
118A ASN* 3.0 27.1 + - - +
137A HIS* 5.2 14.4 - - + +
138A TRP* 3.5 21.0 - - + +
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Residues in contact with ARG 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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109A GLU 4.9 1.2 + - - -
112A GLY* 3.0 41.9 + - - +
113A VAL* 3.7 5.8 - - - +
115A LYS* 1.3 79.4 - - + +
117A ARG* 1.3 60.0 + - - +
118A ASN* 3.3 10.2 + - - -
61B SER* 6.4 1.6 - - - -
62B ASP* 2.8 45.4 + - - +
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Residues in contact with ARG 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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113A VAL* 3.1 19.3 + - + +
114A LEU* 3.8 3.6 - - - +
115A LYS 3.2 0.4 - - - -
116A ARG* 1.3 78.3 - - - +
118A ASN* 1.4 64.8 + - - +
119A ILE* 3.4 12.4 + - + +
61B SER 4.6 8.6 - - - +
62B ASP* 2.8 43.1 + - - +
64B VAL* 3.3 21.9 - - - +
117B ARG* 2.9 72.1 + - + +
118B ASN* 2.9 32.1 + - - +
119B ILE* 3.9 13.7 - - + +
120B ASP* 4.4 2.8 + - - -
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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