Contacts of the helix formed by residues 116 - 132 (chain A) in PDB entry 6J7Z
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 THR 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ILE* 4.1 1.8 - - - -
84A LYS* 5.7 2.2 - - - -
115A ILE* 1.3 79.4 - - - +
117A LEU* 1.3 69.2 + - - +
118A GLN* 3.5 16.6 + - + +
119A GLN* 3.4 35.1 - - + +
120A ALA* 3.0 23.6 + - - +
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Residues in contact with LEU 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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83A ILE* 3.6 24.5 - - + +
84A LYS 6.3 0.2 - - - -
116A THR* 1.3 76.9 + - - +
118A GLN* 1.3 74.2 + - - +
120A ALA* 3.8 1.8 - - - +
121A GLU* 2.9 30.2 + - - +
150A PHE* 5.1 10.1 - - + -
154A TYR* 3.6 51.8 - - + +
155A MET* 3.8 23.3 - - + -
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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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116A THR* 3.3 17.5 + - + +
117A LEU* 1.3 95.0 - - - +
119A GLN* 1.3 59.5 + - + +
121A GLU* 3.3 17.4 + - - +
122A TYR* 2.9 27.9 + - - +
154A TYR 5.9 0.2 + - - -
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Residues in contact with GLN 119 (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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115A ILE* 4.3 12.8 - - + -
116A THR* 3.4 27.1 + - + +
118A GLN* 1.3 78.4 - - + +
120A ALA* 1.3 57.6 + - - +
122A TYR* 3.2 16.3 + - - +
123A GLU* 2.9 35.6 + - + +
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Residues in contact with ALA 120 (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 LEU* 3.7 24.2 - - + -
83A ILE* 3.6 29.2 - - + -
115A ILE* 3.8 6.1 - - + +
116A THR 3.0 17.6 + - - +
117A LEU 3.8 2.9 - - - +
119A GLN* 1.3 73.8 - - - +
121A GLU* 1.3 66.6 + - - +
123A GLU* 3.2 2.1 + - - +
124A PHE* 3.0 31.6 + - + -
155A MET* 4.0 5.8 - - + -
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Residues in contact with GLU 121 (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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117A LEU 2.9 17.5 + - - +
118A GLN* 3.6 17.6 - - - +
120A ALA* 1.3 77.8 - - - +
122A TYR* 1.3 56.3 + - - +
124A PHE* 3.8 1.7 - - - +
125A LEU* 2.9 33.6 + - + +
154A TYR 4.6 3.1 - - - +
155A MET* 3.2 45.7 - - + +
156A PRO* 3.3 6.2 - - - +
157A GLN* 2.9 43.4 + - + +
158A PHE* 4.1 9.8 - - + +
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Residues in contact with TYR 122 (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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118A GLN 2.9 14.8 + - - +
119A GLN* 3.2 19.9 + - - +
121A GLU* 1.3 76.8 - - - +
123A GLU* 1.3 63.6 + - + +
125A LEU* 3.8 9.6 - - + +
126A SER* 2.9 54.2 + - - -
129A ARG* 5.1 11.2 - - - -
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Residues in contact with GLU 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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79A PRO* 3.9 16.8 - - + +
81A LEU* 3.4 34.0 - - + +
115A ILE* 3.7 16.4 - - - +
119A GLN* 2.9 21.3 + - - +
120A ALA 3.2 6.5 + - - +
122A TYR* 1.3 84.8 - - + +
124A PHE* 1.3 63.3 + - - +
126A SER* 3.3 4.9 + - - -
127A PHE* 3.0 23.2 + - - +
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Residues in contact with PHE 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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63A MET* 3.4 60.3 - - + -
65A CYS* 3.7 27.8 - - + -
79A PRO* 3.3 36.3 - - + -
81A LEU* 3.7 25.1 - - + -
83A ILE* 4.9 0.2 - - + -
120A ALA* 3.0 30.7 + - + +
121A GLU* 4.0 2.9 - - - +
123A GLU* 1.3 76.4 - - - +
125A LEU* 1.3 58.3 + - - +
127A PHE* 3.3 6.0 + + - +
128A VAL* 3.0 32.9 + - - +
155A MET* 4.2 4.7 - - + -
158A PHE* 3.8 20.4 - + + -
