Contacts of the helix formed by residues 157 - 169 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B VAL* 4.0 18.6 - - + -
127B VAL* 3.8 25.6 - - + -
129B LEU* 4.0 17.9 - - + -
155B ILE 4.3 1.3 - - - +
156B GLN* 1.3 82.7 - - + +
158B VAL* 1.3 64.6 + - - +
159B GLU* 3.2 7.9 - - - +
160B ASP* 3.1 22.4 + - + +
161B VAL* 2.9 22.3 + - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ILE* 5.1 6.5 - - + -
146B MET 4.3 6.1 - - - +
147B ALA* 3.9 30.1 - - + +
156B GLN* 2.9 14.7 + - + +
157B PRO* 1.3 70.3 - - - +
159B GLU* 1.3 64.4 + - - +
161B VAL* 3.7 8.5 - - - +
162B THR* 2.7 41.4 + - - +
176B VAL* 4.0 29.8 - - + -
187B PHE* 5.3 3.4 - - + -
192B LEU* 4.2 24.2 - - + -
194B VAL* 4.3 0.7 - - + -
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B GLN 4.7 1.4 - - - +
157B PRO* 3.8 4.7 - - - +
158B VAL* 1.3 83.8 + - - +
160B ASP* 1.3 65.5 + - - +
162B THR* 3.1 8.4 + - - -
163B ARG* 2.9 28.7 + - - +
192B LEU* 4.1 27.4 - - + +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.8 28.2 - - + +
157B PRO* 3.1 18.0 + - + +
159B GLU* 1.3 78.8 - - - +
161B VAL* 1.3 68.0 + - - +
162B THR 3.0 0.5 + - - -
163B ARG* 2.7 33.0 + - - +
164B ILE* 2.8 30.6 + - + +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.1 12.1 - - + -
129B LEU* 3.9 18.1 - - + +
132B LEU* 3.8 21.7 - - + +
143B VAL* 4.5 9.0 - - + -
145B ILE* 4.1 33.0 - - + -
157B PRO* 2.9 29.8 + - + +
158B VAL* 3.7 7.9 - - - +
160B ASP* 1.3 74.5 - - - +
162B THR* 1.3 62.3 + - - +
164B ILE* 3.9 1.0 - - - +
165B VAL* 2.8 38.6 + - + +
174B VAL* 5.5 2.9 - - + -
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 2.7 21.8 + - - +
159B GLU 3.3 8.7 - - - -
161B VAL* 1.3 74.9 - - - +
163B ARG* 1.3 67.6 + - - +
165B VAL* 2.9 7.8 + - - +
166B LYS* 2.9 25.7 + - + +
174B VAL* 4.5 19.4 - - + +
192B LEU 3.9 12.6 + - - +
193B GLU* 3.6 34.5 - - + +
194B VAL* 4.0 16.3 - - + +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 5.5 1.0 - - - +
159B GLU 2.9 11.8 + - - +
160B ASP* 2.7 44.4 + - - +
162B THR* 1.3 76.0 - - - +
164B ILE* 1.3 83.3 + - - +
166B LYS* 2.8 48.3 + - - +
167B LYS* 3.1 11.0 + - + +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 3.6 52.3 - - + +
132B LEU* 4.3 9.0 - - + -
133B GLU* 3.8 40.6 - - + +
136B VAL* 6.1 0.2 - - + -
160B ASP* 2.8 22.6 + - + +
161B VAL 3.9 3.6 - - - +
163B ARG* 1.3 91.6 - - - +
165B VAL* 1.3 62.2 + - - +
167B LYS* 3.9 6.0 - - - +
168B LYS* 3.2 21.8 + - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU* 4.4 13.7 - - + -
136B VAL* 4.5 12.1 - - + +
143B VAL* 4.2 19.7 - - + -
161B VAL* 2.8 34.3 + - + +
162B THR* 2.9 8.1 + - - +
164B ILE* 1.3 75.6 - - - +
166B LYS* 1.3 60.1 + - - +
168B LYS* 3.4 4.4 + - - +
169B ASN* 2.9 31.3 + - - +
172B THR* 3.8 35.4 - - + +
174B VAL* 4.3 14.1 - - + -
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B THR* 2.9 14.0 + - + +
163B ARG* 2.8 51.4 - - - +
165B VAL* 1.3 77.8 - - - +
167B LYS* 1.3 64.7 + - - +
169B ASN 3.0 23.1 - - - -
170B LYS* 3.0 18.7 + - + +
172B THR 6.0 0.7 - - - -
193B GLU* 3.9 32.8 + - - +
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ARG* 3.1 14.9 + - + +
164B ILE* 3.9 6.1 - - - +
166B LYS* 1.3 84.4 - - + +
168B LYS* 1.3 68.8 + - - +
169B ASN* 3.0 1.4 + - - -
170B LYS 4.7 0.3 + - - -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLU* 2.7 54.8 + - + +
134B LYS* 3.4 9.9 + - - +
136B VAL* 2.9 49.8 + - + +
137B ASP* 5.0 4.8 - - - +
138B GLU* 5.2 2.8 - - - +
164B ILE 3.2 15.1 + - - +
165B VAL 4.0 2.5 - - - +
167B LYS* 1.3 79.8 - - - +
169B ASN* 1.3 59.8 + - + +
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B VAL* 4.2 9.6 - - + -
137B ASP 3.2 22.5 + - - +
138B GLU* 3.2 33.9 + - - +
140B THR 3.6 5.9 + - - -
165B VAL* 2.9 20.6 + - - +
166B LYS* 3.0 6.6 - - - +
167B LYS 3.0 1.5 - - - -
168B LYS* 1.3 81.7 - - - +
170B LYS* 1.3 63.1 + - - +
171B GLU* 2.7 35.1 + - - +
172B THR* 3.3 31.3 + - - +
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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