Contacts of the helix formed by residues 108 - 130 (chain A) in PDB entry 4X86
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 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PHE* 1.3 76.8 - - - +
109A ALA* 1.3 58.7 + - - +
110A ALA* 3.8 5.5 + - - +
111A ASP* 3.2 31.4 + - - +
112A ALA* 2.8 27.4 + - - +
1078B ARG 5.6 0.2 + - - -
1080B LEU* 3.8 21.3 - - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 1.3 73.7 - - - +
110A ALA* 1.3 63.8 + - - +
112A ALA* 3.3 5.8 + - - +
113A SER* 3.1 23.2 + - - -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 3.3 5.7 + - - +
109A ALA* 1.3 80.6 - - - +
111A ASP* 1.3 61.9 + - - +
113A SER* 3.4 6.0 + - - -
114A ARG* 3.1 51.7 + - - +
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 4.0 11.2 - - + -
108A SER* 3.2 23.5 + - - +
110A ALA* 1.3 77.2 - - - +
112A ALA* 1.3 59.8 + - - +
114A ARG* 3.1 25.8 + - - +
115A VAL* 2.8 35.5 + - - +
1075B ALA 5.1 1.2 - - - +
1076B GLY 4.8 2.3 - - - +
1077B ALA* 3.8 32.3 - - + +
1078B ARG 4.2 10.7 + - - +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER* 5.6 1.6 - - - +
103A LEU* 3.7 38.8 - - + +
104A ALA* 4.7 4.7 - - + +
107A PHE* 3.8 7.7 - - + +
108A SER 2.8 21.2 + - - +
109A ALA* 3.3 7.6 + - - +
111A ASP* 1.3 71.1 - - - +
113A SER* 1.3 63.0 + - - +
115A VAL* 3.4 2.6 + - - -
116A LEU* 3.0 24.8 + - - +
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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
----------------------------------------------------------
109A ALA 3.1 10.4 + - - -
110A ALA* 3.7 9.0 - - - -
112A ALA* 1.3 80.5 - - - +
114A ARG* 1.3 63.1 + - - +
116A LEU* 3.3 7.8 + - - +
117A GLU* 3.0 39.5 + - - +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA* 3.1 40.1 + - - +
111A ASP* 3.1 28.2 + - - +
113A SER* 1.3 76.6 - - - +
115A VAL* 1.3 58.1 + - - +
117A GLU* 3.5 11.3 + - - +
118A GLN* 3.0 30.7 + - - +
1075B ALA* 4.2 26.1 + - + +
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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
----------------------------------------------------------
103A LEU* 4.1 24.5 - - + -
107A PHE* 4.4 8.7 - - + -
111A ASP 2.8 25.2 + - - +
112A ALA* 3.8 4.9 - - - +
114A ARG* 1.3 74.2 - - - +
116A LEU* 1.3 56.7 + - - +
118A GLN* 3.3 5.7 + - - +
119A LEU* 2.8 30.3 + - + +
1068B VAL* 4.4 11.9 - - + -
1071B ALA* 4.0 15.6 - - + +
1072B ALA* 4.0 17.7 - - + +
1075B ALA* 4.5 3.1 - - + -
1077B ALA* 3.5 27.4 - - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 4.1 39.7 - - + +
99A ILE* 4.5 13.9 - - + -
100A SER* 4.4 20.6 - - - +
103A LEU* 4.0 9.2 - - + +
112A ALA 3.0 18.2 + - - +
113A SER* 3.7 7.0 - - - +
115A VAL* 1.3 76.8 - - - +
117A GLU* 1.3 59.2 + - + +
119A LEU* 3.3 5.5 + - + +
120A GLN* 3.0 49.5 + - - +
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Residues in contact with GLU 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 SER* 3.0 33.5 + - - +
114A ARG* 3.9 10.1 - - - +
116A LEU* 1.3 78.8 - - + +
118A GLN* 1.3 63.1 + - - +
120A GLN* 3.4 13.7 + - - +
121A ARG* 3.0 38.6 + - - +
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Residues in contact with GLN 118 (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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114A ARG 3.0 19.1 + - - +
115A VAL 3.7 3.8 - - - +
117A GLU* 1.3 77.6 - - - +
119A LEU* 1.3 58.0 + - - +
121A ARG* 3.4 23.4 + - - +
122A ASP* 2.9 61.3 + - - +
1071B ALA* 3.4 33.4 - - + +
1074B ALA* 3.8 24.2 - - + +
1075B ALA* 4.5 5.8 + - + +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.9 15.5 - - + -
99A ILE* 3.7 43.3 - - + -
103A LEU* 5.8 0.9 - - + -
115A VAL* 2.8 18.9 + - + +
116A LEU* 3.3 8.3 + - + +
118A GLN* 1.3 77.8 - - - +
120A GLN* 1.3 57.5 + - - +
