Contacts of the helix formed by residues 126 - 138 (chain D) in PDB entry 2B5L
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 SER 126 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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842B GLU* 6.2 0.4 - - - -
909B ILE* 4.0 6.3 - - - +
111D THR* 6.3 1.3 - - - -
113D THR* 3.5 2.3 + - - -
125D GLY* 1.3 75.9 - - - +
127D TYR* 1.3 70.5 + - - +
128D LYS* 4.3 4.2 - - - +
129D GLY* 2.7 31.3 + - - -
130D VAL* 2.9 21.7 + - - +
175D TYR* 4.9 1.3 - - - -
188D GLU* 3.4 18.0 + - - -
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Residues in contact with TYR 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841B ALA* 3.6 21.0 + - + -
842B GLU* 3.7 27.2 + - - +
909B ILE* 3.6 24.0 + - + +
910B MET* 4.6 5.4 - - + -
926B LEU* 4.1 28.9 - - + -
927B MET* 4.6 5.8 - - + -
953B TRP* 6.4 0.7 - + - -
21D LEU* 5.5 8.1 + - - +
23D THR* 3.4 35.8 + - + +
26D TYR* 6.0 2.8 - - - +
38D LEU* 5.6 3.2 - - + +
44D PRO* 5.8 2.0 - - + -
126D SER* 1.3 76.3 - - - +
128D LYS* 1.3 74.3 + - + +
130D VAL* 2.9 2.9 + - - +
131D LYS* 2.8 62.2 + - + +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841B ALA* 3.7 27.4 - - + +
842B GLU* 3.1 44.2 + - - +
44D PRO* 5.4 4.0 - - + -
47D VAL* 4.8 9.0 - - + -
126D SER* 3.3 3.5 - - - +
127D TYR* 1.3 84.5 - - + +
129D GLY* 1.3 64.9 + - - +
131D LYS* 4.2 8.5 - - - -
132D LEU* 2.8 33.6 + - + +
146D GLU* 2.8 34.2 + - - +
175D TYR* 3.3 30.3 - - + +
217D GLU* 6.0 2.2 - - - +
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Residues in contact with GLY 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D THR* 3.4 19.1 - - - -
126D SER* 2.7 28.8 + - - -
128D LYS* 1.3 77.0 - - - +
130D VAL* 1.3 55.4 + - - +
132D LEU* 3.8 1.6 - - - +
133D ALA* 3.1 22.9 + - - +
175D TYR* 4.3 7.8 - - - -
186D VAL* 3.7 11.4 - - - +
188D GLU* 4.2 5.8 - - - -
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909B ILE* 4.2 21.1 - - + -
927B MET* 4.0 26.9 - - + -
113D THR* 3.5 19.3 - - + -
115D LEU* 3.3 30.3 - - + +
123D PRO* 4.4 9.9 - - + -
124D SER 4.4 3.4 - - - +
126D SER 2.9 15.4 + - - +
127D TYR 3.6 4.9 - - - +
129D GLY* 1.3 73.6 - - - +
131D LYS* 1.3 70.8 + - + +
133D ALA* 2.9 13.9 + - - +
134D LYS* 3.2 10.8 + - - +
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Residues in contact with LYS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B MET* 5.9 2.7 - - + -
953B TRP* 5.9 3.4 - - + -
21D LEU* 5.5 1.5 - - - +
38D LEU* 3.1 46.1 - - + +
42D THR* 6.1 2.3 - - - -
44D PRO* 4.0 25.1 - - + -
127D TYR* 2.8 71.0 + - + +
128D LYS* 3.8 4.7 - - - +
130D VAL* 1.3 79.4 - - + +
132D LEU* 1.3 64.1 + - - +
133D ALA 3.0 0.5 + - - -
134D LYS* 3.2 21.4 + - - +
135D PHE* 3.2 13.5 + - - +
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE* 5.2 0.4 - - + -
