Contacts of the helix formed by residues 128 - 142 (chain D) in PDB entry 5BUG
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 128 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ALA* 4.6 13.2 - - + +
127D GLY* 1.3 76.3 - - - +
129D GLY* 1.3 56.2 + - - +
132D GLY 2.8 20.1 + - - -
155D TYR* 2.8 27.0 + - + +
159D ARG* 5.4 0.4 - - + -
160D THR* 4.6 11.0 - - + -
164D LYS* 3.2 27.4 - - - +
165D GLY* 2.7 32.1 + - - +
167D THR* 3.4 27.2 + - - +
168D ILE* 6.1 0.6 - - - +
401D TLA 2.5 19.8 + - - +
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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
----------------------------------------------------------
128D LYS* 1.3 75.9 - - - +
130D ARG* 1.3 58.3 + - - -
132D GLY* 3.3 0.7 + - - -
133D VAL* 2.9 33.3 + - - +
165D GLY 4.2 8.7 - - - -
166D VAL* 3.9 7.1 - - - +
171D GLN* 3.3 22.6 - - - +
401D TLA 2.2 18.4 + - - -
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Residues in contact with ARG 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LEU* 3.2 23.9 + - + -
71D CYS* 3.8 2.8 - - - +
72D ALA 3.9 0.8 - - - +
73D GLU* 3.2 21.4 + - - -
90D PHE* 2.6 66.2 + - + -
91D GLU* 3.7 9.4 - - - +
92D ASP* 3.4 32.1 + - - +
124D CYS* 3.1 28.9 - - - +
125D LYS* 4.7 5.1 - - - +
129D GLY* 1.3 67.6 - - - -
131D THR* 1.3 65.5 + - - +
133D VAL* 3.2 4.8 + - - +
134D MET* 3.2 27.2 + - - +
171D GLN* 3.9 9.0 - - - +
401D TLA 2.7 37.3 + - - +
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Residues in contact with THR 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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34D ALA* 4.1 11.4 - - + -
70D LEU* 3.7 9.9 - - - +
122D ILE* 3.6 25.6 - - + +
123D HIS* 3.7 5.7 - - - -
124D CYS 3.6 10.2 + - - -
127D GLY* 3.9 5.5 - - - +
130D ARG* 1.3 81.0 - - - +
132D GLY* 1.3 56.4 + - - +
134D MET* 3.4 2.1 + - - +
135D ILE* 2.9 54.6 + - + +
155D TYR* 4.0 6.7 - - - +
401D TLA 2.8 29.9 + - - -
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Residues in contact with GLY 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LYS 2.8 21.8 + - - -
129D GLY 3.6 1.6 - - - -
131D THR* 1.3 74.8 - - - +
133D VAL* 1.3 59.2 + - - +
135D ILE 4.5 0.4 - - - -
136D CYS* 3.0 36.0 + - - -
155D TYR* 3.5 26.2 + - - -
166D VAL* 3.8 8.9 - - - +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE* 4.7 1.3 - - + -
96D PRO* 3.8 33.2 - - + -
101D ILE* 4.9 5.8 - - + -
129D GLY 2.9 21.4 + - - +
130D ARG* 3.2 8.7 + - - +
132D GLY* 1.3 74.8 - - - +
134D MET* 1.3 61.9 + - - +
137D ALA* 2.9 29.4 + - + +
166D VAL* 4.2 3.8 - - + -
171D GLN* 3.6 42.4 - - + +
174D TYR* 4.8 5.4 - - + -
175D VAL* 3.9 20.6 - - + +
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Residues in contact with MET 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LEU* 3.8 23.6 - - + -
90D PHE* 3.9 22.4 - - + -
96D PRO* 4.2 17.7 - - - -
100D LEU* 4.9 4.9 - - - -
101D ILE* 3.9 28.7 - - + -
104D PHE* 3.3 57.0 - - + -
122D ILE* 5.2 0.4 - - + -
130D ARG 3.2 15.3 + - - +
131D THR 3.8 3.4 - - - +
133D VAL* 1.3 77.6 - - - +
135D ILE* 1.3 65.5 + - + +
137D ALA* 3.7 2.5 - - + +
138D TYR* 3.1 23.4 + - - +
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Residues in contact with ILE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 4.1 24.0 - - + -
32D ILE* 4.1 20.0 - - + -
34D ALA* 3.9 20.2 - - + -
108D LEU* 6.0 0.4 - - + -