122A ASP* 3.9 5.8 - - + +
123A TYR* 3.0 31.3 + - + +
1064B LEU* 4.6 2.7 - - + -
1067B ALA* 3.5 44.4 - - + +
1068B VAL* 3.9 14.6 - - + +
1071B ALA* 3.8 6.0 - - + +
1099B TYR* 6.2 2.5 - - + -
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.6 61.9 - - + +
116A LEU* 3.0 33.2 + - + +
117A GLU* 3.9 12.7 - - - +
119A LEU* 1.3 77.1 - - - +
121A ARG* 1.3 61.9 + - - +
123A TYR* 3.7 1.6 - - - +
124A GLU* 3.1 29.8 + - - +
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 3.0 32.2 + - - +
118A GLN* 3.7 20.6 + - - +
120A GLN* 1.3 77.2 - - - +
122A ASP* 1.3 70.3 + - - +
124A GLU* 3.5 4.0 + - - +
125A ARG* 3.1 25.0 + - + +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 2.9 51.5 + - - +
119A LEU* 3.9 6.1 - - + +
121A ARG* 1.3 76.2 - - - +
123A TYR* 1.3 58.8 + - - +
125A ARG* 3.4 9.1 + - - +
126A SER* 2.9 35.5 + - - +
1067B ALA 5.0 1.4 - - - +
1070B ARG* 4.7 5.5 - - - +
1071B ALA* 3.9 17.3 + - - +
1074B ALA* 5.2 1.4 - - - +
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Residues in contact with TYR 123 (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 TRP* 4.0 27.4 - + + -
119A LEU* 3.0 19.4 + - + +
120A GLN 3.7 3.4 - - - +
122A ASP* 1.3 77.7 - - - +
124A GLU* 1.3 77.9 + - - +
126A SER* 3.2 9.0 + - - -
127A LEU* 3.0 41.0 + - + +
1060B PRO* 6.2 2.9 - - + -
1099B TYR* 4.3 31.6 - + - -
1102B GLN* 3.4 24.2 + - + +
1103B LEU* 3.5 26.3 - - + +
1106B ASP* 2.6 35.0 + - - +
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Residues in contact with GLU 124 (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 TRP* 5.4 2.9 - - - -
120A GLN* 3.1 18.7 + - - +
121A ARG* 4.1 4.0 - - - +
122A ASP 3.3 0.2 - - - -
123A TYR* 1.3 88.0 - - - +
125A ARG* 1.3 64.2 + - - +
127A LEU* 3.4 24.9 + - - +
128A SER* 2.9 29.7 + - - +
1106B ASP* 5.1 2.4 - - - +
1110B ARG* 4.0 20.2 + - - +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.1 20.7 + - + +
122A ASP* 3.7 8.3 - - - +
124A GLU* 1.3 77.4 - - - +
126A SER* 1.3 61.4 + - - +
128A SER* 3.1 8.5 + - - -
129A ARG* 3.1 40.6 + - + +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 2.9 17.1 + - - +
123A TYR* 3.4 12.3 - - - -
125A ARG* 1.3 78.8 - - - +
127A LEU* 1.3 61.6 + - - +
129A ARG* 3.5 10.5 + - - +
130A LEU* 3.4 24.8 + - - +
1059B GLY* 4.1 6.7 + - - -
1060B PRO* 3.9 33.7 - - - +
1061B GLN 5.0 0.9 + - - -
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Residues in contact with LEU 127 (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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123A TYR* 3.0 44.9 + - + +
124A GLU* 3.6 23.6 - - - +
126A SER* 1.3 76.8 - - - +
128A SER* 1.3 63.1 + - - +
130A LEU* 3.3 28.3 - - + +
1060B PRO* 5.2 4.3 - - + -
1103B LEU* 4.4 12.8 - - + -
1106B ASP* 3.6 31.9 - - + +
1107B ILE* 4.4 19.5 - - + -
1110B ARG* 3.4 32.3 - - - +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 2.9 19.8 + - - +
125A ARG* 3.1 12.8 + - - -
127A LEU* 1.3 78.6 - - - +
129A ARG* 1.3 61.3 + - - +
130A LEU 3.1 5.8 + - - +
1110B ARG* 4.3 16.7 + - - +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 3.1 36.6 + - + +
126A SER* 4.0 8.7 - - - +
127A LEU 3.3 0.2 - - - -
128A SER* 1.3 75.9 - - - +
130A LEU* 1.3 65.1 + - - +
131A THR* 3.4 15.1 + - - +
134A ASP* 3.9 4.3 - - - +
1058B GLU 6.3 0.9 - - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER 3.4 6.8 + - - +
127A LEU* 3.3 28.5 + - + +
128A SER 3.1 7.3 - - - +
129A ARG* 1.3 79.5 - - - +
131A THR* 1.3 63.0 + - - +
134A ASP* 3.9 24.7 - - + +
135A ILE* 4.5 15.3 - - + -
138A LEU* 5.7 4.0 - - + -
1059B GLY* 5.5 0.4 - - - -
1060B PRO* 3.6 33.2 - - + -
1107B ILE* 4.0 39.9 - - + -
1110B ARG* 5.6 6.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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