Contacts of the helix formed by residues 131 - 146 (chain A) in PDB entry 2ABJ
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 ASP 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 3.1 35.8 + - + +
23A PHE* 4.9 0.5 - - - -
130A PHE* 1.3 75.9 - - - +
132A LYS* 1.3 63.2 + - - +
133A GLU* 3.0 23.7 + - - +
134A GLU* 3.3 22.6 + - + +
135A LEU 3.1 18.2 + - - -
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Residues in contact with LYS 132 (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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112A ASN* 5.7 0.4 - - - +
115A MET* 3.3 50.0 - - + +
116A ASP* 2.9 29.4 + - - +
119A TYR* 3.7 36.5 - - + +
120A ARG* 5.8 1.4 - - - +
130A PHE* 4.0 10.8 - - + -
131A ASP* 1.3 73.4 + - - +
133A GLU* 1.3 63.6 + - + +
135A LEU 3.6 0.3 + - - -
136A LEU* 3.1 26.3 + - - +
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Residues in contact with GLU 133 (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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112A ASN* 2.8 31.4 + - - +
131A ASP* 3.0 11.0 + - - +
132A LYS* 1.3 78.0 - - + +
134A GLU* 1.3 61.5 + - + +
136A LEU* 3.5 13.1 + - - +
137A GLU* 3.0 28.6 + - - +
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Residues in contact with GLU 134 (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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22A THR* 4.3 1.8 - - + +
23A PHE* 3.5 26.5 - - + +
24A LYS* 3.8 18.2 + - + +
25A ALA* 2.6 38.3 + - - +
26A LYS* 4.3 1.6 + - - +
131A ASP* 3.3 29.3 + - + +
133A GLU* 1.3 75.8 - - - +
135A LEU* 1.3 65.1 + - - +
137A GLU* 3.3 4.9 + - - +
138A CYS* 3.0 26.9 + - - -
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Residues in contact with LEU 135 (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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23A PHE* 3.8 22.8 - - + -
56A LEU* 4.1 12.8 - - + -
115A MET* 3.8 15.5 - - + -
118A MET* 3.7 26.5 - - + -
130A PHE* 3.4 28.3 - - + -
131A ASP 3.1 13.7 + - - +
132A LYS 3.9 3.1 - - - +
133A GLU 3.4 0.2 - - - -
134A GLU* 1.3 71.9 - - - +
136A LEU* 1.3 66.8 + - - +
138A CYS* 3.1 2.4 + - - +
139A ILE* 2.9 37.8 + - + +
162A PRO* 5.3 0.4 - - + -
181A LEU* 3.8 27.6 - - + -
183A VAL* 4.6 1.3 - - + -
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Residues in contact with LEU 136 (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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96A LEU* 5.9 0.7 - - + -
108A LEU* 4.1 14.8 - - + -
111A PRO* 3.8 33.9 - - + -
112A ASN* 3.5 35.7 - - - +
115A MET* 3.9 16.0 - - + -
132A LYS 3.1 18.1 + - - +
133A GLU* 3.6 15.9 - - - +
134A GLU 3.3 0.2 - - - -
135A LEU* 1.3 77.2 - - - +
137A GLU* 1.3 56.7 + - - +
139A ILE* 3.3 7.7 + - + +
140A GLN* 2.9 42.1 + - + +
381A ILE* 5.3 4.0 - - + -
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Residues in contact with GLU 137 (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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25A ALA* 3.5 25.8 - - + -
133A GLU 3.0 16.9 + - - +
134A GLU* 3.3 2.0 + - - +
135A LEU 3.2 0.2 - - - -
136A LEU* 1.3 73.7 - - - +
138A CYS* 1.3 60.0 + - - +
140A GLN* 3.4 6.1 + - - +
141A GLN* 2.8 59.6 + - + +
384A SER* 2.9 25.0 + - - -
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Residues in contact with CYS 138 (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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23A PHE* 4.1 14.6 - - - -
25A ALA* 3.9 21.3 - - - -
28A LEU* 4.1 13.2 - - - -
56A LEU* 3.8 25.4 - - + +
69A PRO* 4.0 24.5 - - - -
71A ILE* 4.1 4.3 - - - +
134A GLU 3.0 18.5 + - - -
135A LEU* 3.1 9.1 + - - +
137A GLU* 1.3 72.6 - - - +
139A ILE* 1.3 61.6 + - - +
141A GLN* 3.4 3.1 + - - +
142A LEU* 3.0 26.5 + - - +
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Residues in contact with ILE 139 (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 LEU* 5.0 0.9 - - + -
