Contacts of the helix formed by residues 144 - 156 (chain D) in PDB entry 5BMU
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 PRO 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D ILE* 4.0 34.3 - - + +
100D ASN* 5.5 2.0 - - - +
103D ASN* 3.7 23.3 - - + +
134D TRP* 5.1 4.0 - - - +
137D GLN* 3.6 18.4 - - - +
143D ALA* 1.4 84.3 - - - +
145D VAL* 1.3 64.6 + - + +
146D HIS 3.4 2.8 + - - -
147D VAL* 3.5 14.2 + - + +
148D LYS* 3.5 8.5 + - - +
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Residues in contact with VAL 145 (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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103C GLU* 3.6 41.2 - - + +
104C ASP* 5.6 0.3 - - - -
103D ASN* 3.7 4.9 + - - +
143D ALA 4.8 2.7 - - - +
144D PRO* 1.3 74.2 - - + +
146D HIS* 1.3 87.3 + - + +
148D LYS* 3.3 39.3 + - - +
149D ARG* 3.3 10.0 + - - +
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Residues in contact with HIS 146 (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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103C GLU* 4.9 3.4 + - - +
140C LEU* 3.5 28.5 - - + +
141C ASN* 3.6 24.0 + - - -
103D ASN* 2.7 34.0 + - - +
106D LEU* 3.6 14.1 - - + +
107D SER* 3.3 29.8 + - - -
145D VAL* 1.3 88.3 - - + +
147D VAL* 1.3 60.9 + - - -
149D ARG* 3.5 32.4 + - - +
150D TRP* 3.2 22.7 + - - +
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ILE* 4.4 9.9 - - + +
102D LEU* 3.7 18.8 - - + -
103D ASN* 3.4 37.9 + - + +
106D LEU* 3.7 9.0 - - + -
128D LEU* 3.7 31.2 - - + -
134D TRP* 4.5 13.9 - - - +
144D PRO* 3.9 8.3 - - + +
145D VAL 3.4 0.6 - - - -
146D HIS* 1.3 73.0 - - - +
148D LYS* 1.3 54.9 + - - +
150D TRP* 3.2 8.3 + - + +
151D PHE* 2.5 41.8 + - + +
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Residues in contact with LYS 148 (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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104C ASP* 6.0 6.5 - - + -
111C TYR* 4.4 0.9 + - - -
134D TRP* 5.7 4.9 - - + -
138D LEU* 6.5 0.9 - - + -
143D ALA* 3.9 35.5 + - + +
144D PRO 3.5 6.9 + - - +
145D VAL* 3.3 31.7 - - - +
147D VAL* 1.3 80.1 - - - +
149D ARG* 1.3 56.0 + - - +
151D PHE* 3.9 5.9 - - - +
152D GLY* 3.1 22.3 + - - -
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Residues in contact with ARG 149 (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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103C GLU 3.5 19.5 - - - +
104C ASP* 3.8 22.0 - - - +
105C LYS 3.7 9.2 - - - +
106C VAL* 4.3 12.0 - - + +
111C TYR* 3.1 9.8 + - - +
144C ARG* 3.1 55.4 - - - +
106D LEU* 2.2 34.2 + - - +
107D SER 4.0 0.8 + - - -
109D ARG 3.4 8.1 + - - -
110D THR* 4.5 6.7 + - - +
145D VAL 3.3 5.0 + - - +
146D HIS* 3.5 30.5 + - - +
147D VAL 3.3 0.2 - - - -
148D LYS* 1.3 75.8 - - - +
150D TRP* 1.3 64.8 + - - +
153D PHE* 2.7 37.6 + - - +
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Residues in contact with TRP 150 (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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102D LEU* 5.2 0.2 - - + -
106D LEU* 3.4 38.5 - - + +
110D THR 3.4 22.6 + - - -
111D TYR* 4.3 0.2 - - - +
112D LEU* 4.2 8.7 - - + +
121D ASP* 3.1 35.0 + - - -
124D VAL* 3.9 10.5 - - + -
125D TRP* 3.6 40.4 - + + -
128D LEU* 4.1 21.3 - - + -
146D HIS 3.2 15.6 + - - +
147D VAL* 3.2 9.8 + - + -
149D ARG* 1.3 87.0 - - - +
151D PHE* 1.3 81.1 + - - +
153D PHE* 4.0 6.0 - + - +
154D LEU* 3.0 49.8 + - + +
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Residues in contact with PHE 151 (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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125D TRP* 2.9 64.4 + + - +
128D LEU* 3.9 9.4 - - + -
129D LYS* 3.5 24.9 - - + -
134D TRP* 3.2 48.5 - + + -
138D LEU* 5.2 4.0 - - + -
147D VAL* 2.5 23.6 + - + +
148D LYS* 3.9 5.2 - - - +
150D TRP* 1.3 85.2 - + + +
152D GLY* 1.3 52.2 + - - +
155D GLU* 2.8 53.2 + - - +
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Residues in contact with GLY 152 (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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111C TYR* 3.3 13.8 - - - -
148D LYS 3.1 16.2 + - - -
149D ARG 3.9 0.2 - - - -
151D PHE* 1.3 76.3 - - - +
153D PHE* 1.3 58.2 + - - +
155D GLU* 3.6 13.3 - - - +
156D ALA* 2.8 32.9 + - - +
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Residues in contact with PHE 153 (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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106C VAL* 3.6 24.2 - - + -
107C TYR* 3.7 30.7 - + - -
111C TYR* 3.3 46.1 - + + +
110D THR* 4.3 13.9 - - + -
111D TYR* 3.5 37.0 - + - -
149D ARG 2.7 23.9 + - - +
150D TRP* 4.0 4.3 - + - +
152D GLY* 1.3 73.6 - - - +
154D LEU* 1.3 71.0 + - + +
156D ALA* 3.5 8.3 + - - +
157D GLN* 3.6 34.4 + - + +
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Residues in contact with LEU 154 (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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111D TYR* 4.3 13.7 - - + -
117D LEU* 4.0 26.5 - - + -
121D ASP* 4.0 11.7 - - + +
125D TRP* 3.5 24.0 - - + +
150D TRP* 3.0 60.4 + - + +
153D PHE* 1.3 76.7 - - + +
155D GLU* 1.3 67.2 + - - +
156D ALA 3.1 1.0 + - - -
157D GLN* 3.2 19.9 + - - +
160D PHE* 3.1 36.2 - - + -
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Residues in contact with GLU 155 (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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125D TRP* 3.7 18.7 - - + +
129D LYS* 3.9 23.7 + - - -
151D PHE* 2.8 40.9 + - - +
152D GLY* 3.6 11.0 - - - +
154D LEU* 1.3 73.7 - - - +
156D ALA* 1.3 56.7 + - - +
157D GLN 3.1 6.9 + - - +
160D PHE* 3.7 11.6 - - - +
161D GLN* 3.7 17.9 + - - +
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Residues in contact with ALA 156 (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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111C TYR* 3.7 27.6 - - + -
152D GLY 2.8 19.6 + - - +
153D PHE 3.9 3.8 - - - +
154D LEU 3.1 1.0 + - - -
155D GLU* 1.3 71.8 - - - +
157D GLN* 1.3 60.9 + - - +
158D GLN 4.1 0.2 + - - -
161D GLN* 4.1 14.6 - - - +
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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