Contacts of the helix formed by residues 159 - 171 (chain B) in PDB entry 3ECS
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 LEU 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLU* 3.2 31.0 - - + +
155B SER 2.9 6.1 + - - +
156B GLN* 3.9 29.8 - - - +
157B PRO 3.3 7.6 - - - +
158B ASP* 1.3 83.6 + - - +
160B SER* 1.3 64.8 + - - +
161B GLY 3.1 3.4 - - - -
162B LYS* 3.0 45.3 + - + +
163B LYS* 3.8 5.1 + - - +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 3.5 15.4 - - - +
130B TYR* 3.5 26.3 + - - +
154B GLU 3.4 1.0 + - - -
155B SER* 3.7 0.9 + - - -
158B ASP* 3.4 17.5 + - - -
159B LEU* 1.3 75.3 - - - +
161B GLY* 1.3 63.1 + - - +
162B LYS 3.1 0.2 - - - -
163B LYS* 3.2 17.0 + - - +
164B MSE 3.1 17.2 + - - -
209B LYS* 3.3 20.6 + - - -
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.8 13.9 - - - -
152B VAL* 3.8 6.9 - - - +
153B THR 3.0 27.8 - - - -
154B GLU* 2.7 18.0 + - - -
155B SER* 3.9 0.6 - - - -
160B SER* 1.3 75.3 + - - +
162B LYS* 1.3 56.5 + - - +
164B MSE 3.2 4.4 + - - +
165B ALA* 2.8 27.0 + - - +
177B VAL* 5.1 1.3 - - - -
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Residues in contact with LYS 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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154B GLU* 3.8 29.9 + - + -
159B LEU* 3.0 38.8 + - + +
161B GLY* 1.3 75.8 - - - +
163B LYS* 1.3 65.9 + - + +
165B ALA* 3.1 9.7 + - - +
166B LYS* 2.9 39.9 + - - +
177B VAL* 4.6 16.2 - - + -
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TYR* 3.8 28.4 + - + -
158B ASP 5.8 1.8 - - - +
159B LEU 4.4 3.8 - - - +
160B SER* 3.2 23.1 + - - +
162B LYS* 1.3 77.1 - - + +
164B MSE 1.3 56.8 + - - +
166B LYS* 3.3 24.4 + - - +
167B ALA* 3.0 27.7 + - - +
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Residues in contact with MSE 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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127B THR* 4.7 6.3 - - + +
129B ALA 3.5 22.0 - - - +
130B TYR* 3.3 23.0 - - + -
131B SER 4.0 23.3 - - - +
134B VAL* 3.7 32.5 - - + -
135B LEU* 3.8 31.9 - - + +
138B LEU* 4.3 10.8 - - + -
152B VAL* 4.2 11.4 - - + -
160B SER 3.1 5.9 + - - +
161B GLY* 3.2 9.9 - - - +
162B LYS 3.1 0.2 - - - -
163B LYS* 1.3 75.0 - - - +
165B ALA* 1.3 65.1 + - - +
167B ALA* 3.2 4.2 + - - +
168B LEU* 3.0 35.3 + - + +
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Residues in contact with ALA 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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152B VAL* 4.4 1.8 - - + +
161B GLY 2.8 8.7 + - - +
162B LYS* 3.4 8.5 - - - +
164B MSE 1.3 77.1 - - - +
166B LYS* 1.3 51.0 + - + +
168B LEU* 3.4 2.6 + - - +
169B CYS* 2.7 35.6 + - - +
175B VAL* 3.7 26.9 - - + +
177B VAL* 3.5 32.1 - - + -
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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 LYS* 2.9 30.7 + - - +
163B LYS* 3.5 25.0 - - + +
165B ALA* 1.3 73.3 - - + +
167B ALA* 1.3 55.0 + - - +
169B CYS* 3.0 8.4 + - - +
170B HIS* 2.8 57.4 + - + +
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Residues in contact with ALA 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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130B TYR* 4.4 11.2 - - + +
135B LEU* 4.0 26.2 - - + -
163B LYS 3.0 12.9 + - - +
164B MSE 3.4 11.9 - - - +
166B LYS* 1.3 74.3 - - - +
168B LEU* 1.3 62.9 + - - +
170B HIS* 3.0 24.1 + - - +
171B LEU* 3.3 15.0 + - - +
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Residues in contact with LEU 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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135B LEU* 3.8 18.8 - - + -
138B LEU* 3.8 28.5 - - + -
150B VAL* 3.9 35.4 - - + -
152B VAL* 5.3 0.7 - - + -
164B MSE 3.0 32.9 + - + +
165B ALA 3.6 4.0 - - - +
167B ALA* 1.3 76.4 - - - +
169B CYS* 1.3 63.5 + - - +
171B LEU* 3.1 10.3 + - + +
172B ASN 3.2 0.2 + - - -
173B VAL* 3.0 48.6 + - + +
175B VAL* 3.9 19.5 - - + -
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Residues in contact with CYS 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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165B ALA 2.7 22.7 + - - +
166B LYS* 3.2 13.0 - - - +
168B LEU* 1.3 74.7 - - - +
170B HIS* 1.3 61.4 + - - +
172B ASN* 2.9 20.8 + - - -
173B VAL 4.4 9.0 - - - +
175B VAL* 4.2 5.8 - - + +
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Residues in contact with HIS 170 (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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166B LYS* 2.8 43.5 + - + +
167B ALA* 3.0 11.7 + - - +
169B CYS* 1.3 81.2 - - + +
171B LEU* 1.3 62.9 + - + +
172B ASN* 3.1 4.2 + - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.6 11.2 - - + -
139B GLU* 3.5 44.6 - - + +
142B VAL* 5.2 11.0 - - + +
167B ALA 3.3 12.1 + - - +
168B LEU* 3.1 10.8 + - + +
170B HIS* 1.3 80.8 - - + +
172B ASN* 1.3 72.1 + - - +
173B VAL* 3.4 16.4 + - + +
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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