Contacts of the helix formed by residues 156 - 167 (chain B) in PDB entry 1S4Z
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 CYS 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.4 32.3 - - + -
119B PRO* 5.3 5.8 - - + -
136B MET* 3.6 17.9 - - - -
152B ALA 3.0 10.6 + - - -
153B ASN 3.7 1.1 - - - -
154B VAL 3.3 0.2 - - - -
155B LYS* 1.3 79.2 - - - +
157B PRO* 1.3 69.8 - - - +
158B GLN* 3.2 4.5 + - + +
159B VAL* 3.5 24.6 + - + +
160B VAL* 3.3 16.3 + - - +
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Residues in contact with PRO 157 (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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157A PRO* 3.5 35.9 - - + -
161A ILE* 4.0 6.7 - - + -
153B ASN* 2.9 24.0 - - + +
154B VAL* 4.0 7.2 - - - +
155B LYS 4.2 0.2 - - - -
156B CYS* 1.3 82.6 - - - +
158B GLN* 1.3 67.0 + - + +
160B VAL* 4.0 7.4 - - + -
161B ILE* 2.7 41.3 + - + +
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Residues in contact with GLN 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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153A ASN* 3.1 52.1 + - - +
154A VAL* 4.4 8.3 - - - +
156B CYS* 3.2 2.2 - - + -
157B PRO* 1.3 87.5 - - + +
159B VAL* 1.3 62.7 + - + +
161B ILE* 4.0 3.8 - - - +
162B SER* 2.9 33.3 + - - -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 4.9 19.1 - - + -
121B ARG* 5.6 3.4 - - - -
122B ILE* 3.4 29.8 - - + +
136B MET* 5.0 1.6 - - + -
156B CYS* 3.5 30.0 + - + +
157B PRO 3.4 0.2 - - - -
158B GLN* 1.3 78.0 - - + +
160B VAL* 1.3 58.3 + - - +
162B SER* 3.8 5.3 - - - -
163B PHE* 2.9 28.8 + - + +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 3.5 37.7 - - + -
122B ILE* 4.1 15.9 - - + -
134B PHE* 4.1 21.1 - - + -
136B MET* 4.7 5.2 - - + -
152B ALA* 4.2 28.7 - - + +
153B ASN* 4.6 1.8 - - + -
156B CYS 3.3 13.8 + - - +
157B PRO* 3.2 9.2 + - + +
158B GLN 3.2 0.4 - - - -
159B VAL* 1.3 75.0 - - - +
161B ILE* 1.3 67.8 + - - +
163B PHE* 3.3 8.0 + - - +
164B TYR* 3.0 26.4 - - + -
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 6.3 0.2 - - + -
134A PHE* 4.8 15.9 - - + -
149A ALA* 5.6 3.6 - - + +
153A ASN* 3.6 29.2 - - + +
157A PRO* 3.5 22.9 - - + -
160A VAL* 3.5 31.6 - - + -
161A ILE* 3.4 21.8 - - + +
164A TYR* 4.9 8.1 + - + +
157B PRO* 2.7 27.5 + - + +
158B GLN* 4.0 2.7 - - - +
160B VAL* 1.3 72.3 - - - +
162B SER* 1.3 63.3 + - - +
163B PHE 3.4 0.2 + - - -
164B TYR* 3.4 9.5 + - - +
165B GLU* 3.2 19.7 + - + +
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Residues in contact with SER 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 GLN 2.9 19.2 + - - -
159B VAL* 3.8 6.1 - - - -
161B ILE* 1.3 76.8 - - - +
163B PHE* 1.3 66.4 - - - +
165B GLU* 3.0 34.0 + - - +
166B GLU* 3.3 17.7 + - - +
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Residues in contact with PHE 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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122B ILE* 3.4 40.8 - - + -
123B ILE 3.6 2.9 - - - -
124B GLY* 3.4 42.2 - - - -
125B ALA* 5.1 0.2 - - + -
134B PHE* 4.8 2.9 - + - -
159B VAL* 2.9 15.3 + - + +
160B VAL 3.4 10.5 - - - +
161B ILE 3.3 0.2 - - - -
162B SER* 1.3 77.8 - - - +
164B TYR* 1.3 77.0 + + + +
166B GLU* 3.3 16.8 + - - +
167B ARG* 3.3 53.3 + - + +
226C LEU* 3.9 18.2 - - + -
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Residues in contact with TYR 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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161A ILE* 5.3 6.7 - - + +
164A TYR* 3.3 55.2 - + + -
165A GLU* 4.8 3.9 - - - +
168A LEU* 4.6 6.3 - - + -
125B ALA* 4.6 4.5 - - - +
132B LEU* 4.2 15.5 - - + +
134B PHE* 3.1 43.6 - + - -
160B VAL* 3.0 29.6 - - + -
161B ILE* 3.4 6.3 + - - +
162B SER 3.3 0.6 - - - -
163B PHE* 1.3 84.0 - + + +
165B GLU* 1.3 67.2 + - - +
166B GLU 3.1 0.2 + - - -
167B ARG* 3.2 4.7 + - - +
168B LEU* 3.0 27.4 + - - +
224C VAL* 3.7 25.1 - - + -
226C LEU* 4.5 13.7 - - + +
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Residues in contact with GLU 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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127A ASP* 5.1 1.0 - - - +
130A GLY 4.8 1.4 - - - +
131A GLU* 4.1 3.5 - - - -
132A LEU* 3.5 50.8 + - + +
149A ALA* 4.5 8.6 - - - +
150A LYS* 3.2 29.4 + - - +
164A TYR* 4.6 1.0 - - - -
161B ILE* 3.2 11.6 + - + +
162B SER* 3.0 28.5 + - - +
164B TYR* 1.3 78.2 - - - +
166B GLU* 1.3 62.5 + - + +
168B LEU* 3.4 14.1 - - - +
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Residues in contact with GLU 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 SER* 3.3 19.4 + - - +
163B PHE* 3.7 17.2 - - - +
164B TYR 3.1 0.6 - - - -
165B GLU* 1.3 78.7 - - + +
167B ARG* 1.3 63.3 + - + +
168B LEU 2.9 14.8 + - - +
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Residues in contact with ARG 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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122B ILE 5.6 1.0 + - - -
123B ILE 4.4 10.6 + - - -
163B PHE* 3.3 47.4 + - + +
164B TYR* 3.2 7.2 + - - +
166B GLU* 1.3 77.3 - - + +
168B LEU* 1.3 58.9 + - - +
224C VAL* 3.2 21.0 - - + +
225C VAL* 3.5 23.3 + - + +
226C LEU* 3.8 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