Contacts of the helix formed by residues 144 - 157 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99H ILE* 4.4 37.7 - - + +
100H ASN* 6.0 0.7 - - - -
103H ASN* 3.8 22.4 - - + +
134H TRP* 5.3 1.9 - - + -
137H GLN* 5.0 6.7 - - + +
142H LYS 3.4 11.3 - - - +
143H ALA* 1.4 83.7 - - + +
145H VAL* 1.3 66.5 + - + +
146H HIS 3.4 2.3 + - - -
147H VAL* 3.5 6.5 + - + +
148H LYS 3.3 14.7 + - - -
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Residues in contact with VAL 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G GLU* 3.6 52.1 - - + +
104G ASP* 5.7 0.3 - - - -
103H ASN* 3.9 1.0 + - - +
143H ALA 4.1 6.3 - - - +
144H PRO* 1.3 73.0 - - + +
146H HIS* 1.3 86.2 + - + +
148H LYS* 3.3 17.9 + - - +
149H ARG* 3.2 22.9 + - - +
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Residues in contact with HIS 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G GLU* 5.4 4.0 + - + -
140G LEU* 3.8 20.7 - - + +
141G ASN* 3.5 26.7 + - - -
103H ASN* 3.2 35.1 + - - +
106H LEU* 4.2 7.7 - - + +
107H SER* 3.0 29.5 + - - -
145H VAL* 1.3 95.1 - - + +
147H VAL* 1.3 64.1 + - - +
148H LYS 3.3 0.3 + - - -
149H ARG* 3.5 30.4 + - - +
150H TRP* 3.3 22.5 + - - +
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Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ILE* 3.9 12.6 - - + +
102H LEU* 3.6 33.7 - - + +
103H ASN* 3.4 41.0 + - + +
106H LEU* 3.8 6.5 - - + -
128H LEU* 3.8 9.2 - - + -
134H TRP* 3.6 24.7 - - + -
144H PRO* 3.5 7.9 + - + +
145H VAL 3.4 0.2 - - - -
146H HIS* 1.3 76.2 - - - +
148H LYS* 1.3 61.3 + - - +
150H TRP* 3.7 4.2 - - + -
151H PHE* 3.1 22.7 + - - +
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Residues in contact with LYS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ASP* 5.5 14.2 - - - +
111G TYR* 4.6 1.2 + - - -
134H TRP* 3.9 9.5 - - + -
138H LEU* 4.1 27.4 - - + -
143H ALA* 4.2 15.3 + - + +
144H PRO 3.3 12.0 + - - +
145H VAL* 3.3 21.6 + - - +
146H HIS 3.2 1.0 - - - -
147H VAL* 1.3 77.6 - - - +
149H ARG* 1.3 61.8 + - - +
151H PHE* 3.9 0.9 - - - +
152H GLY* 3.2 21.1 + - - -
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Residues in contact with ARG 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G GLU 3.8 16.2 + - - +
104G ASP* 3.8 21.1 - - - +
105G LYS* 3.7 17.3 - - - -
106G VAL* 4.3 8.6 - - + +
111G TYR* 3.6 11.7 + - + -
144G ARG* 3.1 48.4 - - - +
106H LEU 2.5 31.7 + - - -
107H SER* 3.8 6.3 + - - +
109H ARG 3.4 14.6 + - - -
110H THR* 4.2 6.7 + - - +
145H VAL 3.2 5.3 + - - +
146H HIS* 3.5 23.3 + - - +
148H LYS* 1.3 78.2 - - - +
150H TRP* 1.3 73.8 - - - +
153H PHE* 2.8 37.4 + - - +
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Residues in contact with TRP 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G VAL* 5.4 0.2 - - - -
102H LEU* 4.3 6.1 - - + -
106H LEU* 3.4 39.5 - - + -
110H THR 3.4 21.8 - - - -
111H TYR* 4.5 0.9 - + - -
112H LEU* 4.0 18.5 - - + +
121H ASP* 3.1 31.8 + - - -
124H VAL* 3.9 13.0 - - + -
125H TRP* 3.8 25.6 - + + -
128H LEU* 3.7 25.1 - - + -
146H HIS 3.3 9.7 + - - +
