Contacts of the helix formed by residues 126 - 143 (chain A) in PDB entry 1EZW
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 GLY 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 4.1 10.1 - - - +
125A VAL* 1.3 77.5 - - - +
127A PRO* 1.3 69.7 - - - +
128A ALA* 3.2 3.1 - - - -
129A THR* 2.9 12.5 + - - -
130A ALA* 2.9 23.6 + - - +
152A LYS* 5.9 0.6 - - - +
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Residues in contact with PRO 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.4 23.1 + - + +
97A PRO* 4.0 15.5 - - + +
111A PRO* 4.3 19.7 - - + -
112A CYS 4.0 12.1 - - - +
113A LYS* 4.5 9.6 - - + -
125A VAL 3.9 2.7 - - - +
126A GLY* 1.3 82.9 - - - +
128A ALA* 1.3 57.4 + - - +
130A ALA* 3.2 2.0 + - + +
131A ILE* 2.9 33.6 + - - +
182A MET* 3.6 18.4 - - + -
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY 3.2 1.6 - - - -
127A PRO* 1.3 80.2 - - - +
129A THR* 1.3 59.1 + - - +
131A ILE* 3.4 4.4 + - - +
132A ARG* 3.0 34.8 + - - +
181A ILE* 4.0 17.3 - - + -
182A MET* 3.3 25.1 - - + +
185A THR* 3.8 26.2 - - + +
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Residues in contact with THR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 3.6 19.5 - - + -
126A GLY* 2.9 14.6 + - - -
128A ALA* 1.3 76.7 - - - +
130A ALA* 1.3 65.2 + - - +
132A ARG* 3.1 17.3 + - + +
133A GLU* 3.0 40.9 + - + +
152A LYS* 4.1 15.7 - - + +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 4.3 4.7 - - + -
69A TYR* 3.5 29.2 - - + +
125A VAL* 4.1 3.5 - - + +
126A GLY 2.9 10.8 + - - +
127A PRO 3.2 3.3 + - - +
129A THR* 1.3 76.7 - - - +
131A ILE* 1.3 56.7 + - - +
133A GLU* 3.2 2.9 + - - +
134A VAL* 2.9 34.5 + - - +
153A TYR* 3.7 37.8 - - + -
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Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 3.9 21.3 - - + -
95A MET* 4.0 7.6 - - + +
96A GLY* 3.6 31.0 - - - +
97A PRO* 3.8 6.1 - - + -
127A PRO 2.9 20.3 + - - +
128A ALA* 3.7 4.7 - - - +
129A THR 3.2 0.2 - - - -
130A ALA* 1.3 73.7 - - - +
132A ARG* 1.3 66.0 + - - +
134A VAL* 3.4 3.2 + - - +
135A LYS* 2.9 22.0 + - - +
173A PHE* 4.0 13.1 - - + -
175A MET* 3.8 36.1 - - + -
176A GLY 5.2 1.3 - - - +
182A MET* 3.9 23.8 - - + -
189A ILE* 4.5 2.0 - - + -
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Residues in contact with ARG 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 ALA* 3.0 23.0 + - - +
129A THR* 3.1 18.2 + - + +
131A ILE* 1.3 75.0 - - - +
133A GLU* 1.3 64.9 + - + +
135A LYS* 3.3 4.7 + - - +
136A GLU* 3.1 27.2 + - + +
149A TYR* 5.4 0.2 - - - -
185A THR* 4.0 27.8 + - + +
188A GLU* 3.0 43.8 + - - -
189A ILE* 3.5 31.6 - - + +
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 3.0 32.7 + - + +
130A ALA 3.6 6.5 - - - +
132A ARG* 1.3 76.8 - - + +
134A VAL* 1.3 66.7 + - - +
136A GLU* 3.1 3.8 + - - +
137A VAL* 3.0 26.8 + - - +
149A TYR* 3.5 27.0 + - + +
151A GLY* 3.5 10.3 - - - -
152A LYS* 2.7 28.0 + - - +
153A TYR* 2.7 36.4 + - + -
154A VAL* 3.1 14.3 + - + +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 3.3 19.5 - - + -
73A PRO* 3.8 22.7 - - + -
76A THR* 5.2 1.6 - - + -
95A MET* 3.8 19.3 - - + -
130A ALA 2.9 21.0 + - - +
131A ILE* 3.9 5.8 - - - +
133A GLU* 1.3 76.2 - - - +
135A LYS* 1.3 64.3 + - - +
137A VAL* 3.2 1.6 + - - +
138A ILE* 2.9 43.3 + - + +
153A TYR* 3.0 32.7 - - + +
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Residues in contact with LYS 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 ILE 2.9 14.2 + - - +
132A ARG* 3.5 10.3 - - - +
133A GLU 3.1 0.2 - - - -
134A VAL* 1.3 76.8 - - - +
136A GLU* 1.3 73.6 + - - +
138A ILE* 3.3 2.9 + - - -
139A TYR* 3.0 55.8 + - + +
173A PHE* 3.7 41.4 - - + -
189A ILE* 2.8 44.1 + - + +
191A ASN* 6.0 1.3 - - - +
