Contacts of the helix formed by residues 137 - 147 (chain A) in PDB entry 1CX4
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 ASP 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS 5.3 0.2 - - - +
136A THR* 1.3 75.7 - - - +
138A ASP* 1.3 62.4 + - - +
140A ARG* 3.3 8.1 + - - +
141A ASN* 2.9 36.4 + - - +
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Residues in contact with ASP 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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136A THR* 3.2 9.1 + - - +
137A ASP* 1.3 79.1 - - - +
139A GLN* 1.3 61.2 + - - +
141A ASN* 3.7 8.9 + - - +
142A ARG* 3.1 60.4 + - - +
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Residues in contact with GLN 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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134A PRO 4.2 1.9 - - - +
135A LYS* 3.1 23.3 - - + +
136A THR* 2.9 45.0 + - - +
138A ASP* 1.3 76.5 - - - +
140A ARG* 1.3 55.3 + - - +
142A ARG* 3.3 10.2 + - - +
143A LEU* 2.7 38.0 + - - +
170A GLU* 2.8 41.9 + - - +
243A TRP* 3.4 14.5 - - + -
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Residues in contact with ARG 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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135A LYS* 3.8 31.0 - - + +
136A THR 3.1 14.2 + - - +
137A ASP* 3.8 9.2 - - - +
139A GLN* 1.3 75.8 - - - +
141A ASN* 1.3 59.6 + - - +
143A LEU* 3.8 5.8 - - - +
144A GLN* 3.0 58.8 + - - +
162A SER* 5.6 1.0 + - - +
165A LEU* 3.5 52.1 + - - +
166A ASP* 3.7 19.1 + - - -
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Residues in contact with ASN 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 ASP* 2.9 27.5 + - - +
138A ASP* 4.0 7.7 - - - +
140A ARG* 1.3 79.6 - - - +
142A ARG* 1.3 63.0 + - + +
144A GLN* 3.6 9.2 + - - +
145A GLU* 3.1 26.8 + - - +
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Residues in contact with ARG 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 ASP* 3.1 45.0 + - - +
139A GLN* 3.8 16.5 - - - +
141A ASN* 1.3 78.5 - - + +
143A LEU* 1.3 59.2 + - - +
145A GLU* 3.6 10.5 + - - +
146A ALA* 3.0 29.5 + - - +
170A GLU* 2.6 40.2 + - - -
193A ASP* 3.2 41.8 + - - +
194A ARG* 3.9 12.2 - - - +
216A ARG* 5.2 0.9 + - - -
243A TRP* 3.5 6.6 - - - -
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Residues in contact with LEU 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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135A LYS* 3.8 18.2 - - + -
139A GLN 2.7 22.8 + - - +
140A ARG* 3.8 9.2 - - - +
142A ARG* 1.3 72.5 - - - +
144A GLN* 1.3 61.6 + - + +
146A ALA* 3.2 1.9 + - - +
147A CYS* 3.0 35.0 + - - -
165A LEU* 3.8 26.7 - - + +
168A MET* 3.5 46.0 - - + -
243A TRP* 3.5 40.1 - - + +
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Residues in contact with GLN 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 ARG* 3.0 53.4 + - - +
141A ASN* 4.0 8.1 + - - +
143A LEU* 1.3 78.4 - - + +
145A GLU* 1.3 61.0 + - - +
147A CYS* 3.4 5.4 + - - +
148A LYS* 3.2 22.5 + - - +
165A LEU* 4.5 23.3 - - + -
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ASN 3.1 18.8 + - - +
142A ARG* 4.0 10.7 - - - +
144A GLN* 1.3 78.4 - - - +
146A ALA* 1.3 58.8 + - - +
148A LYS* 3.1 38.4 - - + +
216A ARG* 4.2 20.4 + - - +
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Residues in contact with ALA 146 (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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142A ARG 3.0 19.1 + - - +
143A LEU 3.2 4.7 + - - +
145A GLU* 1.3 78.7 - - - +
147A CYS* 1.3 59.1 + - - +
149A ASP* 4.6 2.6 + - - +
150A ILE* 3.7 10.4 - - - +
191A VAL* 3.6 15.6 - - + +
192A ILE 3.8 8.5 - - - +
193A ASP* 4.2 2.7 - - - +
216A ARG* 3.7 37.0 + - - +
243A TRP* 4.0 18.8 - - + +
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Residues in contact with CYS 147 (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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143A LEU* 3.0 27.7 + - - +
144A GLN* 3.4 5.6 + - - +
145A GLU 3.3 0.2 - - - -
146A ALA* 1.3 78.1 - - - +
148A LYS* 1.3 64.1 + - - +
149A ASP 3.1 4.1 + - - -
150A ILE* 3.2 20.7 + - - +
153A PHE* 3.8 25.9 - - + +
154A LYS* 5.2 0.2 + - - -
161A MET* 5.6 3.8 - - + +
165A LEU* 4.5 12.6 - - + -
168A MET* 3.4 33.4 - - - -
191A VAL* 4.3 7.0 - - - -
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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