Contacts of the helix formed by residues 129 - 146 (chain A) in PDB entry 1R9F
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLN* 4.7 5.4 - - - +
125A GLY* 4.0 1.7 - - - -
126A GLY 2.8 25.7 + - - +
128A ARG* 1.3 82.5 - - + +
130A LEU* 1.3 66.2 + - - +
131A GLN* 3.2 3.4 - - - -
132A HIS* 2.9 22.8 + - + +
133A LEU* 2.9 34.0 + - - +
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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
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63A TRP* 4.3 9.9 - - + -
65A PHE* 4.8 1.3 - - + -
95A VAL* 4.1 17.3 - - + -
96A ASN* 4.0 30.5 - - + +
99A ALA* 3.7 27.6 - - + -
103A PHE* 4.1 9.0 - - + -
110A CYS* 4.4 11.9 - - + -
126A GLY 3.7 1.6 + - - -
127A SER* 3.3 16.8 + - - +
128A ARG 3.4 1.2 - - - -
129A THR* 1.3 77.7 + - - +
131A GLN* 1.3 56.4 + - - +
133A LEU* 3.3 20.8 - - + +
134A CYS* 2.8 38.7 + - - -
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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
----------------------------------------------------------
128A ARG 5.2 1.1 + - - +
129A THR* 3.0 1.4 + - - -
130A LEU* 1.3 77.2 - - - +
132A HIS* 1.3 67.7 + - + +
134A CYS* 3.3 7.0 + - - +
135A GLU* 3.0 30.7 + - + +
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 2.9 23.3 + - + +
131A GLN* 1.3 81.4 - - + +
133A LEU* 1.3 67.8 + - + +
135A GLU* 3.1 29.6 + - - +
136A MSE 3.0 31.3 + - + +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TRP* 4.9 7.2 - - + -
110A CYS* 3.8 31.6 - - + +
123A VAL* 3.7 23.9 - - + +
124A SER* 3.4 28.5 - - - +
125A GLY* 3.7 13.9 - - - +
126A GLY 4.0 3.8 - - - +
129A THR* 2.9 31.0 + - - +
130A LEU* 3.3 19.3 - - + +
132A HIS* 1.3 78.4 - - + +
134A CYS* 1.3 56.7 + - - +
136A MSE 3.3 1.4 + - + -
137A ALA* 2.8 31.4 + - - +
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Residues in contact with CYS 134 (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 TRP* 3.9 10.1 - - - -
90A TRP* 3.8 7.2 - - + -
92A GLY* 4.3 22.0 - - - -
95A VAL* 3.6 38.1 - - - -
96A ASN* 6.3 0.2 - - - -
130A LEU* 2.8 24.9 + - - +
131A GLN* 3.6 7.0 - - - +
133A LEU* 1.3 74.0 - - - +
135A GLU* 1.3 60.1 + - - +
137A ALA* 3.6 6.5 - - - +
138A ILE* 2.9 31.9 + - - +
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Residues in contact with GLU 135 (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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131A GLN* 3.0 19.2 + - + +
132A HIS* 3.1 33.6 + - - +
134A CYS* 1.3 75.1 - - + +
136A MSE 1.3 75.3 + - + +
138A ILE* 3.1 24.0 - - - +
139A ARG* 3.3 24.4 - - - +
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Residues in contact with MSE 136 (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 VAL* 3.9 17.0 - - + -
132A HIS* 3.0 21.1 + - + +
133A LEU* 3.7 4.3 - - + +
135A GLU* 1.3 84.2 - - + +
137A ALA* 1.3 58.1 + - - +
139A ARG* 3.2 40.1 + - - +
140A SER* 2.7 39.3 + - - +
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Residues in contact with ALA 137 (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 TRP* 4.1 2.2 - - + -
90A TRP* 3.7 14.1 - - + -
112A TYR* 3.6 37.1 - - + -
123A VAL* 4.0 12.3 - - + +
133A LEU 2.8 18.1 + - - +
134A CYS* 3.6 8.3 - - - +
135A GLU 3.3 0.2 - - - -
136A MSE 1.3 78.2 - - - +
138A ILE* 1.3 56.1 + - - +
140A SER* 3.3 2.9 + - - -
141A LYS* 2.9 29.5 + - - +
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Residues in contact with ILE 138 (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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87A LEU* 4.2 35.9 - - + +
