Contacts of the helix formed by residues 126 - 146 (chain A) in PDB entry 2X7G
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 ALA 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 3.5 2.8 - - + +
125A SER* 1.3 81.2 - - - +
127A GLN* 1.3 67.2 + - - +
128A HIS* 3.4 3.6 - - + +
129A TYR* 3.2 31.1 + - + +
130A THR* 3.2 16.1 + - - -
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER 3.5 2.8 + - - -
126A ALA* 1.3 71.7 - - - +
128A HIS* 1.3 71.2 + - - +
130A THR* 3.1 10.9 + - + +
131A GLU* 2.9 36.4 + - + +
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA* 3.3 3.6 + - + +
127A GLN* 1.3 87.4 + - - +
129A TYR* 1.3 78.9 + + + +
131A GLU* 3.2 11.1 + - + +
132A THR* 3.1 38.6 + - - -
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Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.6 43.2 - + + -
123A VAL* 3.6 24.0 - - + +
124A LYS* 3.7 37.0 - - + +
126A ALA* 3.2 29.5 + - + +
128A HIS* 1.3 90.5 - - + +
130A THR* 1.3 57.1 + - - +
132A THR* 3.3 8.5 + - - -
133A ALA* 3.1 26.2 + - - +
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 4.9 0.4 - - - -
124A LYS 3.9 5.8 + - - -
125A SER 3.8 4.4 + - - -
126A ALA 3.2 11.0 + - - -
127A GLN* 3.1 12.2 + - + +
129A TYR* 1.3 74.3 - - - +
131A GLU* 1.3 65.8 + - - +
133A ALA* 3.1 8.2 + - - +
134A LEU* 2.9 41.4 + - + +
164A LYS* 6.4 0.2 - - - -
171A ILE* 3.7 29.3 + - + +
173A VAL* 3.9 19.7 + - + +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN* 2.9 29.2 + - + +
128A HIS* 3.5 14.4 - - + +
130A THR* 1.3 74.5 - - + +
132A THR* 1.3 62.7 + - - +
134A LEU* 3.3 20.8 + - - +
135A ASP* 3.0 40.9 + - - +
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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
----------------------------------------------------------
103A PHE* 6.4 2.7 - - + -
128A HIS* 3.1 30.9 + - - -
129A TYR* 3.7 10.6 - - - -
130A THR 3.2 0.4 - - - -
131A GLU* 1.3 75.0 - - - +
133A ALA* 1.3 53.7 + - - +
135A ASP* 3.2 8.8 + - + +
136A GLU* 2.8 35.2 + - + +
543A GLY* 3.6 28.4 - - - +
544A ASN* 5.3 4.9 - - - +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 4.1 7.9 - - + -
129A TYR 3.1 13.9 + - - +
130A THR* 3.1 8.9 + - - +
132A THR* 1.3 73.8 - - - +
134A LEU* 1.3 55.0 + - - +
136A GLU* 3.0 11.6 + - - +
137A ILE* 2.7 39.7 + - - +
173A VAL* 3.5 33.4 - - + -
175A MET* 4.1 13.5 - - + -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 2.9 32.4 + - + +
131A GLU* 3.7 26.2 - - - +
133A ALA* 1.3 73.8 - - - +
135A ASP* 1.3 65.5 + - - +
137A ILE* 3.0 19.7 + - + +
138A LYS* 3.0 20.2 + - + +
164A LYS* 3.8 34.5 - - - +
173A VAL* 4.4 9.9 - - + -
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Residues in contact with ASP 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 GLU* 3.0 31.4 + - - +
132A THR* 3.6 9.7 - - + +
134A LEU* 1.3 77.5 - - - +
136A GLU* 1.3 63.1 + - - +
138A LYS* 3.3 18.0 + - - +
139A LEU* 3.0 30.2 + - + +
543A GLY 5.9 2.0 - - - +
547A TRP* 5.1 1.3 - - - -
552A PHE* 3.5 42.7 - - + -
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 2.9 32.5 + - - -
123A VAL* 5.5 0.2 - - - +
132A THR* 2.8 16.8 + - - +
133A ALA* 3.3 9.6 - - - +
135A ASP* 1.3 77.2 - - - +
137A ILE* 1.3 57.1 + - - +
139A LEU* 3.5 9.1 + - - +
140A LEU* 2.9 47.4 + - + +
175A MET* 3.1 21.5 - - - +
541A ASP* 4.9 0.9 - - - -
542A LEU* 4.3 3.8 - - + +
543A GLY* 4.0 28.1 + - - +
1708A EDO 2.5 29.4 + - - +
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Residues in contact with ILE 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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133A ALA 2.7 24.1 + - - +
134A LEU* 3.0 14.1 + - + +
136A GLU* 1.3 72.6 - - - +
138A LYS* 1.3 58.4 + - + +
140A LEU* 3.2 2.5 + - - +
141A LYS* 2.9 59.2 + - + +
159A LEU* 4.1 12.1 - - + -
