Contacts of the helix formed by residues 140 - 151 (chain A) in PDB entry 4B23
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 LYS 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A SER* 3.0 34.7 + - - +
135A LYS 4.9 0.2 - - - -
136A ILE 3.0 11.3 + - - -
137A LYS* 4.5 0.6 - - - +
139A VAL* 1.3 88.5 + - - +
141A ARG* 1.3 68.2 + - - +
143A THR* 3.4 1.2 + - - -
144A ILE* 3.0 28.6 + - - +
8X A 3.1 35.8 + - - +
9X T 2.8 43.8 + - - +
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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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130A MET* 3.5 24.8 - - + +
134A SER* 4.7 2.2 + - - -
140A LYS* 1.3 79.0 - - + +
142A TRP* 1.3 64.2 + - - +
144A ILE 3.3 0.2 + - - -
145A GLU* 3.0 49.4 + - - +
158A MET 4.4 4.2 + - - -
160A ALA* 4.1 8.9 - - - +
161A ASP* 3.7 17.9 - - - +
181A THR* 3.6 26.4 - - - +
185A GLU* 2.7 28.3 + - - +
8X A 4.3 2.0 + - - +
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Residues in contact with TRP 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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48A ALA 3.9 3.8 - - - -
51A SER* 3.4 39.7 - - - -
52A GLN* 3.8 17.7 - - + -
140A LYS 3.5 0.8 - - - -
141A ARG* 1.3 77.9 - - - +
143A THR* 1.3 71.7 + - - +
145A GLU* 3.1 14.6 + - - +
146A MET* 3.0 54.3 + - + +
161A ASP* 3.5 20.2 + - - +
162A ASP* 2.8 42.6 + - + +
7X A 3.4 59.7 + - - +
8X A 3.6 7.1 + - - +
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.6 2.0 - - + +
48A ALA* 3.5 32.8 - - + +
49A ILE* 3.9 10.3 - - + +
52A GLN* 2.7 27.7 + - - +
139A VAL* 4.0 15.9 - - + -
140A LYS 3.8 9.2 - - - -
142A TRP* 1.3 83.0 - - - +
144A ILE* 1.3 58.3 + - - +
146A MET* 3.4 1.4 + - - -
147A TYR* 3.0 26.4 + - + +
7X A 3.6 2.4 + - - -
8X A 2.7 22.9 + - - -
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Residues in contact with ILE 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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126A GLU* 4.0 7.6 - - - +
129A LEU* 4.4 11.4 - - + +
130A MET* 3.7 41.3 - - + +
133A LEU* 3.8 19.7 - - + -
134A SER* 3.3 42.2 - - - +
139A VAL* 3.5 17.0 - - + -
140A LYS 3.0 17.0 + - - +
141A ARG 3.8 0.2 - - - +
143A THR* 1.3 73.5 - - - +
145A GLU* 1.3 56.9 + - - +
147A TYR* 3.6 7.4 - - + +
148A SER* 2.7 39.5 + - - +
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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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126A GLU* 4.5 1.3 - - - -
130A MET* 3.7 13.3 - - + +
141A ARG* 3.0 44.2 + - - +
142A TRP* 3.1 12.6 + - - +
144A ILE* 1.3 77.0 - - - +
146A MET* 1.3 66.9 + - + +
148A SER* 3.2 4.4 + - - -
149A ILE* 3.0 34.0 + - - +
157A ILE* 4.0 20.4 - - + +
158A MET 3.6 6.8 - - - +
159A PRO* 3.5 22.0 - - + +
161A ASP* 2.4 34.5 - - - +
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Residues in contact with MET 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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48A ALA* 4.4 11.4 - - + -
51A SER* 4.8 3.6 - - - +
142A TRP* 3.0 60.9 + - + +
143A THR 3.7 5.6 - - - +
145A GLU* 1.3 82.0 - - + +
147A TYR* 1.3 58.6 + - - +
149A ILE* 4.3 3.1 - - + -
150A PHE* 2.8 61.3 + - + +
159A PRO* 3.6 32.1 - - + -
203A TRP* 3.9 19.7 - - + -
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Residues in contact with TYR 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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39A HIS 5.3 0.3 + - - -
41A PRO* 3.4 36.3 - - + +
44A GLY* 3.7 22.4 - - - -
45A ILE* 3.9 8.7 - - + -
48A ALA* 4.3 11.3 - - + +
118A LYS* 5.6 1.2 - - - +
121A ILE* 3.6 15.7 - - + +
129A LEU* 4.7 1.8 - - + -
133A LEU* 4.0 29.6 - - + -
143A THR* 3.0 17.5 + - + +
144A ILE* 3.6 8.5 - - + +
146A MET* 1.3 76.3 - - - +
148A SER* 1.3 59.5 + - - +
151A THR* 3.0 45.2 + - + +
152A LEU* 3.0 56.8 + - + +
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Residues in contact with SER 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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126A GLU* 2.7 33.9 + - - -
129A LEU* 3.8 11.1 - - - +
144A ILE 2.7 21.2 + - - -
145A GLU 3.2 6.3 + - - -
147A TYR* 1.3 77.5 - - - +
149A ILE* 1.3 58.8 + - - +
152A LEU* 3.2 15.7 - - - +
153A GLY 3.0 22.3 + - - -
154A ARG* 3.0 15.2 + - - -
157A ILE* 4.0 12.6 - - - -
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Residues in contact with ILE 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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33A LEU* 4.1 16.5 - - + +
35A PRO* 3.5 10.4 - - - +
145A GLU 3.0 19.6 + - - +
146A MET* 3.8 7.2 - - + +
148A SER* 1.3 77.6 - - - +
150A PHE* 1.3 83.5 + - + +
153A GLY* 3.4 16.3 + - - -
154A ARG 4.5 5.3 - - - +
157A ILE* 3.7 33.0 - - + +
159A PRO* 4.1 20.2 - - + -
196A THR* 3.9 24.2 - - + +
199A ALA* 5.3 0.4 - - + -
203A TRP* 4.2 20.6 - - + -
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Residues in contact with PHE 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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33A LEU* 3.7 28.5 - - + -
34A THR 4.6 3.8 - - - +
35A PRO* 3.2 6.1 - - - +
36A HIS* 2.9 28.1 + - - +
56A ASP* 6.1 1.3 - - - -
146A MET* 2.8 58.2 + - + +
149A ILE* 1.3 86.0 - - + +
151A THR* 1.3 59.9 + - - +
200A TRP* 5.8 1.1 - + - -
203A TRP* 3.8 24.9 - + - -
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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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36A HIS* 3.2 17.2 + - - +
37A PRO* 2.8 32.7 - - + +
39A HIS* 4.0 22.1 + - + +
44A GLY* 3.3 24.8 + - - -
47A ARG* 5.4 2.6 - - - +
147A TYR* 3.0 42.6 + - + +
150A PHE* 1.3 80.0 + - - +
152A LEU* 1.3 68.2 + - + +
153A GLY 3.3 2.0 + - - -
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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