147H VAL* 3.7 7.2 - - + -
149H ARG* 1.3 86.7 - - - +
151H PHE* 1.3 88.4 + + + +
153H PHE* 3.8 7.8 - + - +
154H LEU* 3.2 48.1 + - + +
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Residues in contact with PHE 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TRP* 2.8 65.1 + + - +
128H LEU* 3.8 22.0 - - + -
129H LYS* 3.8 17.0 - - + -
134H TRP* 3.3 47.6 - + + -
135H GLN* 5.6 1.3 - - - -
138H LEU* 5.5 3.1 - - + -
147H VAL 3.1 20.6 + - - +
148H LYS 3.9 0.9 - - - +
150H TRP* 1.3 85.2 - + + +
152H GLY* 1.3 56.9 + - - +
154H LEU 3.3 1.9 + - - -
155H GLU* 2.8 44.5 + - - -
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Residues in contact with GLY 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G TYR* 3.6 16.2 - - - -
148H LYS 3.2 12.9 + - - -
149H ARG 3.8 0.4 - - - -
151H PHE* 1.3 77.7 - - - +
153H PHE* 1.3 63.1 + - - +
155H GLU* 3.7 21.5 - - - +
156H ALA* 3.2 24.4 + - - +
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Residues in contact with PHE 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G VAL* 3.8 24.2 - - + -
107G TYR* 4.6 11.0 - + - -
111G TYR* 3.3 53.3 - + + -
110H THR* 4.1 20.9 - - + -
111H TYR* 3.5 38.8 - + - -
149H ARG 2.8 21.2 + - - +
150H TRP* 3.8 7.4 - + - +
152H GLY* 1.3 76.3 - - - +
154H LEU* 1.3 73.0 + - + +
156H ALA* 3.4 8.8 + - - +
157H GLN* 3.5 25.3 + - + +
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Residues in contact with LEU 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H TYR* 4.1 15.9 - - + -
117H LEU* 3.5 27.8 - - + -
121H ASP* 3.8 19.3 - - + +
125H TRP* 3.5 27.1 - - + +
150H TRP* 3.2 36.6 + - + +
151H PHE 3.5 7.0 - - - +
153H PHE* 1.3 83.3 - - + +
155H GLU* 1.3 63.1 + - - +
157H GLN* 2.9 29.8 + - - +
160H PHE* 3.2 28.5 - - + +
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Residues in contact with GLU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TRP* 3.6 24.9 - - + +
151H PHE* 2.8 33.7 + - + +
152H GLY* 3.7 17.2 - - - +
153H PHE 3.3 0.4 - - - -
154H LEU* 1.3 73.0 - - - +
156H ALA* 1.3 56.5 + - - +
157H GLN 3.5 0.3 + - - -
160H PHE* 3.9 2.2 - - - +
161H GLN* 2.8 44.9 + - - +
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Residues in contact with ALA 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G TYR* 4.2 20.9 - - + -
152H GLY 3.2 15.6 + - - +
153H PHE 3.8 4.9 - - - +
154H LEU 3.2 0.4 - - - -
155H GLU* 1.3 74.9 - - - +
157H GLN* 1.3 66.8 + - - +
158H GLN* 4.7 0.3 - - - -
161H GLN* 3.5 17.3 - - - +
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Residues in contact with GLN 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H HIS* 5.6 6.7 - - + +
111H TYR* 4.2 12.8 + - - -
117H LEU* 4.1 8.0 - - - +
153H PHE* 3.6 33.1 - - + +
154H LEU* 2.9 34.8 + - - +
155H GLU 3.8 0.2 - - - +
156H ALA* 1.3 82.2 - - - +
158H GLN* 1.3 60.3 + - - +
159H ALA 3.5 1.1 - - - +
160H PHE* 3.5 18.5 + - + -
161H GLN* 2.9 28.6 + - - +
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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