Contacts of the helix formed by residues 150 - 163 (chain A) in PDB entry 4M8J
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 TYR 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 6.5 0.2 - - - -
146A PRO 4.2 3.1 - - - -
147A TRP* 3.5 32.8 - + - +
148A ALA 3.1 0.8 - - - -
149A THR* 1.3 90.2 + - - +
151A SER* 1.3 61.4 + - - +
152A PHE 3.2 2.7 - - - -
153A LEU* 3.1 6.2 + - - -
154A SER* 2.9 25.6 + - - -
323A TRP 4.2 0.2 + - - -
324A TRP* 2.5 63.1 + + + -
327A TYR* 3.5 10.5 - - - +
328A ALA* 3.5 29.8 + - + -
331A MET* 4.1 26.9 - - + -
332A SER* 3.3 13.3 + - - +
335A LEU* 4.9 2.9 - - + -
351A MET* 3.5 10.1 - - + -
601A NM2 4.2 6.5 - - - -
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Residues in contact with SER 151 (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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66A TRP* 3.8 13.9 - - - -
69A LEU* 3.7 2.7 - - - +
148A ALA 3.4 13.8 + - - -
150A TYR* 1.3 80.2 - - - +
152A PHE* 1.3 56.1 + - - +
154A SER* 3.0 9.8 + - - -
155A VAL* 2.9 32.7 + - - +
347A LEU* 5.3 0.2 - - - +
348A CYS* 2.4 40.4 - - - +
351A MET* 3.5 17.5 - - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE 5.9 0.2 - - - -
62A MET* 4.3 33.7 - - + +
65A GLY* 3.6 36.1 - - - -
66A TRP 5.7 1.2 - - - +
68A TRP* 3.9 18.4 - + - -
69A LEU* 4.1 15.7 - - + +
148A ALA 4.5 2.2 + - - -
149A THR 5.4 1.3 - - - +
150A TYR 3.2 1.2 - - - +
151A SER* 1.3 77.8 - - - +
153A LEU* 1.3 67.7 + - + +
155A VAL* 4.1 1.6 - - - +
156A ALA* 3.1 22.3 + - - +
491A THR* 4.5 10.9 - - + +
494A PHE* 3.5 32.7 - + - -
495A ILE* 3.6 31.6 - - + -
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Residues in contact with LEU 153 (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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58A TYR* 4.7 5.4 - - - +
62A MET* 3.9 18.4 - - - -
149A THR 4.1 13.2 - - - +
150A TYR* 3.1 3.1 + - - +
152A PHE* 1.3 77.2 - - + +
154A SER* 1.3 60.2 + - - +
155A VAL 3.1 1.6 - - - -
156A ALA* 3.2 5.3 - - - +
157A PHE* 2.8 44.8 + - + -
328A ALA* 4.2 15.9 - - + -
329A ILE* 3.9 29.2 - - + +
332A SER* 3.4 18.4 - - - +
487A ASN* 4.0 20.6 - - + +
490A VAL* 4.7 4.9 - - + -
491A THR* 3.7 24.9 - - + -
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Residues in contact with SER 154 (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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150A TYR 2.9 11.6 + - - -
151A SER* 3.0 22.5 + - - -
153A LEU* 1.3 77.1 - - - +
155A VAL* 1.3 55.6 + - - +
158A ALA* 3.2 28.2 + - - +
332A SER* 3.4 25.2 - - - -
335A LEU* 3.9 24.7 - - - -
336A ALA* 3.3 6.7 - - - +
347A LEU* 4.1 12.5 - - - +
351A MET* 3.9 8.7 - - - -
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Residues in contact with VAL 155 (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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69A LEU* 3.6 22.9 - - + -
74A TYR* 6.5 0.2 - - + -
79A LEU* 4.6 3.7 - - + +
151A SER* 2.9 21.6 + - - +
152A PHE 4.2 1.3 - - - +
154A SER* 1.3 77.3 + - - +
156A ALA* 1.3 59.3 + - - +
158A ALA* 3.7 2.3 - - - +
159A TYR* 2.8 28.8 + - - +
344A VAL* 4.1 33.2 - - + -
347A LEU* 3.7 23.1 - - + -
348A CYS* 4.1 8.7 - - - -
494A PHE* 4.0 23.3 - - + -
502A TRP* 4.9 2.0 - - + -
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Residues in contact with ALA 156 (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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152A PHE 3.1 21.0 + - - +
153A LEU* 3.0 11.8 + - - +
155A VAL* 1.3 75.4 - - - +
157A PHE* 1.3 61.7 + - + +
159A TYR* 3.1 4.7 - - - +
