Contacts of the helix formed by residues 155 - 164 (chain A) in PDB entry 1SHZ
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 ASP 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A TRP* 3.5 20.0 - - + -
111A GLY 3.2 10.9 + - - -
112A ASP* 3.2 21.9 + - - +
115A ASN* 2.6 31.5 + - + +
151A ALA 3.2 5.5 + - - +
152A LEU* 3.4 17.9 - - - +
153A TRP 3.2 3.0 - - - +
154A GLU* 1.3 81.4 - - - +
156A SER* 1.3 64.3 + - - +
157A GLY* 3.1 19.8 + - - -
158A ILE* 3.5 9.2 + - + +
159A GLN* 3.5 20.3 + - - +
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Residues in contact with SER 156 (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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109A PRO 4.9 0.7 + - - -
110A TRP 4.4 0.7 + - - -
111A GLY* 3.1 22.5 - - - -
154A GLU 3.5 2.5 + - - -
155A ASP* 1.3 74.0 + - - +
157A GLY* 1.3 69.9 + - - +
159A GLN* 3.3 9.2 + - - +
160A ASN* 3.1 29.0 + - - -
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Residues in contact with GLY 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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103A ARG* 4.0 6.2 - - - +
108A ILE* 3.3 24.2 - - - +
109A PRO 3.5 25.1 - - - -
110A TRP* 4.4 1.6 - - - -
111A GLY 3.7 1.6 - - - +
155A ASP* 3.1 10.0 + - - -
156A SER* 1.3 81.9 + - - +
158A ILE* 1.3 59.6 + - - +
160A ASN* 3.3 2.5 + - - -
161A ALA* 3.3 12.6 + - - +
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Residues in contact with ILE 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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96A MET* 4.5 12.3 - - + -
99A LEU* 4.3 17.5 - - + +
100A VAL* 4.6 9.9 - - + -
103A ARG* 3.6 31.6 - - + -
110A TRP* 3.8 24.5 - - + -
152A LEU* 3.0 35.4 - - + +
153A TRP* 4.1 22.9 - - + +
155A ASP* 3.5 7.1 + - + +
156A SER 3.3 0.4 - - - -
157A GLY* 1.3 73.0 - - - +
159A GLN* 1.3 68.2 + - - +
161A ALA* 3.1 16.2 + - - +
162A TYR* 3.1 12.0 + - - +
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Residues in contact with GLN 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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153A TRP* 3.5 55.5 + - - +
154A GLU* 4.2 12.6 + - - +
155A ASP 3.5 10.2 + - - +
156A SER* 3.3 13.0 + - - +
158A ILE* 1.3 81.8 - - - +
160A ASN* 1.3 65.9 + - - +
162A TYR* 3.0 12.3 + - + +
163A ASP* 3.0 32.9 + - - +
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Residues in contact with ASN 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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108A ILE* 4.1 18.7 - - + +
156A SER* 3.1 15.8 + - - +
157A GLY* 3.7 8.7 - - - +
158A ILE 3.3 0.2 - - - -
159A GLN* 1.3 79.8 - - - +
161A ALA* 1.3 62.3 + - - +
163A ASP* 3.5 15.0 + - - +
164A ARG* 3.3 26.7 + - - +
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Residues in contact with ALA 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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99A LEU* 4.2 22.9 - - + +
102A ALA* 4.5 7.6 - - + -
103A ARG* 4.4 14.4 - - + +
106A LEU* 5.3 2.9 - - + -
108A ILE* 4.9 9.1 - - + +
157A GLY 3.3 11.3 + - - +
158A ILE* 3.1 13.7 + - - +
159A GLN 3.0 0.4 - - - -
160A ASN* 1.3 74.8 - - - +
162A TYR* 1.3 60.7 + - - +
164A ARG* 2.7 24.5 + - - +
165A ARG 3.3 7.4 + - - -
168A PHE* 3.8 9.4 - - - -
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Residues in contact with TYR 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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99A LEU* 4.3 22.3 - - + +
153A TRP* 4.6 16.4 - + + -
158A ILE 3.1 8.0 + - - +
159A GLN* 3.0 13.8 + - + +
161A ALA* 1.3 79.8 - - - +
163A ASP* 1.3 63.0 + - - +
165A ARG* 2.6 81.0 + - - +
170A LEU* 3.9 23.8 - - + -
172A GLU* 4.1 14.5 + - - +
174A VAL* 4.5 7.0 - - + -
175A LYS* 3.3 51.2 - - + +
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Residues in contact with ASP 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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159A GLN* 3.0 26.9 + - - +
160A ASN* 3.8 18.0 + - - +
161A ALA 3.0 0.6 + - - -
162A TYR* 1.3 89.5 - - - +
164A ARG* 1.3 60.6 + - + +
165A ARG* 3.3 15.1 + - - +
166A ARG* 5.1 1.2 + - - +
302A LYS* 5.2 19.7 - - - -
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Residues in contact with ARG 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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106A LEU* 3.3 37.4 + - + +
108A ILE* 3.6 28.8 - - - +
160A ASN* 3.3 14.7 + - - +
161A ALA 2.7 11.5 + - - +
163A ASP* 1.3 80.9 - - + +
165A ARG* 1.3 62.0 + - - -
166A ARG* 2.9 10.2 + - - +
167A GLU* 2.7 58.8 + - - +
168A PHE* 3.6 3.8 - - - -
266D HIS* 4.5 12.3 + - - -
308D CYS 5.9 0.4 + - - -
310D PRO* 5.2 23.0 - - + +
311D GLU* 5.8 3.4 - - - -
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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