90A TRP* 3.5 30.0 - - + +
134A CYS 2.9 15.8 + - - +
135A GLU* 3.1 18.4 - - - +
137A ALA* 1.3 77.2 - - - +
139A ARG* 1.3 70.3 + - + +
141A LYS* 3.4 6.5 + - + +
142A GLN* 3.1 28.3 + - - +
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Residues in contact with ARG 139 (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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135A GLU* 3.3 27.3 + - - +
136A MSE 3.2 35.8 - - - +
137A ALA 3.2 0.4 - - - -
138A ILE* 1.3 86.4 - - + +
140A SER* 1.3 63.4 + - - +
142A GLN* 3.4 7.7 + - - +
143A GLU* 3.0 30.6 + - + +
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 5.5 1.1 - - - -
114A ILE* 5.1 3.4 - - - -
121A ILE* 3.8 33.3 - - - +
123A VAL* 3.9 10.6 - - - +
136A MSE 2.7 24.4 + - - +
137A ALA* 3.6 6.3 - - - -
139A ARG* 1.3 76.9 - - - +
141A LYS* 1.3 57.3 + - - +
143A GLU* 3.4 6.0 + - - +
144A MSE 2.8 32.3 + - - +
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Residues in contact with LYS 141 (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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59A PHE* 3.9 16.3 - - - -
61A GLU* 2.9 17.2 + - - +
86A VAL 2.8 22.3 + - - -
87A LEU* 4.0 21.0 + - + +
89A SER* 2.6 31.3 + - - +
90A TRP* 3.4 16.7 - - + +
112A TYR* 3.4 20.6 - - - +
114A ILE* 3.8 17.9 - - + -
137A ALA 2.9 17.3 + - - +
138A ILE* 3.6 8.3 - - + +
140A SER* 1.3 77.4 - - - +
142A GLN* 1.3 62.2 + - - +
144A MSE 3.2 1.2 + - - +
145A LEU* 3.0 34.5 + - + +
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.9 3.8 - - + +
87A LEU* 4.2 32.4 - - + +
138A ILE* 3.1 19.2 + - - +
139A ARG* 3.8 6.7 - - - +
140A SER 3.3 0.2 - - - -
141A LYS* 1.3 78.5 - - - +
143A GLU* 1.3 66.0 + - + +
145A LEU* 3.5 2.9 + - - +
146A GLN* 2.8 65.7 + - + +
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Residues in contact with GLU 143 (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 ILE* 5.9 2.7 - - + -
139A ARG* 3.0 22.3 + - + +
140A SER* 3.9 6.1 - - - +
142A GLN* 1.3 78.9 - - + +
144A MSE 1.3 64.8 + - - +
146A GLN* 3.3 21.7 + - - +
147A MSE 3.4 12.3 + - - +
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Residues in contact with MSE 144 (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 ILE* 3.0 47.6 - - + +
116A PHE* 3.6 31.3 - - + +
119A VAL* 3.0 39.7 - - - +
121A ILE* 3.4 35.0 - - + +
140A SER 2.8 19.5 + - - +
141A LYS 3.5 4.3 - - - +
143A GLU* 1.3 77.0 - - - +
145A LEU* 1.3 62.6 + - + +
147A MSE 3.3 28.4 - - - +
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Residues in contact with LEU 145 (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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59A PHE* 3.8 32.5 - - + -
76A TYR* 2.7 47.9 + - + +
78A ARG* 5.2 2.3 - - - +
83A LEU* 3.8 17.3 - - + -
86A VAL* 3.6 30.7 - - + -
87A LEU* 4.8 0.9 - - + -
114A ILE* 4.3 8.7 - - + -
116A PHE* 4.0 21.7 - - + -
141A LYS* 3.0 32.2 + - + +
142A GLN 4.1 0.7 - - - +
144A MSE 1.3 75.3 - - - +
146A GLN* 1.3 56.8 - - - +
147A MSE 3.3 4.5 + - - +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 4.8 0.9 - - - +
83A LEU* 3.6 26.8 - - + +
142A GLN* 2.8 52.7 + - - +
143A GLU* 3.3 15.5 + - - +
144A MSE 3.2 0.6 - - - -
145A LEU* 1.3 79.3 - - - +
147A MSE 1.3 59.6 - - - +
148A ALA 3.7 1.9 + - - -
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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