Contacts of the helix formed by residues 140 - 152 (chain A) in PDB entry 2Z53
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 GLY 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 1.3 76.7 - - - +
141A ILE* 1.3 61.5 + - - -
142A GLN 3.5 2.0 - - - -
143A ILE* 3.5 8.7 + - - +
144A LEU* 2.9 29.6 + - - +
172A MET* 3.4 18.7 - - - +
189A ASN 5.7 0.7 - - - -
192A ARG 4.2 12.3 - - - -
193A ALA* 4.7 2.2 - - - -
194A PHE* 4.6 5.4 - - - -
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Residues in contact with ILE 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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6A PHE* 4.2 23.1 - - + -
8A VAL* 3.5 27.8 - - + +
11A ALA* 4.0 8.3 - - + +
16A TYR* 4.9 1.3 - - + -
140A GLY* 1.3 69.5 - - - -
142A GLN* 1.3 76.1 + - + +
144A LEU* 3.3 2.8 + - - -
145A ASN* 2.9 27.2 + - - +
172A MET* 3.9 20.0 - - + -
186A VAL* 4.7 2.7 - - + -
190A PHE* 3.4 62.2 + - + +
192A ARG 5.0 1.8 + - - -
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Residues in contact with GLN 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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8A VAL 5.0 4.2 + - - -
9A GLY 5.4 4.4 + - - -
141A ILE* 1.3 88.9 + - + +
143A ILE* 1.3 60.9 + - + +
145A ASN* 3.4 18.1 + - - +
146A SER* 2.9 36.4 + - - +
191A ASN 6.1 2.2 - - - +
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Residues in contact with ILE 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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138A GLN* 3.6 47.3 - - + +
139A LEU 3.9 6.1 - - - +
140A GLY* 3.5 8.6 + - - +
141A ILE 3.3 0.4 - - - -
142A GLN* 1.3 80.0 - - + +
144A LEU* 1.3 57.5 + - - +
146A SER* 3.6 4.6 - - - -
147A ASP* 2.8 48.5 + - - +
168A VAL* 4.0 10.8 - - + -
193A ALA* 3.7 20.9 - - + -
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Residues in contact with LEU 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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6A PHE* 5.1 6.1 - - + -
8A VAL* 3.8 29.2 - - + -
54A LEU* 4.3 15.3 - - + -
140A GLY 2.9 17.8 + - - +
141A ILE* 3.3 4.5 + - - +
143A ILE* 1.3 75.5 - - - +
145A ASN* 1.3 63.9 + - - +
147A ASP* 3.2 3.0 + - - -
148A ILE* 3.0 30.5 + - + +
165A PHE* 4.0 27.4 - - + -
168A VAL* 4.0 22.0 - - + -
169A ALA* 4.3 11.9 - - + -
172A MET* 4.3 24.0 - - + -
173A VAL* 5.5 2.9 - - + -
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Residues in contact with ASN 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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8A VAL* 3.7 11.9 - - + +
9A GLY* 3.8 13.8 - - - +
56A ASP* 3.2 37.1 - - - +
57A ALA* 3.3 16.6 - - - +
141A ILE 2.9 13.6 + - - +
142A GLN* 3.5 25.3 - - - +
144A LEU* 1.3 79.3 - - - +
146A SER* 1.3 65.7 + - - +
148A ILE* 3.4 13.9 + - - +
149A GLY* 3.4 8.5 + - - -
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Residues in contact with SER 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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142A GLN* 2.9 22.7 + - - +
143A ILE* 3.6 7.4 - - - -
145A ASN* 1.3 76.7 + - - +
147A ASP* 1.4 66.4 + - - +
149A GLY* 3.1 12.6 + - - -
150A LYS* 3.4 24.0 + - - +
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Residues in contact with ASP 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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143A ILE* 2.8 36.9 + - - +
144A LEU* 3.2 5.6 + - - +
146A SER* 1.4 73.6 - - - +
148A ILE* 1.3 68.2 + - - +
150A LYS* 3.1 42.5 + - - +
151A ILE* 3.5 13.3 + - - +
161A THR* 5.5 1.6 - - + +
164A GLU* 4.1 7.6 - - - +
165A PHE* 3.7 40.9 + - + -
168A VAL* 3.9 9.5 - - - +
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Residues in contact with ILE 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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8A VAL* 4.2 16.8 - - + -
54A LEU* 3.9 31.0 - - + +
56A ASP* 3.8 28.9 - - + +
60A LYS 4.3 8.7 - - - +
61A THR 4.6 1.8 - - - -
62A ILE* 4.0 18.2 - - + -
144A LEU* 3.0 25.0 + - + +
145A ASN* 3.6 6.7 - - - +
147A ASP* 1.3 76.9 - - - +
149A GLY* 1.3 57.1 + - - +
151A ILE 3.2 1.4 + - - -
152A SER* 2.9 44.5 + - - -
165A PHE* 4.1 18.2 - - + -
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Residues in contact with GLY 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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56A ASP* 3.9 12.9 + - - -
60A LYS* 6.0 1.8 - - - -
145A ASN 3.4 5.5 + - - -
146A SER* 3.1 10.5 + - - -
148A ILE* 1.3 79.9 - - - +
150A LYS* 1.3 58.8 + - - +
151A ILE 3.3 0.4 + - - -
152A SER* 4.6 3.8 - - - +
154A VAL* 3.9 11.6 - - - +
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Residues in contact with LYS 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 SER* 3.5 20.1 - - - +
147A ASP* 3.1 33.2 + - - +
149A GLY* 1.3 77.4 - - - +
151A ILE* 1.3 60.5 + - - +
154A VAL* 3.5 20.4 - - - +
157A PHE* 4.1 9.7 - - - +
161A THR* 3.8 25.6 - - + +
164A GLU* 5.0 8.5 + - - -
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Residues in contact with ILE 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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62A ILE* 3.9 16.2 - - + -
76A TYR* 3.8 27.1 - - + +
78A ASP* 5.1 1.3 - - - +
85A ARG* 3.4 10.4 + - - +
147A ASP 3.9 9.2 - - - +
148A ILE 3.2 1.2 + - - -
149A GLY 3.3 0.4 - - - -
150A LYS* 1.3 84.4 - - - +
152A SER* 1.3 68.5 + - - +
153A GLY 3.2 1.0 + - - -
154A VAL* 3.0 19.2 + - - +
157A PHE* 3.9 19.0 - - + -
161A THR* 4.0 12.8 - - + +
162A GLU* 4.0 19.7 - - + -
165A PHE* 3.4 42.2 - - + -
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Residues in contact with SER 152 (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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60A LYS* 3.8 22.0 - - - +
61A THR 2.7 34.4 + - - -
62A ILE* 3.8 8.7 - - - +
78A ASP* 3.6 11.0 - - - +
79A LEU 4.9 3.1 + - - -
148A ILE* 2.9 28.6 + - - +
149A GLY* 4.7 4.0 - - - +
151A ILE* 1.3 73.1 - - - +
153A GLY* 1.3 62.6 + - - +
154A VAL* 3.4 6.8 + - - +
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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