Contacts of the helix formed by residues 144 - 159 (chain A) in PDB entry 4BU2
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A SER 4.4 8.8 + - - -
80A LEU* 3.7 17.5 - - - +
81A PHE* 3.8 25.4 - - + -
82A LYS* 6.2 0.4 - - - +
85A ASP* 3.0 39.8 + - + +
89A LEU* 5.3 3.6 - - + -
140A PRO* 3.0 15.4 + - + +
141A GLN 3.7 2.9 - - - +
143A PHE* 1.3 84.6 - - + +
145A ASP* 1.3 66.3 + - - +
146A GLU* 3.5 2.5 - - + +
147A LEU* 3.5 14.4 + - + +
148A TRP* 3.1 17.2 + - - +
401A ARG* 3.6 5.1 + - - -
903A EDO 3.5 28.5 + - - +
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Residues in contact with ASP 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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143A PHE 3.3 10.4 - - - +
144A LYS* 1.3 69.6 - - - +
146A GLU* 1.3 65.9 + - - +
148A TRP* 3.0 5.6 + - - +
149A ARG* 2.8 24.8 + - - +
342A TYR* 3.9 24.2 + - + +
344A ALA* 4.3 14.0 - - - +
401A ARG* 3.3 23.8 + - - +
903A EDO 2.8 28.4 + - - +
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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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35A PHE* 3.2 24.3 - - - -
76A TYR* 2.6 41.1 + - + +
79A SER* 5.4 1.6 - - - +
80A LEU* 3.5 24.5 - - + -
144A LYS* 3.5 2.8 - - + -
145A ASP* 1.3 78.6 - - - +
147A LEU* 1.3 58.3 + - - +
149A ARG* 3.2 19.8 + - - +
150A ILE* 2.9 32.1 + - - +
342A TYR* 5.3 3.5 + - - -
903A EDO 4.1 4.4 + - - +
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Residues in contact with LEU 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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80A LEU* 4.0 41.1 - - + +
81A PHE* 5.0 3.1 - - + -
140A PRO* 3.6 34.8 - - + -
141A GLN* 4.3 5.8 - - - -
144A LYS* 3.5 13.5 + - + +
145A ASP 3.2 0.8 - - - -
146A GLU* 1.3 76.9 - - - +
148A TRP* 1.3 57.3 + - - +
150A ILE* 2.9 19.2 + - + +
151A GLN* 2.7 53.2 + - - +
254A VAL* 4.4 22.2 - - + -
256A ILE* 4.8 11.2 - - + -
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Residues in contact with TRP 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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141A GLN* 3.5 17.4 - - - +
144A LYS 3.1 4.6 + - - -
145A ASP* 3.0 8.0 + - - +
147A LEU* 1.3 75.7 - - - +
149A ARG* 1.3 57.3 + - - +
152A GLU* 3.0 28.6 + - + +
339A LEU* 3.6 30.1 - - + +
340A PRO* 2.9 32.8 + - + +
341A PRO 3.3 20.0 - - - -
342A TYR* 3.6 31.0 - + - +
343A SER* 3.6 26.9 - - - -
344A ALA* 4.8 3.4 - - + -
401A ARG* 2.9 56.8 - - + +
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Residues in contact with ARG 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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35A PHE* 3.3 59.5 - - + +
145A ASP 2.8 12.0 + - - +
146A GLU* 3.3 23.7 + - - +
148A TRP* 1.3 78.6 - - - +
150A ILE* 1.3 62.6 + - - +
152A GLU* 4.0 1.8 - - - +
153A LYS* 3.6 27.0 + - - +
342A TYR* 3.2 55.3 + - + -
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Residues in contact with ILE 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* 3.9 21.3 - - + -
35A PHE* 3.8 21.5 - - + -
41A LEU* 3.6 12.0 - - + +
45A LEU* 5.1 11.2 - - + -
76A TYR* 4.0 2.5 - - - +
80A LEU* 3.9 28.7 - - + -
146A GLU 2.9 17.9 + - - +
147A LEU* 2.9 18.1 + - + +
149A ARG* 1.3 75.3 - - - +
151A GLN* 1.3 66.9 + - + +
152A GLU 3.2 0.2 + - - -
153A LYS 3.3 2.9 + - - -
154A LEU* 3.0 38.0 + - + +
188A LEU* 5.5 3.6 - - + -
256A ILE* 4.3 14.8 - - + -
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Residues in contact with GLN 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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141A GLN* 3.3 38.4 - - - +
147A LEU* 2.7 30.5 + - - +
150A ILE* 1.3 75.5 - - + +
152A GLU* 1.3 57.9 + - - +
154A LEU* 3.2 11.2 + - - +
155A GLU* 2.9 32.7 + - - +
162A VAL* 2.8 39.9 + - + +
163A GLY 3.6 7.3 - - - -
164A SER* 2.7 30.8 + - - -
256A ILE* 4.5 9.0 - - + +
339A LEU* 4.1 9.6 - - + -
404A HIS* 4.4 0.2 - - - -
