Contacts of the helix formed by residues 118 - 138 (chain A) in PDB entry 2CXO
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 VAL 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.6 1.3 - - + -
102A ALA* 3.8 29.2 - - + -
111A ILE* 2.9 30.1 + - + +
113A VAL* 3.8 26.5 - - + -
116A LYS 3.9 7.0 - - - +
117A ASP* 1.3 73.0 - - - +
119A MET* 1.3 69.6 + - - +
120A PRO 3.5 0.7 - - - -
121A GLU* 3.2 9.6 + - - +
122A VAL* 3.0 22.0 + - + +
267A TRP* 5.5 0.2 - - - -
269A TRP* 3.6 33.1 - - + +
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA* 3.3 40.8 - - - +
105A ASN* 3.5 35.0 - - - +
108A ASN* 3.5 22.9 - - + +
109A THR 3.7 19.5 - - - +
111A ILE* 4.3 3.4 - - - +
117A ASP* 3.5 15.9 - - - +
118A VAL* 1.3 77.1 - - - +
120A PRO* 1.3 74.3 - - + +
122A VAL* 3.2 15.9 + - + +
123A ASN* 2.8 37.8 + - - +
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Residues in contact with PRO 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 3.5 28.5 - - + +
118A VAL 3.6 2.5 - - - -
119A MET* 1.3 93.3 - - + +
121A GLU* 1.3 61.3 + - + +
123A ASN* 3.8 5.8 - - + +
124A ARG* 2.9 29.3 + - - +
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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
----------------------------------------------------------
116A LYS* 6.5 1.1 - - - -
117A ASP 5.3 1.3 + - - +
118A VAL* 3.2 10.2 + - - +
119A MET 3.2 0.4 - - - -
120A PRO* 1.3 78.7 - - + +
122A VAL* 1.3 68.0 + - - +
124A ARG* 2.8 49.8 + - - +
125A VAL* 3.1 29.5 + - - +
265A GLU* 4.6 4.7 - - - +
267A TRP* 3.7 27.0 + - + +
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 3.8 19.7 - - - +
103A LEU* 3.7 31.0 - - + +
118A VAL* 3.0 22.8 + - + +
119A MET* 3.5 18.4 - - + +
121A GLU* 1.3 77.5 - - - +
123A ASN* 1.3 59.3 + - - +
125A VAL* 3.4 2.9 + - - +
126A LEU* 3.1 36.9 + - + +
267A TRP* 3.6 13.8 - - + -
269A TRP* 3.9 25.8 - - + -
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Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN 5.4 0.2 - - - +
106A ARG* 5.1 4.3 + - - -
108A ASN* 2.8 37.2 + - - +
119A MET* 2.8 34.3 + - - +
120A PRO* 3.9 5.5 - - + +
122A VAL* 1.3 72.1 - - - +
124A ARG* 1.3 60.0 + - - +
126A LEU* 3.4 18.1 + - - +
127A ASP* 2.9 38.4 + - - +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO 2.9 18.5 + - - +
121A GLU* 2.8 43.4 + - - +
123A ASN* 1.3 77.0 - - - +
125A VAL* 1.3 75.6 + - - +
127A ASP* 3.3 10.6 + - + +
128A LYS* 3.0 40.2 + - + +
265A GLU* 3.5 21.8 + - - +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU 3.1 17.6 + - - +
122A VAL 3.9 3.1 - - - +
124A ARG* 1.3 93.8 - - - +
126A LEU* 1.3 60.7 + - + +
128A LYS* 3.1 9.8 + - + +
129A MET* 2.8 38.0 + - + +
264A PHE* 4.5 5.6 - - + -
265A GLU* 3.4 39.5 - - + +
267A TRP* 3.8 13.5 - - + -
279A ALA* 4.0 19.5 - - + +
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Residues in contact with LEU 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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103A LEU 4.0 10.3 - - - +
106A ARG* 4.1 19.3 - - - +
122A VAL* 3.1 35.3 + - + +
123A ASN* 3.7 21.8 - - - +
125A VAL* 1.3 77.2 - - + +
127A ASP* 1.3 59.0 + - - +
129A MET* 3.2 13.4 + - - +
130A LYS* 2.9 24.3 + - - +
277A TRP 4.7 6.3 - - - +
278A SER 5.9 0.7 - - - -
290A PHE* 3.4 25.5 - - + -
293A PHE* 3.8 18.6 - - + -
297A LEU* 3.8 19.7 - - + -
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 2.9 25.9 + - - +
124A ARG* 3.5 8.7 - - + +
126A LEU* 1.3 76.9 - - - +
128A LYS* 1.3 58.1 + - - +
130A LYS* 3.3 13.1 + - - +
131A SER* 3.0 29.5 + - - -
290A PHE* 6.1 0.2 - - - -
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Residues in contact with LYS 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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124A ARG* 3.0 27.1 + - + +
125A VAL* 3.1 14.1 + - + +
127A ASP* 1.3 76.2 - - - +
129A MET* 1.3 56.4 + - - +
131A SER* 3.4 6.3 + - - -
132A PHE* 3.0 29.1 + - - +
260A PRO 4.9 0.4 + - - -
261A GLN* 2.7 33.7 + - - +
