Contacts of the helix formed by residues 140 - 151 (chain A) in PDB entry 1ZHH
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 HIS 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.8 19.8 - - + +
116A GLN* 3.1 41.4 + - + -
117A SER* 5.0 2.0 + - - -
120A LEU* 4.1 11.8 - - + +
133A PHE* 3.7 19.3 - + + -
135A LEU* 3.5 36.8 - - + +
136A ASP 3.1 25.0 + - - +
137A THR 3.9 3.8 - - - -
139A ARG* 1.3 87.3 - - + +
141A ARG* 1.3 63.4 + - - +
142A LYS 3.3 3.1 - - - +
143A PHE* 3.1 17.7 + - + +
144A VAL* 3.1 14.2 + - - +
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Residues in contact with ARG 141 (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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28A TYR* 3.6 22.8 + - - -
137A THR* 3.0 28.7 + - - +
138A THR* 3.2 21.8 + - + +
139A ARG 3.4 1.6 + - - -
140A HIS* 1.3 76.7 - - - +
142A LYS* 1.3 63.3 + - - +
144A VAL* 3.3 3.6 - - - +
145A GLU* 3.0 62.9 + - - +
164A VAL* 4.0 22.1 - - - +
166A GLU* 3.4 27.3 + - - -
167A TRP* 3.6 19.0 - - - -
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Residues in contact with LYS 142 (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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139A ARG 5.2 0.6 + - - +
140A HIS* 3.3 1.2 - - - -
141A ARG* 1.3 78.7 - - - +
143A PHE* 1.3 61.2 + - - +
145A GLU* 3.9 5.3 - - - +
146A HIS* 3.0 25.9 + - + +
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Residues in contact with PHE 143 (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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72A VAL* 5.2 0.2 - - + -
117A SER* 5.9 2.0 - - - +
120A LEU* 3.7 50.3 - - + -
121A MET* 6.2 0.4 - - - -
123A ALA* 4.5 4.3 - - + -
124A LEU* 4.0 25.1 - - + -
131A LEU* 4.1 20.6 - - + -
133A PHE* 3.6 40.2 - + + -
140A HIS* 3.1 12.6 + - + +
142A LYS* 1.3 78.3 - - - +
144A VAL* 1.3 62.7 + - + +
146A HIS* 3.2 11.4 + + + +
147A VAL* 3.0 46.9 + - + +
155A LEU* 5.8 0.2 - - + -
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Residues in contact with VAL 144 (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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133A PHE* 3.7 40.4 - - + -
137A THR* 4.1 9.6 - - + +
140A HIS 3.1 10.2 + - - +
141A ARG* 3.3 17.9 - - - +
143A PHE* 1.3 79.7 - - + +
145A GLU* 1.3 60.1 + - - +
147A VAL* 3.3 7.9 + - - +
148A LEU* 3.1 31.6 + - - +
155A LEU* 4.1 13.7 - - + +
157A LEU* 4.2 11.9 - - + -
167A TRP* 3.8 27.1 - - + -
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Residues in contact with GLU 145 (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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141A ARG* 3.0 51.6 + - - +
142A LYS* 4.1 4.8 - - - +
144A VAL* 1.3 73.6 - - - +
146A HIS* 1.3 59.5 + - - +
148A LEU* 3.4 6.4 + - + +
149A ASP* 2.9 47.7 + - - +
166A GLU* 3.8 12.2 - - - +
167A TRP* 3.0 31.4 + - + +
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Residues in contact with HIS 146 (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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124A LEU* 4.6 21.6 - - + +
142A LYS* 3.0 16.4 + - + +
143A PHE* 3.3 13.9 - + + +
145A GLU* 1.3 75.3 - - - +
147A VAL* 1.3 61.9 + - + +
149A ASP* 4.8 0.4 - - - -
150A SER* 2.8 63.2 + - - -
151A THR* 3.9 15.8 - - + +
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Residues in contact with VAL 147 (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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124A LEU* 4.5 9.2 - - + -
131A LEU* 4.5 8.3 - - + -
143A PHE* 3.0 48.8 + - + +
144A VAL* 3.3 8.9 + - - +
146A HIS* 1.3 77.1 - - + +
148A LEU* 1.3 62.7 + - - +
151A THR* 2.6 32.1 + - + +
153A THR* 3.5 33.6 - - + +
155A LEU* 4.0 30.5 - - + -
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Residues in contact with LEU 148 (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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144A VAL 3.1 20.2 + - - +
145A GLU* 3.8 5.6 - - - +
146A HIS 3.2 0.2 - - - -
147A VAL* 1.3 79.5 - - + +
149A ASP* 1.3 66.1 + - - +
150A SER 3.8 0.2 + - - -
151A THR 4.8 3.1 - - - +
155A LEU* 4.0 17.9 - - + +
167A TRP* 3.7 50.0 - - + +
170A HIS* 3.1 47.0 + - + +
171A GLN 4.2 1.8 - - - +
172A PRO* 3.8 30.7 - - + -
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Residues in contact with ASP 149 (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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145A GLU* 2.9 32.1 + - - +
146A HIS* 4.8 0.4 - - - -
148A LEU* 1.3 83.4 - - - +
150A SER* 1.3 66.2 + - - +
151A THR 3.9 0.9 - - - -
170A HIS* 5.1 2.8 + - - +
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Residues in contact with SER 150 (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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146A HIS* 2.8 40.3 + - - -
149A ASP* 1.3 90.3 + - - +
151A THR* 1.3 65.1 + - - +
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Residues in contact with THR 151 (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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124A LEU* 4.6 15.5 - - + -
146A HIS* 3.8 17.5 - - + +
147A VAL* 2.6 40.9 + - + +
148A LEU 4.8 3.3 - - - +
149A ASP 3.9 0.5 - - - -
150A SER* 1.3 85.3 + - - +
152A ASN* 1.3 61.4 + - - +
153A THR* 3.5 24.4 + - - +
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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