160A PHE* 2.9 39.1 + - + -
490A VAL* 4.7 11.0 - - + +
491A THR* 5.2 2.2 - - - -
494A PHE* 3.8 32.1 - - + -
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Residues in contact with PHE 157 (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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153A LEU* 2.8 37.8 + - + +
156A ALA* 1.3 71.4 - - + +
158A ALA* 1.3 54.2 + - - +
159A TYR 3.0 4.9 - - - -
160A PHE* 3.1 6.1 + + + +
161A PHE* 2.7 49.4 + + + -
168A VAL* 3.5 32.5 - - + -
171A PRO* 5.5 4.0 - - + -
174A THR* 4.3 9.9 - - + -
329A ILE* 3.5 37.2 - - + -
332A SER* 4.4 5.8 - - - +
333A ILE* 3.5 26.2 - - + -
336A ALA* 3.6 16.4 - - + -
490A VAL* 3.7 29.2 - - + -
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Residues in contact with ALA 158 (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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79A LEU* 3.6 36.9 - - + +
154A SER 3.2 19.3 + - - +
155A VAL* 3.9 0.9 - - - +
157A PHE* 1.3 77.5 - - - +
159A TYR* 1.3 56.7 + - - +
162A PHE* 3.2 37.1 - - - +
336A ALA* 3.3 22.5 - - + +
339A SER 4.9 0.7 - - - +
347A LEU* 4.7 4.3 - - + -
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Residues in contact with TYR 159 (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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79A LEU* 4.6 2.2 - - + -
155A VAL 2.8 18.5 + - - +
156A ALA 3.1 5.8 - - - +
158A ALA* 1.3 76.8 - - - +
160A PHE* 1.3 73.7 + + - +
163A VAL* 2.7 65.9 + - + +
164A ARG* 3.1 26.5 + - + -
494A PHE* 3.6 26.2 - + + -
497A ASP* 2.3 48.1 + - + -
498A ALA* 3.6 8.8 - - + -
501A HIS* 3.9 10.1 - - + +
502A TRP* 3.7 35.0 - + + -
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Residues in contact with PHE 160 (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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156A ALA* 2.9 33.2 + - + -
157A PHE* 3.7 9.2 - + + +
159A TYR* 1.3 89.4 - + - +
161A PHE* 1.3 65.5 + - + +
164A ARG* 3.3 8.3 - - + -
165A LYS 3.1 17.0 + - - -
166A MET* 3.1 52.8 + - + +
168A VAL* 5.1 4.7 - - + -
174A THR* 4.1 38.4 - - + -
177A PRO* 5.0 4.7 - - + -
490A VAL* 4.5 8.5 - - + -
493A SER* 4.1 3.8 - - - -
494A PHE* 4.1 35.2 - - + -
497A ASP* 4.6 12.3 - - + -
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Residues in contact with PHE 161 (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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157A PHE* 2.7 47.9 + + + +
158A ALA* 4.6 0.2 - - - -
160A PHE* 1.3 75.2 - - + +
162A PHE* 1.3 84.1 + + + +
165A LYS* 3.2 19.8 + - - +
166A MET 3.7 16.3 - - - +
167A GLU* 4.0 10.0 - - - +
168A VAL* 3.4 47.8 - - + -
333A ILE* 4.4 8.5 - - + -
336A ALA* 4.2 10.8 - - + -
337A ARG* 3.1 47.1 - - - -
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Residues in contact with PHE 162 (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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79A LEU* 3.8 12.3 - - + -
80A GLY* 3.5 30.8 - - - +
158A ALA* 3.2 24.8 + - + +
159A TYR 3.3 1.4 + - - -
161A PHE* 1.3 98.1 - + + +
163A VAL* 1.3 63.2 + - - +
165A LYS* 3.6 26.1 + - - +
336A ALA 3.0 28.9 - - - -
337A ARG* 3.9 22.0 - - - -
340A LYS* 3.5 43.7 - - + -
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG 4.5 1.8 - - - +
79A LEU* 3.7 31.0 - - + -
80A GLY* 3.9 2.5 - - - +
159A TYR* 2.7 55.7 + - + +
162A PHE* 1.3 73.2 - - - +
164A ARG* 1.3 59.2 + - + +
165A LYS* 3.3 6.2 + - - +
501A HIS* 5.1 7.4 - - + +
502A TRP* 3.8 24.2 - - + +
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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