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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
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132A ARG* 3.1 16.0 + - + +
133A GLU 3.1 7.1 + - - +
135A LYS* 1.3 87.5 + - - +
137A VAL* 1.3 63.6 + - - +
139A TYR* 4.0 3.4 - - - +
140A GLN* 3.0 37.1 + - - +
149A TYR* 4.0 32.5 - - + +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 4.0 24.7 - - + +
74A LEU* 3.6 33.9 - - + -
77A ALA* 5.2 0.7 - - + -
133A GLU 3.0 17.3 + - - +
134A VAL 3.7 6.5 - - - +
136A GLU* 1.3 77.2 - - - +
138A ILE* 1.3 64.5 + - - +
140A GLN* 3.8 2.1 - - - +
141A TYR* 3.0 21.3 + - - +
147A VAL* 4.1 12.5 - - + +
149A TYR* 4.1 20.4 - - + -
154A VAL* 4.0 22.7 - - + -
156A THR* 4.6 5.6 - - + -
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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
----------------------------------------------------------
73A PRO 4.2 6.3 - - - +
76A THR* 4.0 19.1 - - + -
77A ALA* 4.0 26.7 - - + +
80A ILE* 5.2 3.4 - - + -
93A ILE* 3.8 32.3 - - + -
95A MET* 4.0 9.6 - - + -
134A VAL* 2.9 42.5 + - + +
135A LYS 3.7 4.3 - - - +
137A VAL* 1.3 76.6 - - - +
139A TYR* 1.3 62.8 + - + +
141A TYR* 3.1 5.4 + - - +
142A LEU* 2.9 39.1 + - + +
173A PHE* 4.8 7.0 - - + -
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Residues in contact with TYR 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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93A ILE* 3.5 21.2 - - + +
135A LYS* 3.0 39.6 + - + +
136A GLU* 4.4 3.8 - - - +
138A ILE* 1.3 76.4 - - + +
140A GLN* 1.3 66.5 + - - +
142A LEU* 3.7 15.9 - - + +
143A GLU* 2.9 32.1 + - + +
169A SER* 3.4 40.8 - - - -
171A ILE 2.6 22.7 + - - -
173A PHE* 3.3 42.5 + + + +
191A ASN* 4.6 1.7 + - - -
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Residues in contact with GLN 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* 3.0 28.4 + - - +
137A VAL 3.8 3.6 - - - +
139A TYR* 1.3 74.8 - - - +
141A TYR* 1.3 60.3 + - - +
143A GLU* 3.3 13.2 + - - +
144A GLY 3.4 0.2 + - - -
145A GLY* 3.0 24.4 + - - -
146A PRO 3.7 4.9 - - - +
147A VAL* 3.2 18.7 - - + -
148A GLU* 2.9 44.7 + - - +
149A TYR* 3.9 21.0 - - - +
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Residues in contact with TYR 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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74A LEU* 4.1 27.1 - - + -
77A ALA* 3.4 28.7 - - + -
78A SER* 3.4 23.1 + - - -
81A ALA* 3.8 25.4 - - + -
137A VAL 3.0 13.9 + - - +
138A ILE 3.1 8.5 + - - +
140A GLN* 1.3 77.2 - - - +
142A LEU* 1.3 62.5 + - + +
144A GLY* 2.9 20.6 + - - -
147A VAL* 3.6 9.6 - - + +
160A ASP 5.5 0.9 - - - -
161A VAL* 3.6 43.8 - - + +
163A ALA* 3.5 23.1 + - - +
164A ARG* 5.8 0.2 - - - -
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Residues in contact with LEU 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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77A ALA 4.8 1.3 - - - +
80A ILE* 4.8 2.0 - - + -
81A ALA* 4.0 21.1 - - + +
93A ILE* 4.7 2.2 - - + -
138A ILE* 2.9 36.1 + - + +
139A TYR* 3.3 25.3 + - + +
141A TYR* 1.3 80.3 - - + +
143A GLU* 1.3 59.6 + - - +
144A GLY* 3.1 0.9 + - - -
164A ARG* 5.4 5.8 - - - -
165A SER* 3.8 27.2 + - - +
168A GLY* 3.6 41.1 - - - +
169A SER* 4.3 1.3 - - - +
171A ILE* 3.8 23.1 - - + -
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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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139A TYR* 2.9 28.6 + - + +
140A GLN* 3.7 8.3 - - - +
141A TYR 3.2 0.8 - - - -
142A LEU* 1.3 76.1 - - - +
144A GLY* 1.3 58.0 + - - +
145A GLY 3.5 2.7 + - - +
164A ARG* 5.3 0.8 + - - -
169A SER* 2.9 34.2 + - - -
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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