162A ASP* 3.8 30.3 - - + +
164A LYS* 5.3 2.7 - - - +
173A VAL* 4.5 11.4 - - + -
175A MET* 3.4 37.7 - - + -
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.0 20.4 + - + +
135A ASP* 3.3 19.3 + - - +
137A ILE* 1.3 77.0 - - + +
139A LEU* 1.3 63.9 - - - +
141A LYS* 3.2 13.2 + - + +
142A CYS* 3.1 26.4 + - - -
547A TRP* 4.5 21.0 - - + -
552A PHE* 6.6 0.2 - - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP* 3.0 26.1 + - + +
136A GLU* 3.8 5.4 - - - +
138A LYS* 1.3 76.3 - - - +
140A LEU* 1.3 62.4 + - - +
142A CYS* 3.0 14.4 + - - +
143A VAL* 3.1 17.4 + - - +
221A ILE* 3.7 26.0 - - + +
542A LEU* 3.6 29.2 - - + +
543A GLY 5.3 2.5 - - - +
545A ALA* 3.2 41.3 - - + +
546A CYS 4.1 3.4 - - - +
547A TRP* 3.8 29.2 - - + -
552A PHE* 4.4 6.3 - - + -
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Residues in contact with LEU 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 GLU* 2.9 41.8 + - + +
137A ILE 3.8 2.9 - - - +
139A LEU* 1.3 77.9 - - - +
141A LYS* 1.3 61.2 + - - +
143A VAL* 3.5 8.4 + - + +
144A ARG* 3.2 23.2 + - - +
157A VAL 3.9 21.5 - - - +
158A GLN* 5.0 0.5 - - - +
159A LEU* 3.8 31.7 + - + +
175A MET* 4.3 7.6 - - - -
177A PHE* 4.0 26.0 - - + -
542A LEU* 4.1 21.1 - - + -
1708A EDO 4.2 15.3 - - - +
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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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137A ILE* 2.9 43.6 + - + +
138A LYS* 3.2 10.7 + - + +
140A LEU* 1.3 79.2 - - - +
142A CYS* 1.3 56.8 + - - +
144A ARG* 3.4 32.1 - - - +
145A GLU* 2.9 50.5 + - - +
159A LEU* 4.5 2.9 - - + -
162A ASP* 3.9 16.7 + - - -
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Residues in contact with CYS 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 LYS* 3.1 16.8 + - - -
139A LEU 3.0 9.0 + - - +
141A LYS* 1.3 74.5 - - - +
143A VAL* 1.3 58.0 + - - +
145A GLU* 3.0 8.8 + - - -
146A SER* 2.5 43.5 + - - +
219A CYS* 4.5 2.2 - - + +
221A ILE* 4.2 14.1 - - + -
547A TRP* 3.8 27.1 - - - +
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Residues in contact with VAL 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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139A LEU 3.1 12.5 + - - +
140A LEU* 3.7 10.5 - - + +
141A LYS 3.4 0.2 - - - -
142A CYS* 1.3 74.7 - - - +
144A ARG* 1.3 59.6 + - - +
153A LYS* 5.0 0.9 - - - +
156A VAL* 4.0 15.7 - - + -
157A VAL 4.7 2.9 - - - +
158A GLN* 3.5 29.6 + - - +
214A TYR* 2.5 41.7 + - + -
215A LEU* 3.5 27.6 - - + -
219A CYS* 3.8 8.0 - - - -
221A ILE* 3.8 10.1 - - + -
542A LEU* 3.9 15.3 - - + -
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Residues in contact with ARG 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 LEU 3.2 10.6 + - - +
141A LYS* 3.4 44.8 - - - +
143A VAL* 1.3 81.0 - - - +
145A GLU* 1.3 70.7 + - + +
146A SER 3.9 0.3 + - - -
148A PRO* 3.8 19.2 - - - +
153A LYS* 5.1 6.4 + - - +
158A GLN* 3.6 16.2 - - + +
159A LEU* 3.0 48.8 + - - +
160A ILE 4.3 9.1 + - - -
161A ASP* 4.5 2.6 - - - +
162A ASP* 4.8 4.0 + - - -
214A TYR* 4.5 0.9 + - - -
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 2.9 40.3 + - - +
142A CYS* 3.0 8.2 + - - +
144A ARG* 1.3 91.6 + - + +
146A SER* 1.3 66.0 + - - +
147A ASP 3.5 1.6 - - - -
148A PRO* 3.5 13.8 - - - +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A CYS* 2.5 29.3 + - - +
144A ARG 3.6 1.6 - - - -
145A GLU* 1.3 73.8 - - - +
147A ASP* 1.3 63.0 + - - +
148A PRO* 4.4 0.3 - - - +
214A TYR* 3.7 9.7 + - - -
218A LYS* 3.5 25.2 + - - +
219A CYS* 3.4 23.4 - - - -
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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) + - + + + + + -
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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