263A MET 3.4 25.6 - - - +
264A PHE* 3.7 30.7 - - + -
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Residues in contact with MET 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 2.8 24.2 + - + +
126A LEU* 3.4 24.0 - - - +
128A LYS* 1.3 73.1 - - - +
130A LYS* 1.3 59.2 + - - +
132A PHE* 3.4 1.4 + - - +
133A CYS* 2.9 35.2 + - - -
264A PHE* 3.8 24.2 - - + -
278A SER 3.6 18.2 - - - +
279A ALA* 3.8 20.9 - - - -
281A GLY 4.0 0.9 - - - +
282A LEU* 3.7 36.1 - - + +
285A ALA* 4.8 2.5 - - + -
290A PHE* 3.9 8.3 - - + -
293A PHE* 3.8 20.4 - - + -
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU 2.9 16.1 + - - +
127A ASP* 3.6 14.1 - - - +
128A LYS 3.3 0.2 - - - -
129A MET* 1.3 75.0 - - - +
131A SER* 1.3 62.9 + - - +
133A CYS* 3.4 2.1 + - - +
134A GLN* 3.1 23.9 + - + +
290A PHE* 3.6 43.1 - - + +
291A ASP* 5.0 9.8 + - - -
294A GLU* 5.1 8.8 + - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP 3.0 16.8 + - - -
128A LYS* 3.8 6.7 - - - -
130A LYS* 1.3 76.4 - - - +
132A PHE* 1.3 62.3 + - - +
134A GLN* 3.3 8.3 + - - +
135A ARG* 3.1 37.5 + - - +
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Residues in contact with PHE 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 LYS* 3.0 17.9 + - + +
129A MET 3.7 2.9 - - - +
131A SER* 1.3 77.4 - - - +
133A CYS* 1.3 61.7 + - - +
135A ARG* 3.2 9.0 + - + +
136A VAL* 3.0 45.8 + - + +
141A TRP* 3.5 40.8 - + - -
205A LEU* 3.6 25.6 - - + -
244A VAL* 3.8 19.1 - - + -
262A ASN* 5.6 0.7 - - - -
264A PHE* 3.6 25.8 - + + -
282A LEU* 3.9 28.9 - - + -
286A LEU* 4.1 7.6 - - + -
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Residues in contact with CYS 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 MET 2.9 28.6 + - - +
130A LYS 3.7 4.5 - - - +
132A PHE* 1.3 72.7 - - - +
134A GLN* 1.3 58.0 + - - +
137A ARG* 2.8 43.1 + - - +
282A LEU* 4.0 6.5 - - - -
285A ALA* 3.5 48.5 - - - +
286A LEU* 3.6 22.4 - - - -
290A PHE* 4.5 11.0 - - + +
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Residues in contact with GLN 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 LYS* 3.1 13.8 + - + +
131A SER* 3.6 9.5 + - - +
133A CYS* 1.3 75.6 - - - +
135A ARG* 1.3 77.1 + - - +
137A ARG* 4.9 2.5 - - - +
138A SER* 2.8 47.7 + - - -
140A ASP* 4.3 9.5 + - - +
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Residues in contact with ARG 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 SER* 3.1 28.0 + - - +
132A PHE* 3.2 10.7 + - - +
134A GLN* 1.3 89.9 - - - +
136A VAL* 1.3 60.4 + - - +
138A SER* 3.2 3.1 + - - -
140A ASP* 3.1 18.3 + - + +
141A TRP* 2.9 66.3 + - + +
1701A GOL 4.0 19.4 + - - -
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Residues in contact with VAL 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 PHE* 3.0 49.5 + - + +
135A ARG* 1.3 75.2 - - - +
137A ARG* 1.3 66.1 + - - +
139A GLY* 3.0 15.4 + - - -
141A TRP* 3.8 19.8 + - + +
149A ILE* 4.1 29.3 + - + +
152A ILE* 3.8 28.3 - - + -
179A PRO* 4.9 4.5 - - + -
205A LEU* 4.3 4.0 - - + -
286A LEU* 3.7 12.3 - - + -
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Residues in contact with ARG 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 CYS* 2.8 29.2 + - - +
134A GLN* 4.4 2.0 - - - +
136A VAL* 1.3 74.7 - - - +
138A SER* 1.3 60.3 + - - +
139A GLY* 3.1 1.1 + - - -
174A TYR 5.2 1.0 + - - -
176A LYS 4.5 12.5 + - - -
177A GLY 4.6 12.2 - - - +
178A GLY* 3.4 14.5 - - - +
179A PRO* 4.0 13.5 - - + -
285A ALA 3.9 10.8 - - - -
286A LEU* 2.8 44.4 + - + +
287A HIS 3.0 19.6 + - - -
288A VAL 3.9 5.9 + - - -
289A GLY* 3.4 25.2 - - - +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 2.8 36.8 + - - -
135A ARG 3.2 9.9 + - - -
137A ARG* 1.3 76.0 - - - +
139A GLY* 1.3 56.5 + - - +
140A ASP* 3.2 26.9 + - - +
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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
------------------------------------------------------------
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