Contacts of the helix formed by residues 125 - 144 (chain A) in PDB entry 6J8G
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 HIS 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS* 4.3 7.0 - - + +
122A ILE* 3.8 29.2 - - + +
123A LEU 3.6 3.7 + - - +
124A VAL* 1.3 77.1 - - - +
126A SER* 1.3 94.6 + - - +
127A LEU* 3.2 27.8 + - + +
128A PHE* 3.7 14.5 + - + +
129A SER* 3.8 11.3 + - - -
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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
----------------------------------------------------------
125A HIS* 1.3 90.2 + - - +
127A LEU* 1.3 67.1 + - - +
128A PHE 3.6 0.2 + - - -
129A SER* 3.8 4.9 + - - -
130A MET* 3.7 20.8 + - - +
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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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125A HIS* 3.2 22.8 + - + +
126A SER* 1.3 84.9 - - - +
128A PHE* 1.3 53.2 + - - +
130A MET* 3.2 20.0 + - + +
131A LEU* 2.7 37.1 + - + +
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Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.8 38.1 - - + +
123A LEU* 4.2 14.4 - - + +
125A HIS* 3.7 14.5 + - + +
126A SER 3.4 1.4 - - - -
127A LEU* 1.3 74.5 - - - +
129A SER* 1.3 69.3 + - - +
131A LEU* 3.7 19.9 - - + +
132A ILE* 2.9 36.2 + - + +
165A PHE* 4.2 22.9 - + - -
166A GLU* 3.6 33.0 - - + -
169A VAL* 4.2 20.0 - - + -
170A LYS* 5.7 6.5 - - + -
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A HIS 3.8 7.7 + - - -
126A SER 3.8 7.9 + - - -
127A LEU 3.4 0.6 - - - -
128A PHE* 1.3 79.4 - - - +
130A MET* 1.3 62.7 + - - +
132A ILE* 3.5 4.8 + - - +
133A MET* 3.1 24.4 + - - +
227A VAL* 4.0 22.5 + - - +
229A PRO* 6.1 0.2 - - - +
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Residues in contact with MET 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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126A SER* 3.7 14.1 + - - +
127A LEU* 3.2 25.0 + - + +
129A SER* 1.3 79.9 - - - +
131A LEU* 1.3 56.6 + - - +
133A MET* 3.4 10.6 + - + +
134A CYS* 2.9 30.5 + - - +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 2.7 21.0 + - + +
128A PHE* 3.2 22.4 + - + +
130A MET* 1.3 71.3 - - - +
132A ILE* 1.3 88.5 + - + +
133A MET 3.4 0.2 + - - -
134A CYS* 3.5 6.8 + - + +
135A THR* 3.4 27.2 + - - +
162A ILE* 4.4 18.6 - - + -
165A PHE* 6.0 3.8 - - + -
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Residues in contact with ILE 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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128A PHE* 2.9 31.7 + - + +
129A SER* 3.9 4.3 - - - +
131A LEU* 1.3 90.1 - - + +
133A MET* 1.3 61.5 + - - +
135A THR* 3.6 4.8 + - - -
136A ILE* 3.4 18.9 + - + +
162A ILE* 4.3 9.1 - - + +
163A TYR* 5.1 3.0 - - + -
166A GLU* 2.4 77.1 - - + +
223A LYS* 4.6 7.4 - - - +
227A VAL* 3.3 26.0 - - + -
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Residues in contact with MET 133 (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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129A SER 3.1 17.4 + - - +
130A MET* 3.8 9.9 - - + +
132A ILE* 1.3 76.8 - - - +
134A CYS* 1.3 69.7 + - - +
136A ILE* 2.6 34.6 - - + +
137A LEU* 3.2 31.4 + - + -
224A THR* 6.2 0.2 - - - -
227A VAL* 4.0 24.2 - - + -
228A ILE* 4.7 18.8 - - + +
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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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130A MET 2.9 17.8 + - - +
131A LEU* 4.0 7.4 - - + +
132A ILE 3.4 0.4 - - - -
133A MET* 1.3 83.5 - - - +
135A THR* 1.3 55.7 + - - +
137A LEU* 3.5 5.6 + - - +
138A THR* 2.6 33.7 + - - -
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Residues in contact with THR 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 LEU* 3.4 22.3 + - - +
132A ILE 3.9 7.6 - - - -
133A MET 3.3 0.6 - - - -
134A CYS* 1.3 78.4 - - - +
136A ILE* 1.3 58.7 + - - +
138A THR* 3.2 9.2 + - - -
139A ASN* 2.9 25.1 + - - +
159A PHE* 3.5 29.4 - - + -
162A ILE* 4.1 32.9 - - + +
163A TYR* 4.4 12.6 - - + +
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Residues in contact with ILE 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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132A ILE* 3.4 9.3 + - + +