96A LEU* 5.1 4.9 - - + -
108A LEU* 5.0 9.2 - - + -
115A MET* 3.8 30.3 - - + -
135A LEU* 2.9 28.0 + - + +
136A LEU* 3.6 10.3 - - + +
138A CYS* 1.3 73.3 - - - +
140A GLN* 1.3 60.9 + - - +
142A LEU* 3.1 8.9 + - + +
143A VAL* 2.9 38.5 + - + +
160A ILE* 3.9 28.5 - - + -
162A PRO* 4.2 19.3 - - + -
183A VAL* 4.1 21.1 - - + -
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Residues in contact with GLN 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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108A LEU* 4.0 24.1 - - + +
111A PRO* 5.9 0.2 - - - +
136A LEU* 2.9 38.8 + - + +
137A GLU* 3.4 12.6 - - - +
139A ILE* 1.3 76.6 - - - +
141A GLN* 1.3 51.8 + - - +
143A VAL* 3.4 2.0 + - - -
144A LYS* 2.8 32.4 + - - +
381A ILE* 4.0 18.8 - - - +
382A VAL 4.2 1.5 + - - +
383A LEU* 3.3 30.3 - - - +
384A SER* 3.0 48.7 + - - +
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Residues in contact with GLN 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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25A ALA* 5.7 0.4 - - + -
28A LEU* 3.7 25.4 - - + -
71A ILE* 3.8 8.1 - - + +
137A GLU* 2.8 44.7 + - + +
138A CYS 3.7 5.4 - - - +
139A ILE 3.2 0.2 - - - -
140A GLN* 1.3 75.8 - - - +
142A LEU* 1.3 57.5 + - - +
144A LYS* 3.7 27.0 + - - +
145A LEU* 3.1 28.1 + - - +
384A SER* 3.9 16.4 - - - -
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Residues in contact with LEU 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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54A HIS* 3.7 39.0 - - + +
55A MET* 3.9 9.9 - - - +
56A LEU* 3.9 7.2 - - + +
71A ILE* 3.6 18.3 - - + +
138A CYS 3.0 14.3 + - - +
139A ILE* 3.5 9.0 - - - +
141A GLN* 1.3 75.2 - - - +
143A VAL* 1.3 64.8 + - + +
145A LEU* 3.3 4.2 + - - +
146A ASP* 3.1 20.8 + - - +
183A VAL* 3.6 46.0 - - + +
185A LEU* 3.7 21.5 - - + -
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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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98A ALA* 4.0 21.5 - - + -
106A ILE* 4.5 0.2 - - + -
108A LEU* 5.0 4.9 - - + -
139A ILE* 2.9 26.2 + - + +
140A GLN* 3.8 4.0 - - - +
142A LEU* 1.3 68.8 - - - +
144A LYS* 1.3 54.3 + - - +
146A ASP 3.2 0.9 + - - -
147A GLN* 2.7 38.6 + - - -
150A VAL* 4.3 13.0 - - + -
158A LEU* 4.4 4.3 - - + -
160A ILE* 4.0 20.4 - - + -
185A LEU* 3.9 31.0 - - + -
383A LEU* 4.2 20.9 - - + -
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Residues in contact with LYS 144 (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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140A GLN 2.8 22.5 + - - +
141A GLN* 3.7 27.6 + - - +
143A VAL* 1.3 74.0 - - - +
145A LEU* 1.3 62.4 + - - +
147A GLN* 3.0 37.8 - - - +
383A LEU* 3.8 18.1 - - + +
384A SER 3.6 24.7 + - - +
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Residues in contact with LEU 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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30A VAL* 4.3 20.2 - - + -
32A PRO* 5.3 7.6 - - + -
54A HIS* 3.7 35.3 - - + +
71A ILE* 3.7 26.5 - - + -
141A GLN 3.1 17.8 + - - +
142A LEU* 3.7 5.6 - - - +
143A VAL 3.2 0.2 - - - -
144A LYS* 1.3 79.0 - - - +
146A ASP* 1.3 60.9 + - - +
147A GLN* 3.4 1.5 + - - +
148A GLU 5.3 0.2 + - - -
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Residues in contact with ASP 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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52A THR* 2.8 25.2 + - - +
53A ASP* 3.9 5.9 - - - +
54A HIS* 2.7 50.7 + - - +
142A LEU 3.1 14.5 + - - +
143A VAL* 3.2 2.7 - - - -
145A LEU* 1.3 77.6 - - - +
147A GLN* 1.3 52.2 + - - +
148A GLU* 3.2 3.4 - - - -
149A TRP* 2.8 50.8 + - + +
150A VAL 4.1 0.7 + - - -
158A LEU* 4.6 3.1 - - - +
185A LEU* 3.9 14.4 - - + +
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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