Contacts of the helix formed by residues 139 - 148 (chain A) in PDB entry 2ZPB
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 GLU 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ARG* 2.8 66.6 + - + +
138A ARG* 1.3 81.0 - - + +
140A PRO* 1.3 64.0 - - - +
141A ARG 3.3 0.5 + - - -
142A LYS* 3.3 24.7 + - + +
143A VAL* 3.0 20.3 + - - +
194B THR* 5.6 0.7 - - - -
195B ASP* 3.1 21.3 - - - +
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Residues in contact with PRO 140 (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 VAL* 5.3 0.7 - - + -
136A VAL* 3.2 35.4 - - + +
137A VAL 4.2 3.6 - - - +
138A ARG 3.4 7.2 - - - +
139A GLU* 1.3 89.5 - - - +
141A ARG* 1.3 57.4 + - - +
143A VAL* 4.3 0.7 - - + -
144A LEU* 2.9 37.6 + - + +
157A ILE* 3.7 30.5 - - + +
159A VAL* 3.8 12.1 - - + -
195B ASP* 3.3 6.1 - - - +
196B GLY* 3.8 21.5 - - - -
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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
----------------------------------------------------------
140A PRO* 1.3 78.4 - - - +
142A LYS* 1.3 57.5 + - - +
144A LEU* 3.9 3.1 - - - +
145A SER* 2.9 31.1 + - - -
149A THR 4.8 0.7 - - - +
151A ILE* 3.6 24.7 + - + +
152A ALA 2.9 28.1 + - - -
153A SER* 3.9 17.4 + - - +
155A ILE 3.2 19.0 + - - -
156A GLU* 5.1 1.0 - - - +
157A ILE* 3.6 29.2 - - + +
195B ASP* 3.0 42.3 + - - +
196B GLY 4.4 10.1 + - - -
197B GLY* 5.4 0.4 - - - -
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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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135A ARG* 3.8 7.7 - - - +
139A GLU* 3.3 27.8 + - + +
141A ARG* 1.3 73.7 - - - +
143A VAL* 1.3 65.2 + - - +
145A SER* 3.3 5.9 + - - -
146A GLU* 2.9 55.1 + - + +
195B ASP* 2.9 18.9 + - - +
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Residues in contact with VAL 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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132A TYR* 4.2 4.0 - - + -
135A ARG* 3.7 51.8 - - + +
136A VAL* 4.2 15.9 - - + -
139A GLU 3.0 20.3 + - - +
140A PRO* 3.9 5.8 - - + +
142A LYS* 1.3 74.8 - - - +
144A LEU* 1.3 64.7 + - + +
146A GLU* 3.2 9.9 + - - +
147A MET* 3.0 47.4 + - - +
16B VAL* 4.0 15.9 - - + -
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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
----------------------------------------------------------
104A LYS* 4.6 3.4 - - + -
106A VAL* 4.0 32.1 - - + -
136A VAL* 4.4 10.1 - - + -
140A PRO 2.9 21.6 + - - +
141A ARG* 4.0 2.9 - - - +
143A VAL* 1.3 79.3 - - + +
145A SER* 1.3 61.7 + - - +
147A MET* 3.1 8.7 + - - +
148A GLY 3.0 6.6 + - - -
149A THR* 2.8 34.9 + - + +
151A ILE* 3.9 29.4 - - + -
157A ILE* 5.0 3.6 - - + -
197A GLY 4.0 9.6 - - - +
198A VAL* 3.9 38.4 - - + +
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ARG* 2.9 20.1 + - - -
142A LYS* 3.5 8.5 - - - -
143A VAL 3.2 0.2 - - - -
144A LEU* 1.3 75.4 - - - +
146A GLU* 1.3 63.3 + - - +
148A GLY* 3.0 15.2 + - - -
149A THR 3.2 10.7 + - - -
150A GLU* 2.5 32.9 + - - +
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Residues in contact with GLU 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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135A ARG* 2.9 43.6 + - - -
142A LYS* 2.9 39.7 + - + +
143A VAL* 3.6 6.2 - - - +
145A SER* 1.3 77.0 - - - +
147A MET* 1.3 62.6 + - + +
148A GLY 3.5 0.5 + - - -
15B LYS* 3.8 49.1 + - + +
16B VAL* 4.6 2.1 + - - +
18B HIS 4.8 0.6 - - - +
19B THR* 4.2 11.3 - - - +
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Residues in contact with MET 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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126A TRP* 3.6 28.3 - - + -
132A TYR* 4.5 2.5 - - - -
143A VAL* 3.0 40.4 + - + +
144A LEU* 3.1 8.0 + - - +
146A GLU* 1.3 78.5 - - + +
148A GLY* 1.3 57.2 + - - +
198A VAL* 4.0 22.9 - - + +
16B VAL* 4.2 16.2 - - + +
18B HIS* 3.6 50.0 - - + +
19B THR* 3.3 8.0 - - - +
20B VAL* 2.8 39.1 + - + +
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Residues in contact with GLY 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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145A SER 3.0 13.3 + - - -
146A GLU 3.2 1.2 + - - -
147A MET* 1.3 79.4 - - - +
149A THR* 1.3 63.5 + - - +
150A GLU* 4.1 3.8 + - - +
20B VAL* 4.1 11.1 - - - +
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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