133A MET* 2.6 38.4 - - + +
135A THR* 1.3 77.7 - - - +
137A LEU* 1.3 73.9 + - + +
139A ASN* 3.1 12.3 + - + +
140A CYS* 3.2 21.8 + - - -
143A MET* 6.0 0.2 - - + -
163A TYR* 3.6 22.9 + - + +
220A ARG* 3.8 17.5 - - + +
221A ALA* 4.2 1.1 - - - -
223A LYS* 4.6 6.7 - - + -
224A THR* 2.5 47.1 - - + +
227A VAL* 4.5 6.7 - - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A MET* 3.2 35.0 + - + +
134A CYS* 3.9 9.0 - - - +
135A THR 3.3 0.2 - - - -
136A ILE* 1.3 98.0 - - + +
138A THR* 1.3 63.2 + - - +
140A CYS* 3.2 23.8 + - + +
141A ILE* 3.5 12.9 + - - +
224A THR* 4.6 9.4 - - + -
228A ILE* 5.8 5.6 - - + -
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Residues in contact with THR 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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134A CYS* 2.6 25.1 + - - -
135A THR* 3.5 9.2 + - - -
136A ILE 3.2 0.4 - - - -
137A LEU* 1.3 77.0 - - - +
139A ASN* 1.3 62.8 + - - +
141A ILE* 3.2 20.3 + - + +
142A PHE* 3.3 26.5 - - + -
159A PHE* 4.2 15.7 - - + -
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Residues in contact with ASN 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 THR 2.9 13.4 + - - +
136A ILE* 3.3 10.5 - - + +
138A THR* 1.3 78.4 - - - +
140A CYS* 1.3 61.7 + - - +
142A PHE* 3.1 14.7 + - - +
143A MET* 3.3 24.6 + - + +
159A PHE* 3.8 30.5 - - + +
163A TYR* 3.3 19.8 + - - +
217A ARG* 5.9 2.8 - - - +
220A ARG* 3.2 33.0 + - + +
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Residues in contact with CYS 140 (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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136A ILE* 3.2 32.4 + - - -
137A LEU* 3.2 15.1 + - + +
138A THR 3.2 0.4 - - - -
139A ASN* 1.3 77.0 - - - +
141A ILE* 1.3 69.8 + - + +
142A PHE 3.2 0.7 + - - -
143A MET* 3.3 30.7 + - - +
144A THR* 3.5 10.7 + - - -
221A ALA* 4.3 7.0 - - - -
224A THR* 4.6 3.1 - - - -
878A PHE* 3.6 34.8 - - + -
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Residues in contact with ILE 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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137A LEU* 3.7 16.4 - - + +
138A THR* 3.2 15.2 + - + +
140A CYS* 1.3 79.7 - - + +
142A PHE* 1.3 69.0 + - + +
144A THR* 3.3 21.9 - - - -
145A MET* 3.9 12.1 - - + +
878A PHE* 6.0 2.5 - - + -
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Residues in contact with PHE 142 (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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138A THR* 3.3 24.9 - - + -
139A ASN* 3.1 15.1 + - - +
140A CYS 3.1 1.0 - - - -
141A ILE* 1.3 82.9 - - + +
143A MET* 1.3 63.5 + - - +
144A THR 3.1 2.2 - - - -
145A MET* 3.2 36.1 + - + +
148A PRO* 5.1 3.6 - - + +
151A TRP* 4.5 13.9 - + - -
152A THR* 3.3 27.8 - - - -
155A VAL* 3.8 31.2 - - + -
159A PHE* 4.1 15.9 - + + -
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Residues in contact with MET 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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136A ILE* 6.0 0.2 - - + -
139A ASN* 3.3 26.0 - - - +
140A CYS* 3.3 26.0 + - - +
142A PHE* 1.3 74.9 - - - +
144A THR* 1.3 58.3 + - - +
145A MET 3.1 4.9 + - - -
146A ASN 4.0 6.1 + - - -
217A ARG* 4.1 24.7 - - - +
218A VAL* 4.2 23.3 - - + -
220A ARG* 4.7 4.7 - - + -
221A ALA* 4.0 31.4 - - + +
878A PHE* 4.7 6.7 - - + -
882A VAL* 3.7 26.8 - - + +
885A MET* 4.3 5.4 - - - +
886A GLN* 4.2 14.8 + - - +
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Residues in contact with THR 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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140A CYS 3.5 11.4 + - - -
141A ILE* 3.3 16.0 - - + -
142A PHE 3.1 0.2 - - - -
143A MET* 1.3 76.8 - - - +
145A MET* 1.3 68.2 - - + +
146A ASN* 3.5 5.7 + - - +
878A PHE* 4.1 10.9 - - - -
882A VAL* 5.3 0.6 - - - +
885A MET* 4.4 9.9 - - - -
913A PHE* 3.4 48.5 + - + +
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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
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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