Contacts of the helix formed by residues 119 - 131 (chain A) in PDB entry 2BKE
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLY 3.1 4.8 - - - -
118A SER* 1.3 77.6 - - - +
120A LYS* 1.3 61.0 + - - +
121A THR 3.4 1.8 - - - -
122A GLN* 3.7 15.6 - - - +
123A LEU* 3.0 34.7 + - - +
287A LEU* 3.7 6.3 - - - -
312A PHE* 5.0 1.9 - - - -
314A LEU* 4.0 13.2 - - - +
319A ILE* 4.7 0.5 - - - +
1325A CL 3.3 9.8 - - - +
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Residues in contact with LYS 120 (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 PHE* 3.8 22.7 - - + +
114A GLY 3.5 20.6 - - - +
115A GLU 3.5 2.0 + - - -
116A PHE* 3.5 24.2 - - - +
117A GLY 3.8 5.1 - - - +
118A SER* 3.5 11.2 - - - +
119A GLY* 1.3 80.3 - - - +
121A THR* 1.3 69.6 + - - +
122A GLN 3.5 0.2 + - - -
123A LEU* 3.5 8.3 + - - +
124A CYS* 3.4 17.7 + - - -
210A ASP* 4.5 0.7 - - - +
211A SER* 5.3 2.2 - - - -
254A THR* 3.6 22.5 - - + +
255A ASN 3.6 21.5 - - - +
256A GLN* 3.3 30.8 + - - +
287A LEU* 3.5 16.2 - - + +
1325A CL 4.1 5.0 - - + +
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Residues in contact with THR 121 (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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120A LYS* 1.3 83.8 + - - +
122A GLN* 1.3 60.2 + - - +
124A CYS* 3.4 8.5 + - - +
125A HIS* 2.7 42.0 + - + -
146A TYR* 3.4 20.9 - - - +
152A THR* 3.5 20.0 + - - +
157A ARG* 5.8 2.0 - - - +
210A ASP* 2.8 29.0 + - - +
1325A CL 3.4 15.1 - - - +
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Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY* 6.1 2.0 - - - -
119A GLY* 3.7 14.1 - - - +
120A LYS 3.3 0.4 - - - -
121A THR* 1.3 76.0 - - - +
123A LEU* 1.3 65.9 + - - +
125A HIS* 3.5 5.5 + - - +
126A GLN 3.2 15.6 + - - -
157A ARG* 3.1 48.0 + - - +
161A MSE 3.5 18.2 - - + +
314A LEU* 4.0 24.9 - - + +
315A THR 5.2 5.0 - - - +
318A GLY* 5.6 0.9 - - - -
319A ILE* 3.5 14.4 - - + +
1325A CL 3.8 16.6 - - + -
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Residues in contact with LEU 123 (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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91A THR* 4.0 18.8 - - + +
96A LEU* 4.0 23.6 - - + -
112A PHE* 3.6 46.4 - - + -
119A GLY 3.0 21.5 + - - +
120A LYS 3.7 5.2 - - - +
122A GLN* 1.3 75.2 - - - +
124A CYS* 1.3 53.9 + - - +
126A GLN* 3.0 4.7 + - + +
127A LEU* 2.8 49.4 + - + +
252A ILE* 6.3 0.2 - - + -
287A LEU* 4.5 7.9 - - + -
312A PHE* 5.0 4.0 - - + -
319A ILE* 3.4 27.5 - - + +
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Residues in contact with CYS 124 (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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120A LYS 3.4 16.4 + - - -
121A THR* 3.5 7.2 - - - +
122A GLN 3.3 0.6 - - - -
123A LEU* 1.3 78.0 - - - +
125A HIS* 1.3 59.4 + - - +
127A LEU* 3.4 5.1 + - - +
128A SER* 2.7 33.6 + - - -
146A TYR* 3.4 22.7 - - + +
208A VAL* 4.1 22.5 - - + +
210A ASP* 3.8 16.2 - - - -
252A ILE* 4.6 7.9 - - - -
254A THR* 3.6 22.0 - - - -
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Residues in contact with HIS 125 (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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121A THR* 2.7 44.4 + - + -
122A GLN 3.7 4.9 - - - +
124A CYS* 1.3 79.3 - - - +
126A GLN* 1.3 65.8 + - - +
128A SER* 3.1 11.6 + - - -
129A VAL* 3.3 8.8 + - - +