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Residues in contact with LEU 125 (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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121A GLU* 2.9 19.7 + - + +
122A TYR* 3.8 11.4 - - + +
124A PHE* 1.3 74.1 - - - +
126A SER* 1.3 60.8 + - - +
128A VAL* 3.2 6.9 - - + +
129A ARG* 2.9 67.2 + - + +
157A GLN* 3.7 29.8 - - + +
158A PHE* 3.9 10.7 - - - -
161A HIS* 3.9 22.2 - - + -
301A CIT 3.5 24.5 - - + +
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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
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122A TYR* 2.9 47.9 + - - -
123A GLU* 3.7 5.2 - - - -
125A LEU* 1.3 74.8 - - - +
127A PHE* 1.3 63.5 + - - +
129A ARG* 3.3 13.7 + - - +
130A GLN* 3.0 37.7 + - - +
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Residues in contact with PHE 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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65A CYS* 4.0 20.4 - - - -
66A LEU* 4.3 1.3 - - - -
67A ILE* 3.5 34.8 - - + -
76A ALA* 3.8 14.6 - - + -
77A GLU 3.6 11.4 - - - -
78A GLY* 3.4 39.9 - - - -
79A PRO* 4.0 11.0 - - + -
123A GLU 3.0 14.4 + - - +
124A PHE* 3.6 7.0 - - - +
125A LEU 3.3 0.2 - - - -
126A SER* 1.3 76.3 - - - +
128A VAL* 1.3 68.5 + - + +
130A GLN* 3.0 23.0 + - + +
131A GLN* 3.0 33.1 + - + +
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Residues in contact with VAL 128 (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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44A VAL* 3.8 26.5 - - + -
65A CYS* 4.4 1.3 - - - -
67A ILE* 4.5 2.5 - - + -
124A PHE 3.0 16.1 + - - +
125A LEU* 3.2 15.5 - - + +
127A PHE* 1.3 88.5 - - + +
129A ARG* 1.3 56.5 + - - +
131A GLN* 4.1 6.7 - - - +
132A THR* 2.7 32.6 + - - +
158A PHE* 3.4 32.3 - - + -
161A HIS* 3.0 33.4 + - + -
162A LEU* 4.5 1.8 - - + -
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Residues in contact with ARG 129 (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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122A TYR* 5.1 12.1 - - - -
125A LEU* 2.9 47.2 + - + +
126A SER* 3.5 10.5 + - - +
127A PHE 3.2 0.2 - - - -
128A VAL* 1.3 78.5 - - - +
130A GLN* 1.3 62.9 + - + +
131A GLN 3.4 0.2 + - - -
132A THR 3.8 8.1 - - - +
161A HIS* 3.8 8.0 - - + +
301A CIT 3.1 68.3 + - - +
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Residues in contact with GLN 130 (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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42A ARG* 5.1 1.2 + - - -
126A SER* 3.0 26.7 + - - +
127A PHE* 3.0 15.6 + - + +
129A ARG* 1.3 77.3 - - + +
131A GLN* 1.3 73.3 + - - +
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Residues in contact with GLN 131 (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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39A MET* 4.2 5.1 - - - +
42A ARG* 2.7 43.1 + - - +
67A ILE* 3.6 38.2 - - + +
75A LEU* 4.9 3.6 - - - +
76A ALA* 3.7 26.7 - - - +
127A PHE* 3.0 31.6 + - + +
128A VAL* 3.1 1.8 + - - +
130A GLN* 1.3 95.4 + - - +
132A THR* 1.3 62.9 + - + +
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Residues in contact with THR 132 (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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39A MET* 5.3 1.3 - - - -
42A ARG* 4.4 9.4 - - + -
44A VAL* 3.8 24.7 - - + +
67A ILE* 4.2 12.1 - - + -
128A VAL* 2.7 17.7 + - - +
129A ARG 3.8 7.4 - - - +
130A GLN 3.9 0.2 - - - -
131A GLN* 1.3 80.8 - - + +
133A PRO* 1.3 70.5 + - - +
134A PRO* 4.3 0.3 - - - +
137A CYS* 3.6 26.8 - - - +
161A HIS* 2.8 45.6 + - - -
162A LEU* 4.8 0.7 - - - +
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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