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Residues in contact with GLU 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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148A TRP* 3.0 26.9 + - + +
149A ARG 4.0 3.5 - - - +
151A GLN* 1.3 76.3 - - - +
153A LYS* 1.3 71.7 + - - +
155A GLU* 3.0 18.9 + - - +
156A CYS* 3.1 27.2 + - - -
338A ARG* 4.7 0.5 + - - -
339A LEU* 4.0 11.6 - - + +
340A PRO 3.6 19.1 - - - +
341A PRO* 3.7 0.9 - - - -
342A TYR* 2.8 32.7 + - - +
371A HIS* 2.8 32.0 + - + +
901A EDO 3.2 19.4 + - - -
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Residues in contact with LYS 153 (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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35A PHE* 3.2 37.0 + - + +
36A ASP 4.7 2.2 + - - -
37A SER* 3.8 4.7 - - - +
38A PRO* 3.5 43.3 - - + +
41A LEU* 3.3 26.7 - - + -
149A ARG* 3.6 17.2 + - - +
150A ILE 3.3 2.6 + - - +
152A GLU* 1.3 86.6 + - - +
154A LEU* 1.3 57.9 + - - +
156A CYS* 3.2 7.3 + - - +
157A TYR* 2.9 28.3 + - - +
342A TYR* 5.9 1.6 - - - +
901A EDO 3.4 28.9 + - - -
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Residues in contact with LEU 154 (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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41A LEU* 4.3 13.5 - - + -
42A PHE* 3.9 22.0 - - + -
45A LEU* 4.2 18.4 - - + -
150A ILE* 3.0 32.0 + - + +
151A GLN* 3.5 11.7 - - - +
152A GLU 3.1 0.4 - - - -
153A LYS* 1.3 77.9 - - - +
155A GLU* 1.3 55.4 + - - +
157A TYR* 3.6 2.9 - - + +
158A PHE* 2.8 59.3 + - + +
162A VAL* 4.0 11.9 - - + -
186A PHE* 5.8 3.4 - - + -
256A ILE* 3.8 29.8 - - + -
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Residues in contact with GLU 155 (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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151A GLN 2.9 18.5 + - - +
152A GLU* 3.0 8.3 + - - +
154A LEU* 1.3 75.3 - - - +
156A CYS* 1.3 53.7 + - - +
159A GLY* 2.6 34.3 + - - -
160A SER 3.5 20.2 + - - +
161A LEU* 3.4 11.8 - - - +
162A VAL* 2.9 28.2 + - + +
334A PHE* 3.7 12.4 - - + -
338A ARG* 3.7 11.7 + - - +
339A LEU* 2.9 38.6 + - - +
404A HIS* 3.1 21.6 + - - -
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Residues in contact with CYS 156 (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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38A PRO* 3.7 19.5 - - + -
152A GLU* 3.1 33.4 + - - -
153A LYS* 3.4 7.6 - - - +
155A GLU* 1.3 78.5 - - - +
157A TYR* 1.3 62.5 + - - +
159A GLY* 3.8 5.4 + - - -
338A ARG* 3.5 21.8 - - - +
370A ASP* 3.5 41.0 - - + +
371A HIS* 3.9 5.8 - - - -
901A EDO 4.7 3.4 - - - -
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Residues in contact with TYR 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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38A PRO* 4.0 11.2 - - + +
39A SER* 3.3 43.6 + - - -
42A PHE* 3.4 37.4 - + + -
51A THR* 4.4 9.3 - - + +
55A PHE* 3.1 37.1 - + - -
153A LYS 2.9 15.8 + - - +
154A LEU* 3.6 7.4 - - - +
155A GLU 3.3 0.2 - - - -
156A CYS* 1.3 78.5 - - - +
158A PHE* 1.3 79.1 + + - +
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Residues in contact with PHE 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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42A PHE* 3.7 26.2 - + - -
55A PHE* 4.1 16.2 - + - -
59A TRP* 3.8 21.8 - + - -
154A LEU* 2.8 55.9 + - + +
157A TYR* 1.3 89.8 - + - +
159A GLY* 1.3 62.9 + - - +
160A SER* 3.6 10.3 + - - +
162A VAL* 4.8 1.8 - - + -
186A PHE* 4.1 19.5 - + - -
258A THR* 4.4 15.0 - - + +
259A TYR* 3.9 40.7 + + + -
262A ASN* 5.2 0.9 + - - -
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Residues in contact with GLY 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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155A GLU 2.6 19.6 + - - -
156A CYS 3.8 4.7 + - - -
157A TYR 3.5 1.6 - - - -
158A PHE* 1.3 75.0 - - - +
160A SER* 1.3 59.8 + - - +
262A ASN* 4.8 6.6 + - - +
334A PHE* 3.6 27.4 - - - +
904A EDO 4.3 1.9 + - - -
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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