Contacts of the helix formed by residues 157 - 169 (chain A) in PDB entry 1ECX
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 PRO 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 4.1 16.8 - - + -
127A VAL* 3.7 29.4 - - + -
129A LEU* 4.1 11.4 - - + -
155A ILE 4.2 1.1 - - - +
156A GLN* 1.3 85.3 - - + +
158A VAL* 1.3 58.8 + - - +
159A GLU* 3.3 7.0 - - - +
160A ASP* 3.3 22.0 + - + +
161A VAL* 2.8 34.6 + - + +
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Residues in contact with VAL 158 (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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145A ILE* 5.2 7.9 - - + -
146A MET 4.5 3.6 - - - +
147A ALA* 3.9 30.3 - - + -
156A GLN* 2.8 21.7 + - + +
157A PRO* 1.3 69.4 - - - +
159A GLU* 1.3 72.5 + - - +
161A VAL* 3.1 8.4 + - + +
162A THR* 2.8 33.9 + - - +
176A VAL* 4.0 24.5 - - + -
187A PHE* 5.1 3.1 - - + -
192A LEU* 3.8 32.8 - - + -
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Residues in contact with GLU 159 (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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156A GLN 4.7 1.2 - - - +
157A PRO* 4.1 4.3 - - - +
158A VAL* 1.3 84.4 + - - +
160A ASP* 1.3 68.3 + - - +
162A THR* 3.2 5.5 + - - -
163A ARG* 3.0 22.7 + - - +
192A LEU* 3.8 27.5 - - + +
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Residues in contact with ASP 160 (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 LEU* 3.8 24.6 - - + +
157A PRO* 3.3 18.6 + - + +
159A GLU* 1.3 81.1 + - - +
161A VAL* 1.3 55.6 + - - +
163A ARG* 2.9 36.6 + - - +
164A ILE* 2.7 38.0 + - - +
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Residues in contact with VAL 161 (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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127A VAL* 4.1 10.3 - - + -
129A LEU* 3.8 23.8 - - + +
132A LEU* 3.8 21.5 - - + +
143A VAL* 5.0 7.2 - - + -
145A ILE* 4.3 30.5 - - + -
157A PRO* 2.8 38.5 + - + +
158A VAL* 3.5 8.7 - - + +
160A ASP* 1.3 71.3 - - - +
162A THR* 1.3 64.0 + - - +
164A ILE* 4.0 1.7 - - - +
165A VAL* 3.1 29.4 + - + +
174A VAL* 5.7 3.6 - - + -
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Residues in contact with THR 162 (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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158A VAL* 2.8 22.5 + - - +
159A GLU 3.6 7.2 - - - -
161A VAL* 1.3 70.6 - - - +
163A ARG* 1.3 61.8 + - - +
165A VAL* 3.2 6.1 + - - +
166A LYS* 2.9 34.6 + - + +
174A VAL* 4.3 19.4 - - + +
192A LEU 3.9 11.5 + - - +
193A GLU* 3.2 32.8 - - + +
194A VAL* 3.6 19.3 - - + +
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Residues in contact with ARG 163 (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 LEU* 5.0 1.6 - - - +
159A GLU 3.0 11.8 + - - +
160A ASP* 2.9 41.5 + - - +
162A THR* 1.3 75.8 - - - +
164A ILE* 1.3 89.2 + - - +
166A LYS* 2.7 51.1 - - - +
167A LYS* 3.1 12.5 + - + +
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Residues in contact with ILE 164 (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 LEU* 3.7 50.3 - - + +
132A LEU* 4.4 10.1 - - + -
133A GLU* 4.1 37.7 - - + +
136A VAL* 6.1 0.7 - - + -
160A ASP 2.7 20.4 + - - +
161A VAL* 4.0 4.7 - - - +
163A ARG* 1.3 94.9 - - - +
165A VAL* 1.3 63.0 + - - +
167A LYS* 3.6 6.6 + - - +
168A LYS* 3.3 20.6 + - - +
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Residues in contact with VAL 165 (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 LEU* 4.2 13.9 - - + -
136A VAL* 3.9 24.9 - - + +
143A VAL* 4.0 17.5 - - + -
161A VAL* 3.1 24.5 + - + +
162A THR 3.7 3.8 - - - +
164A ILE* 1.3 72.9 - - - +
166A LYS* 1.3 66.7 + - - +
168A LYS* 3.5 4.6 + - - +
169A ASN* 3.1 22.3 + - - +
172A THR* 3.8 35.0 - - + +
174A VAL* 4.2 17.5 - - + -
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Residues in contact with LYS 166 (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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162A THR* 2.9 16.5 + - + +
163A ARG* 2.7 50.3 - - - +
165A VAL* 1.3 77.1 - - - +
167A LYS* 1.3 70.3 + - - +
169A ASN 4.1 5.2 - - - -
170A LYS* 3.2 32.7 + - + +
172A THR 6.1 0.2 - - - -
193A GLU* 4.1 24.5 + - - +
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Residues in contact with LYS 167 (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 GLU* 6.5 1.3 - - + -
163A ARG* 3.1 16.0 + - + +
164A ILE* 3.8 7.4 - - - +
166A LYS* 1.3 87.6 - - + +
168A LYS* 1.3 61.6 + - - +
169A ASN* 3.4 0.5 + - - -
170A LYS 5.0 0.3 + - - -
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Residues in contact with LYS 168 (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 GLU* 2.5 61.4 + - + +
134A LYS* 3.7 9.5 + - - +
136A VAL* 2.7 52.7 + - + +
137A ASP* 4.6 5.8 - - - +
138A GLU* 4.7 5.7 - - - +
164A ILE* 3.3 15.0 + - + +
165A VAL 4.2 0.7 - - - +
166A LYS 3.4 0.2 - - - -
167A LYS* 1.3 78.4 - - - +
169A ASN* 1.3 59.2 + - - +
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Residues in contact with ASN 169 (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 VAL* 4.2 10.5 - - + -
137A ASP 3.2 21.7 + - - +
138A GLU* 3.7 32.1 + - - +
140A THR 4.0 3.6 + - - -
165A VAL 3.1 15.1 + - - +
166A LYS* 3.3 5.0 - - - -
167A LYS 3.2 2.8 - - - -
168A LYS* 1.3 82.3 - - - +
170A LYS* 1.3 59.6 + - - +
171A GLU* 2.6 46.8 + - - +
172A THR* 3.2 29.8 + - - +
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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