Contacts of the helix formed by residues 156 - 167 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.4 34.8 - - + -
119A PRO* 4.7 4.7 - - + -
136A MET* 4.7 2.0 - - - -
152A ALA 3.1 6.6 + - - -
153A ASN 3.8 1.3 - - - -
154A VAL 3.3 0.2 - - - -
155A LYS* 1.3 82.6 - - - +
157A PRO* 1.3 70.5 - - - +
158A GLN* 3.2 3.8 - - + +
159A VAL* 3.2 41.0 + - + +
160A VAL* 3.3 15.3 + - - +
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Residues in contact with PRO 157 (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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153A ASN 2.9 22.6 - - - +
154A VAL* 4.1 7.2 - - - +
156A CYS* 1.3 81.4 - - - +
158A GLN* 1.3 61.7 + - + +
160A VAL* 3.0 11.2 - - + +
161A ILE* 2.8 40.2 + - + +
157B PRO* 3.5 27.4 - - + -
161B ILE* 3.5 15.7 - - + -
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Residues in contact with GLN 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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156A CYS* 3.2 1.7 - - + -
157A PRO* 1.3 84.1 - - + +
159A VAL* 1.3 63.9 + - + +
161A ILE* 4.2 7.9 - - - +
162A SER* 3.2 32.7 + - - +
165A GLU* 5.7 1.8 + - - -
153B ASN* 4.0 30.8 + - - +
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Residues in contact with VAL 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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119A PRO* 4.1 27.6 - - + -
121A ARG* 6.1 2.0 - - - -
122A ILE* 4.1 22.4 - - + +
136A MET* 4.5 2.0 - - + -
156A CYS* 3.2 36.3 + - + -
157A PRO 3.2 0.8 - - - -
158A GLN* 1.3 78.2 - - + +
160A VAL* 1.3 66.3 + - - +
162A SER* 3.4 5.5 + - - -
163A PHE* 3.0 21.1 + - - +
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Residues in contact with VAL 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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122A ILE* 4.0 19.3 - - + -
134A PHE* 4.2 26.2 - - + -
136A MET* 5.5 2.9 - - - -
152A ALA* 4.6 13.7 - - + +
153A ASN* 4.8 1.6 - - - +
156A CYS* 3.3 12.5 + - - +
157A PRO* 3.0 16.6 - - + +
159A VAL* 1.3 72.3 - - - +
161A ILE* 1.3 76.7 + - - +
163A PHE* 3.0 11.1 + - - +
164A TYR* 2.9 30.3 - - + -
161B ILE* 3.5 34.8 - - + -
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Residues in contact with ILE 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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157A PRO* 2.8 33.2 + - + +
158A GLN* 4.2 8.1 - - - +
160A VAL* 1.3 75.2 - - - +
162A SER* 1.3 62.7 + - - +
164A TYR* 3.4 10.8 + - - +
165A GLU* 3.2 29.5 + - + +
134B PHE* 5.1 8.1 - - + -
149B ALA* 6.1 2.2 - - + +
153B ASN* 4.1 22.2 - - + -
157B PRO* 4.0 16.4 - - + -
160B VAL* 3.5 31.9 - - + -
161B ILE* 3.4 26.7 - - + +
164B TYR* 5.3 5.9 - - + +
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Residues in contact with SER 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 GLN* 3.2 24.8 + - - +
159A VAL* 3.6 6.1 - - - -
160A VAL 3.2 0.8 - - - -
161A ILE* 1.3 76.2 - - - +
163A PHE* 1.3 66.2 + - - +
165A GLU* 3.1 36.0 + - - +
166A GLU* 3.5 8.5 + - - +
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Residues in contact with PHE 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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122A ILE* 3.1 67.1 - - + -
123A ILE* 4.5 2.0 - - - -
124A GLY 4.6 4.3 - - - -
125A ALA* 4.9 4.3 - - + -
134A PHE* 5.2 2.7 - + - -
159A VAL 3.0 12.6 + - - +
160A VAL 3.0 10.7 + - - +
162A SER* 1.3 76.1 - - - +
164A TYR* 1.3 77.1 + + - +
166A GLU* 3.1 36.0 - - - +
167A ARG* 3.2 39.0 + - + +
222C PRO* 3.8 36.8 - - + -
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Residues in contact with TYR 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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132A LEU* 3.0 17.0 - - - +
134A PHE* 2.9 43.9 - + - -
160A VAL* 2.9 31.9 + - + -
161A ILE* 3.8 8.1 - - - +
162A SER 3.3 0.4 - - - -
163A PHE* 1.3 84.5 - + + +
165A GLU* 1.3 68.1 + - - +
167A ARG* 3.1 25.7 + - + +
168A LEU* 3.3 7.6 + - - +
161B ILE* 4.9 10.3 + - + -
164B TYR* 3.3 48.0 - + + -
165B GLU* 4.6 1.1 - - - -
168B LEU* 3.8 24.0 - - + +
222C PRO* 6.2 1.3 - - + -
224C VAL* 3.3 22.6 - - + +
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Residues in contact with GLU 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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158A GLN* 5.7 1.7 + - - -
161A ILE* 3.2 22.3 - - + +
162A SER* 3.1 29.4 + - - +
164A TYR* 1.3 78.9 - - - +
166A GLU* 1.3 62.5 + - - +
168A LEU* 3.1 20.1 - - - +
132B LEU* 3.6 33.1 + - + +
134B PHE* 6.0 0.9 - - + -
149B ALA* 4.1 18.2 - - - +
150B LYS* 5.3 5.0 + - - -
164B TYR* 5.0 5.4 - - - +
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Residues in contact with GLU 166 (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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162A SER* 3.5 4.8 + - - +
163A PHE* 3.1 44.4 - - - +
165A GLU* 1.3 75.2 - - - +
167A ARG* 1.3 71.8 + - + +
168A LEU* 2.8 15.7 + - - +
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Residues in contact with ARG 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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122A ILE 5.1 3.8 + - - -
123A ILE* 5.4 7.3 - - - +
163A PHE* 3.2 50.3 + - + +
164A TYR* 3.1 13.2 + - + +
166A GLU* 1.3 86.5 + - + +
168A LEU* 1.3 57.3 + - - +
221C VAL* 3.1 27.9 - - - +
222C PRO* 3.0 29.2 - - + +
223C VAL* 3.1 9.2 - - - -
224C VAL* 2.9 24.9 + - + +
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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