44D PRO* 3.9 29.4 - - + -
47D VAL* 4.1 26.9 - - + -
128D LYS* 2.8 25.6 + - + +
129D GLY* 4.0 3.6 - - - +
131D LYS* 1.3 73.1 - - - +
133D ALA* 1.3 59.6 + - - +
135D PHE* 4.5 7.4 - - + -
136D GLY* 3.1 12.9 + - - -
144D PHE* 4.1 23.9 - - + -
175D TYR* 3.7 42.8 - - + -
177D ILE* 2.9 30.4 - - + +
186D VAL* 5.5 0.2 - - + -
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D THR* 5.2 2.2 - - + -
114D VAL* 6.2 0.2 - - - -
115D LEU* 4.1 14.6 - - + +
129D GLY 3.1 13.2 + - - +
130D VAL* 2.9 15.9 + - - +
132D LEU* 1.3 74.9 - - - +
134D LYS* 1.3 67.9 + - - +
136D GLY* 3.3 7.4 + - - -
137D LYS* 3.4 11.4 + - - +
177D ILE* 4.3 1.7 - - - +
184D VAL* 3.7 27.9 - - + +
186D VAL* 3.7 20.2 - - + -
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Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953B TRP* 4.4 23.6 - - - -
38D LEU* 4.9 17.0 + - - +
39D GLY* 6.6 0.4 - - - -
40D LYS 5.8 3.1 - - - +
115D LEU* 4.3 14.5 - - + +
117D LEU* 4.4 24.7 - - + -
130D VAL* 3.2 6.4 + - - +
131D LYS* 3.2 16.5 + - - +
133D ALA* 1.3 81.7 - - - +
135D PHE* 1.3 65.9 + - - +
136D GLY 3.0 1.4 + - - -
137D LYS* 3.2 2.6 + - - +
138D GLU* 3.1 46.4 + - - +
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 3.9 23.6 - - + -
41D ASN* 3.0 34.1 - - - -
42D THR 3.0 32.5 - - - +
43D ILE* 4.0 21.3 - - + -
44D PRO* 5.5 0.7 - - + -
83D ILE* 5.3 0.9 - - + -
131D LYS 3.2 12.7 + - - +
132D LEU* 4.4 10.1 - - + +
134D LYS* 1.3 80.9 - - - +
136D GLY* 1.3 63.3 + - - +
138D GLU* 4.8 4.3 - - - +
139D ASN* 3.4 40.1 + - - +
141D MET* 4.6 7.2 - - + -
144D PHE* 3.7 32.3 - + - -
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU 3.1 18.7 + - - -
133D ALA 3.8 2.0 - - - -
134D LYS 3.0 1.6 + - - -
135D PHE* 1.3 77.3 - - - +
137D LYS* 1.3 57.5 - - - +
139D ASN 3.0 2.8 + - - -
140D LEU* 2.9 24.8 + - - -
141D MET* 3.3 27.9 + - - -
144D PHE* 4.3 5.4 - - - -
177D ILE* 4.4 4.9 - - - -
179D TRP* 3.8 5.4 - - - -
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 4.3 22.7 - - + -
133D ALA 3.4 7.3 + - - +
134D LYS 3.2 6.8 + - - +
136D GLY* 1.3 73.4 - - - +
138D GLU* 1.3 61.3 + - + +
139D ASN 2.9 5.2 + - - -
140D LEU* 3.4 19.7 + - + +
179D TRP* 3.3 59.4 - - + +
181D GLY* 3.3 32.1 + - - +
184D VAL* 4.5 2.2 - - + -
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Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LYS* 3.8 32.3 + - - +
39D GLY 5.8 0.3 - - - +
40D LYS 4.6 11.1 - - - +
41D ASN* 4.0 10.0 + - - +
117D LEU* 5.8 6.9 - - + +
134D LYS* 3.1 37.3 + - + +
135D PHE* 3.7 4.1 + - - +
136D GLY 3.3 0.2 - - - -
137D LYS* 1.3 79.3 - - + +
139D ASN* 1.3 71.7 + - - +
140D LEU* 3.9 2.7 - - - -
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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