146A TYR* 3.5 14.3 - + - -
152A THR 4.0 8.7 - - - -
153A PHE* 3.6 11.6 - + - -
154A ARG 3.1 41.0 + - - -
157A ARG* 3.7 24.1 + - + -
158A ILE* 3.3 26.5 - - + +
161A MSE 3.7 20.2 - - + -
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Residues in contact with GLN 126 (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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91A THR* 3.3 26.2 - - - +
122A GLN 3.2 10.8 + - - +
123A LEU* 3.0 10.0 + - + +
125A HIS* 1.3 78.1 - - - +
127A LEU* 1.3 58.9 + - + +
129A VAL* 2.9 12.7 + - - +
130A ASN* 2.8 51.3 + - - +
161A MSE 3.4 25.6 - - + +
165A LEU* 4.6 5.3 - - - +
318A GLY* 3.1 13.1 - - - -
319A ILE* 2.8 32.9 + - + +
320A ARG* 3.4 20.7 + - - +
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Residues in contact with LEU 127 (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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89A ILE* 3.9 17.2 - - + +
90A SER 3.3 29.6 - - - +
91A THR* 4.2 5.8 - - + -
104A ILE* 3.8 22.7 - - + -
112A PHE* 4.8 2.2 - - + -
123A LEU* 2.8 43.9 + - + +
124A CYS 3.9 3.6 - - - +
126A GLN* 1.3 72.9 - - + +
128A SER* 1.3 57.7 + - - +
130A ASN* 4.0 3.4 - - + -
131A VAL* 2.9 34.3 + - - +
206A LEU* 4.1 14.1 - - + -
252A ILE* 3.2 31.0 - - + -
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Residues in contact with SER 128 (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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124A CYS 2.7 17.2 + - - -
125A HIS* 3.1 11.2 + - - -
127A LEU* 1.3 75.6 - - - +
129A VAL* 1.3 52.7 + - - +
131A VAL* 3.3 9.5 - - - +
132A GLN* 2.6 29.6 + - - -
144A ALA* 3.7 20.0 - - - +
145A VAL 5.4 0.3 + - - -
146A TYR* 4.1 13.9 - - - +
158A ILE* 4.7 1.6 - - - -
176A ILE* 3.7 24.0 - - - +
206A LEU* 3.9 10.7 - - - +
208A VAL* 4.4 3.1 - - - +
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A HIS 3.3 12.3 + - - +
126A GLN* 2.9 10.5 + - - +
128A SER* 1.3 79.0 - - - +
130A ASN* 1.3 56.9 + - - +
132A GLN* 2.7 39.5 + - - +
133A LEU* 3.8 3.3 + - - +
158A ILE* 4.1 18.2 - - + +
161A MSE 4.2 20.6 - - + +
162A ALA* 4.8 2.5 - - - +
165A LEU* 3.5 31.0 - - + -
167A LEU* 3.9 15.0 - - + -
172A VAL* 4.0 19.5 - - + -
176A ILE* 4.9 0.2 - - + -
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Residues in contact with ASN 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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89A ILE* 3.6 8.3 - - + -
90A SER* 2.7 33.0 + - - +
91A THR* 3.3 23.2 + - - +
92A GLY* 3.5 5.1 - - - +
126A GLN* 2.8 43.8 + - - +
127A LEU* 3.2 4.6 + - - +
129A VAL* 1.3 73.4 - - - +
131A VAL* 1.3 62.1 + - - +
132A GLN 3.2 0.9 + - - -
133A LEU* 3.2 28.8 + - + +
138A GLY 5.0 1.6 - - - +
139A GLY* 3.1 21.0 - - - -
165A LEU* 4.2 6.2 - - - +
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Residues in contact with VAL 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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89A ILE* 3.4 29.3 - - + +
127A LEU 2.9 17.1 + - - +
128A SER 3.3 24.2 - - - +
130A ASN* 1.3 72.1 - - - +
132A GLN* 1.3 61.1 + - + +
140A LEU* 3.0 8.8 + - + +
141A SER 3.0 13.0 + - - -
142A GLY* 2.8 35.8 + - - +
143A LYS 3.8 4.0 - - - +
144A ALA* 3.7 16.2 - - + -
205A LYS* 4.6 7.0 - - + -
206A LEU* 3.3 31.9 - - + +
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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