122D ILE* 3.7 26.5 - - + -
131D THR* 2.9 41.0 + - + +
132D GLY* 4.4 4.3 - - - +
134D MET* 1.3 77.8 - - - +
136D CYS* 1.3 61.6 + - - +
138D TYR* 3.3 6.9 + - - +
139D LEU* 3.1 46.6 + - + +
155D TYR* 4.3 8.5 - - + -
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Residues in contact with CYS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D GLY 3.0 26.7 + - - +
133D VAL 4.0 0.4 - - - +
135D ILE* 1.3 76.2 - - - +
137D ALA* 1.3 64.5 + - - +
139D LEU* 3.3 9.2 + - - +
140D LEU* 3.1 30.0 + - - +
151D ALA* 3.4 36.7 - - + +
152D LEU* 4.0 11.4 - - - -
155D TYR* 3.6 20.9 - - - -
175D VAL* 3.9 19.7 - - + -
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ILE* 3.6 33.7 - - + -
105D CYS* 3.9 3.8 - - - -
133D VAL* 2.9 20.5 + - + +
134D MET* 3.7 6.7 - - + +
136D CYS* 1.3 77.2 - - - +
138D TYR* 1.3 50.8 + - - +
140D LEU* 3.4 9.0 - - - +
141D HIS* 2.8 34.8 + - - +
175D VAL* 4.3 5.5 - - + +
178D TYR* 3.6 16.1 - - + -
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Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ILE* 3.8 30.3 - - + -
104D PHE* 4.7 0.7 - - + -
105D CYS* 3.5 43.9 - - + -
108D LEU* 3.8 18.6 - - + -
109D ASP* 2.8 42.0 + - + -
112D LEU* 3.7 17.1 - - + +
134D MET 3.1 18.9 + - - +
135D ILE* 3.6 5.4 - - - +
136D CYS 3.3 0.2 - - - -
137D ALA* 1.3 78.3 - - - +
139D LEU* 1.3 58.8 + - + +
141D HIS* 3.2 4.9 - + + +
142D ARG* 2.8 57.3 + - + +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 4.5 6.3 - - + -
29D TYR* 3.8 32.8 - - + -
32D ILE* 4.0 19.7 - - + -
135D ILE* 3.1 35.9 + - + +
136D CYS* 3.3 10.3 + - - +
138D TYR* 1.3 79.2 - - + +
140D LEU* 1.3 58.5 + - - +
142D ARG* 3.7 3.0 + - + +
143D GLY 3.2 2.9 + - - -
144D LYS* 2.8 45.1 + - + +
145D PHE* 3.2 36.0 + - + -
151D ALA 5.6 0.7 - - - +
154D PHE* 5.1 2.5 - - + -
155D TYR* 6.2 0.9 - - + -
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Residues in contact with LEU 140 (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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136D CYS 3.1 17.9 + - - +
137D ALA* 3.4 8.7 - - - +
139D LEU* 1.3 74.0 - - - +
141D HIS* 1.3 59.7 - - - +
143D GLY* 2.9 19.4 + - - -
145D PHE* 3.4 27.2 - - + +
146D LEU 4.2 2.0 - - - +
147D LYS 3.8 27.1 - - - +
148D ALA* 4.1 7.4 - - - +
151D ALA* 4.3 5.6 - - + -
175D VAL* 3.7 28.3 - - + +
178D TYR* 5.1 0.4 - - + -
179D SER* 3.9 27.6 - - - +
182D LEU* 3.7 18.9 - - + +
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Residues in contact with HIS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 5.7 0.7 - - - +
102D LYS* 5.0 3.4 - - + -
105D CYS* 3.4 21.2 - - + +
106D GLU* 4.1 23.4 - - + +
109D ASP* 4.3 17.9 + - - +
137D ALA 2.8 18.4 + - - +
138D TYR* 3.2 27.8 - + - +
140D LEU* 1.3 74.5 - - - +
142D ARG* 1.3 58.2 - - + +
143D GLY 3.6 0.5 + - - -
178D TYR* 2.7 29.0 + - + -
182D LEU* 3.6 22.3 - - + +
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Residues in contact with ARG 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.6 27.4 - - - +
43B GLU* 4.6 4.6 - - - +
31D ASN* 5.7 5.5 - - - +
109D ASP* 3.3 28.4 + - - +
112D LEU* 5.0 8.1 - - - +
113D SER* 3.9 14.1 + - - +
138D TYR* 2.8 53.5 + - + +
139D LEU* 3.7 6.0 + - + +
140D LEU 3.2 0.2 - - - -
141D HIS* 1.3 74.6 - - + +
143D GLY* 1.3 59.0 + - - +
144D LYS* 3.2 34.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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