Contacts of the helix formed by residues 126 - 140 (chain A) in PDB entry 1CW0
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 3.9 1.6 - - - +
124A LYS 5.3 1.8 - - - +
125A LEU* 1.3 79.3 - - - +
127A ASP* 1.3 64.3 + - - +
128A GLU* 3.7 14.6 + - - +
129A ALA* 3.1 26.2 + - + +
130A LEU* 2.9 23.2 + - - +
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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
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27A ARG* 2.6 38.1 + - - +
31A LEU* 3.8 16.2 - - + +
126A THR* 1.3 73.4 - - - +
128A GLU* 1.3 71.7 + - - +
130A LEU* 3.8 1.4 - - - +
131A THR* 2.9 36.8 + - - +
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Residues in contact with GLU 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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126A THR* 3.2 11.3 + - - +
127A ASP* 1.3 91.8 + - - +
129A ALA* 1.3 59.2 + - - +
131A THR* 3.8 5.1 - - - +
132A GLU* 3.0 33.8 + - - +
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Residues in contact with ALA 129 (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 LEU* 4.4 12.8 - - + -
126A THR* 3.1 25.9 + - + +
128A GLU* 1.3 80.8 - - - +
130A LEU* 1.3 62.6 + - - +
132A GLU* 4.0 4.0 - - - +
133A ARG* 3.2 52.5 + - - +
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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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27A ARG* 3.2 44.2 - - - +
31A LEU* 3.8 21.5 - - + -
114A VAL* 5.1 3.8 - - + -
118A ALA* 3.8 11.0 - - + +
119A LEU* 4.0 13.2 - - + -
125A LEU* 3.7 31.4 - - + +
126A THR 2.9 13.2 + - - +
127A ASP 3.8 3.1 - - - +
129A ALA* 1.3 74.7 - - - +
131A THR* 1.3 61.1 + - - +
133A ARG* 3.2 5.2 + - - +
134A LEU* 2.9 38.4 + - + +
147A ILE* 4.4 16.3 - - + +
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Residues in contact with THR 131 (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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31A LEU* 3.7 19.6 + - - +
34A GLY 6.5 0.4 - - - -
35A GLN* 3.7 17.7 + - + +
127A ASP* 2.9 27.3 + - - +
128A GLU* 3.8 5.8 - - - +
130A LEU* 1.3 72.5 - - - +
132A GLU* 1.3 58.5 + - - +
134A LEU* 3.7 8.6 - - - +
135A GLU* 3.0 31.9 + - + +
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Residues in contact with GLU 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 GLU 3.0 18.8 + - - +
129A ALA* 4.0 2.6 - - - +
131A THR* 1.3 79.3 - - - +
133A ARG* 1.3 91.2 + - - +
135A GLU* 3.9 6.0 - - - +
136A GLU* 3.0 32.0 + - + +
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Residues in contact with ARG 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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125A LEU* 4.5 17.3 - - - +
129A ALA* 3.2 39.4 + - - +
130A LEU* 3.9 3.6 - - - +
132A GLU* 1.3 108.7 + - - +
134A LEU* 1.3 59.3 + - - +
136A GLU* 4.1 4.6 - - - +
137A TRP* 3.0 30.7 + - - +
147A ILE* 4.3 17.7 - - + -
151A GLY* 3.8 19.7 - - - -
152A ILE* 4.1 31.0 - - + +
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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
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28A LEU* 3.8 31.4 - - + -
31A LEU* 4.1 23.3 - - + -
32A LEU* 4.4 7.0 - - + -
35A GLN* 4.1 8.7 - - - +
61A ILE* 4.4 5.2 - - + -
112A LEU* 3.8 24.9 - - + -
114A VAL* 4.6 2.9 - - + -
130A LEU* 2.9 29.2 + - + +
131A THR* 3.7 6.3 - - - +
133A ARG* 1.3 74.9 - - - +
135A GLU* 1.3 56.3 + - - +
137A TRP* 3.2 2.9 + - - +
138A ILE* 2.8 54.9 + - + +
147A ILE* 4.5 10.8 - - + -
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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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35A GLN* 3.3 29.1 - - + +
131A THR* 3.0 21.2 + - + +
132A GLU* 3.9 6.6 - - - +
134A LEU* 1.3 75.3 - - - +
136A GLU* 1.3 81.0 + - - +
139A CYS* 3.0 47.1 + - - +
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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 GLU* 3.0 19.6 + - + +
133A ARG* 4.1 4.9 - - - +
135A GLU* 1.3 92.0 + - - +
137A TRP* 1.3 58.2 + - + +
139A CYS* 5.2 0.2 - - - -
140A GLY* 3.0 29.7 + - - -
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Residues in contact with TRP 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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59A CYS* 3.6 39.7 - - + -
60A VAL 4.1 3.1 - - - -
61A ILE* 4.7 1.8 - - + -
110A ARG* 2.9 42.7 + - + -
111A VAL 3.5 26.5 - - - -
112A LEU* 3.5 40.6 - - + -
133A ARG 3.0 20.2 + - - +
134A LEU 3.9 1.3 - - - +
136A GLU* 1.3 76.7 - - - +
138A ILE* 1.3 76.5 + - + +
140A GLY* 3.4 6.9 + - - +
142A GLY* 3.7 10.1 + - - +
143A ALA 3.0 24.8 + - - -
145A ALA* 3.8 11.5 - - + +
152A ILE* 3.9 26.5 - - + -
154A LEU* 5.4 1.8 - - + -
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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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32A LEU* 3.8 28.7 - - + -
35A GLN* 4.1 2.9 - - - +
37A LEU* 3.9 15.5 - - + -
54A VAL* 4.3 9.6 - - + -
57A TYR* 3.4 30.4 - - + +
59A CYS* 3.9 14.4 - - - -
61A ILE* 4.0 15.0 - - + -
110A ARG* 2.7 25.4 + - - +
134A LEU* 2.8 35.8 + - + +
135A GLU 4.3 1.1 - - - +
137A TRP* 1.3 93.9 - - + +
139A CYS* 1.3 61.3 + - - +
140A GLY 3.5 0.3 - - - +
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Residues in contact with CYS 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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35A GLN* 4.5 9.0 - - - -
37A LEU* 5.5 2.2 - - - -
57A TYR* 3.8 43.5 - - + +
135A GLU* 3.0 43.1 + - - +
136A GLU 4.8 0.2 - - - +
138A ILE* 1.3 75.2 - - - +
140A GLY* 1.3 64.6 + - - +
141A GLU* 5.4 0.7 - - - +
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Residues in contact with GLY 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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57A TYR* 5.3 1.6 - - - -
110A ARG* 3.5 18.0 + - - -
136A GLU* 3.0 28.0 + - - -
137A TRP 3.4 3.3 + - - -
138A ILE 3.3 1.4 - - - +
139A CYS* 1.3 83.0 - - - +
141A GLU* 1.3 65.7 + - - +
142A GLY 3.5 2.9 - - - -
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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