Contacts of the helix formed by residues 129 - 144 (chain A) in PDB entry 2DB9
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 THR 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PRO* 4.6 17.0 - - + +
11A SER* 3.4 39.5 - - - +
12A GLN 3.1 7.4 - - - +
13A PRO* 4.5 2.7 - - + -
126A GLN* 5.3 7.9 - - - +
127A LEU 3.5 8.2 + - - +
128A PRO* 1.3 74.3 - - - +
130A LEU* 1.3 54.6 + - - +
131A ASP* 2.6 7.3 + - - +
132A GLU* 2.5 47.7 + - - +
133A ILE* 2.8 11.1 + - - -
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Residues in contact with LEU 130 (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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11A SER* 4.5 2.4 - - - +
12A GLN* 2.6 64.2 + - + +
14A VAL* 3.7 13.5 - - - -
15A SER* 3.9 9.0 - - - +
19A GLU* 3.2 48.3 - - + +
129A THR* 1.3 70.0 - - - +
131A ASP* 1.3 60.3 + - - +
133A ILE* 3.7 5.3 - - + +
134A ASN* 3.1 23.9 + - - +
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Residues in contact with ASP 131 (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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9A PRO* 4.7 18.0 - - + +
11A SER* 3.6 24.5 + - - +
129A THR* 2.6 7.9 + - - +
130A LEU* 1.3 73.7 - - - +
132A GLU* 1.3 60.8 + - + +
134A ASN* 3.4 5.3 + - - +
135A LYS* 2.8 51.2 + - + +
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Residues in contact with GLU 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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9A PRO* 6.2 2.9 - - + -
45A GLY 5.5 3.1 - - - +
65A GLU* 5.3 4.7 - - - +
128A PRO* 4.7 14.3 - - + +
129A THR* 2.5 30.2 + - - +
131A ASP* 1.3 73.4 - - + +
133A ILE* 1.3 55.9 + - - +
135A LYS* 4.2 7.9 - - + -
136A LYS* 2.5 45.1 + - + +
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Residues in contact with ILE 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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14A VAL* 2.9 37.0 - - + -
19A GLU* 2.8 44.6 - - + +
20A LEU* 3.8 0.4 - - - -
22A ARG* 4.1 7.4 - - + -
23A VAL* 2.8 37.1 - - + +
128A PRO* 3.6 15.9 - - + +
129A THR 2.8 20.3 + - - +
130A LEU* 3.7 8.7 - - - +
132A GLU* 1.3 76.4 - - - +
134A ASN* 1.3 53.0 + - - +
136A LYS* 4.5 0.9 - - - -
137A GLU* 2.6 32.2 + - + +
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Residues in contact with ASN 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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19A GLU* 5.1 1.4 + - - +
22A ARG* 4.8 18.4 - - - +
130A LEU 3.1 18.0 + - - +
131A ASP* 3.6 5.2 - - - +
133A ILE* 1.3 73.8 - - - +
135A LYS* 1.3 60.5 + - + +
137A GLU* 2.9 6.7 + - - +
138A LEU* 2.6 62.9 + - - +
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Residues in contact with LYS 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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131A ASP* 2.8 42.2 + - + +
132A GLU* 3.8 7.6 - - + +
134A ASN* 1.3 76.4 - - + +
136A LYS* 1.3 65.4 + - - +
138A LEU* 3.3 10.4 + - - +
139A SER* 3.3 13.2 + - - -
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Residues in contact with LYS 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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23A VAL* 3.9 11.2 - - + -
41A LYS 4.0 2.2 + - - -
42A THR* 2.9 35.1 + - + +
44A THR 3.2 15.3 + - - -
45A GLY* 4.1 16.8 - - - +
46A CYS* 3.6 12.1 - - - -
132A GLU* 2.5 31.7 + - + +
133A ILE* 3.7 2.2 - - - +
135A LYS* 1.3 72.2 - - - +
137A GLU* 1.3 53.7 + - - +
139A SER* 2.5 48.4 + - - -
140A ILE* 3.2 19.8 + - + -
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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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22A ARG* 2.4 43.4 - - + +
23A VAL* 3.2 11.5 - - + +
29A LYS* 5.3 1.6 + - - -
133A ILE 2.6 24.1 + - - +
134A ASN* 3.3 8.3 - - - +
136A LYS* 1.3 72.3 - - - +
138A LEU* 1.3 56.7 + - + +
139A SER 2.6 1.4 + - - -
140A ILE* 2.5 61.7 + - - +
141A LYS* 3.0 43.8 + - + +
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Residues in contact with LEU 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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134A ASN* 2.6 57.8 + - - +
135A LYS* 3.4 13.5 - - - +
137A GLU* 1.3 73.3 - - + +
139A SER* 1.3 59.6 + - - +
141A LYS* 3.7 27.0 + - + +
142A GLU* 3.3 31.6 + - + +
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Residues in contact with SER 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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42A THR* 4.6 10.8 + - - +
135A LYS 3.3 6.6 + - - -
136A LYS* 2.5 40.7 + - - -
137A GLU 2.6 0.2 + - - -
138A LEU* 1.3 71.1 - - - +
140A ILE* 1.3 53.3 + - - -
142A GLU* 3.4 7.7 + - - +
143A ALA* 2.8 36.3 + - - +
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Residues in contact with ILE 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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23A VAL* 4.5 5.2 - - + -
25A LEU* 4.6 3.8 - - + -
29A LYS* 3.9 20.4 - - + +
33A TRP* 3.3 39.6 - - + -
42A THR* 4.6 1.6 - - + -
46A CYS* 3.7 12.6 - - - -
136A LYS* 3.2 45.7 + - + +
137A GLU* 2.5 51.3 + - - +
139A SER* 1.3 73.1 - - - +
141A LYS* 1.3 65.2 + - + +
143A ALA* 3.2 4.0 - - - +
144A SER 3.0 21.4 + - - +
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Residues in contact with LYS 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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22A ARG* 5.7 4.8 - - - +
137A GLU* 3.0 58.6 + - - +
138A LEU* 3.8 30.5 - - + +
140A ILE* 1.3 76.5 - - + +
142A GLU* 1.3 66.0 + - + +
144A SER 3.0 12.0 + - - -
145A GLY* 3.1 22.1 + - - +
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Residues in contact with GLU 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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138A LEU* 3.3 19.0 + - + +
139A SER* 3.8 7.1 + - - +
141A LYS* 1.3 81.2 - - + +
143A ALA* 1.3 66.6 + - - +
144A SER* 3.2 0.9 + - - -
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Residues in contact with ALA 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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33A TRP* 4.2 9.0 - - + -
36A MET* 4.2 1.4 - - - +
38A PHE* 3.4 45.0 - - + -
42A THR* 4.1 13.5 - - + +
139A SER 2.8 23.0 + - - +
140A ILE* 3.2 10.8 - - - +
142A GLU* 1.3 75.0 - - - +
144A SER* 1.3 68.9 + - - +
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Residues in contact with SER 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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29A LYS* 4.7 6.9 - - - +
32A ARG* 5.9 3.0 - - - +
33A TRP* 3.5 32.4 + - - -
36A MET* 4.0 13.7 - - - +
140A ILE* 3.0 8.2 + - - +
141A LYS 3.0 6.0 + - - -
142A GLU 4.0 0.9 - - - -
143A ALA* 1.3 86.4 + - - +
145A GLY* 1.3 57.7 + - - +
146A PRO* 4.1 5.1 - - - +
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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