Contacts of the helix formed by residues 87 - 98 (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 SER 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLU 4.3 0.4 + - - -
86A PHE* 1.3 74.9 - - - +
88A THR* 1.3 54.6 + - - +
89A ALA* 3.7 9.2 + - - +
90A SER* 3.3 21.4 + - - -
91A TRP* 2.7 32.2 + - - +
342A ARG* 3.8 0.2 - - - -
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Residues in contact with THR 88 (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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87A SER* 1.3 72.6 - - - +
89A ALA* 1.3 57.2 + - - +
91A TRP* 3.9 15.0 - - + -
92A ILE* 2.8 42.7 + - - +
342A ARG* 3.8 16.9 - - - +
346A GLU* 4.7 8.1 - - - +
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Residues in contact with ALA 89 (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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87A SER* 3.1 8.7 - - - +
88A THR* 1.3 81.6 + - - +
90A SER* 1.3 62.1 + - - +
92A ILE* 4.1 3.1 - - - +
93A PHE* 3.1 24.6 + - - +
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Residues in contact with SER 90 (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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86A PHE* 3.9 21.4 - - - -
87A SER* 3.2 18.0 + - - -
89A ALA* 1.3 78.1 - - - +
91A TRP* 1.3 53.3 + - - +
93A PHE* 3.1 11.0 + - - +
94A MET* 2.8 44.7 + - - +
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Residues in contact with TRP 91 (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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86A PHE* 4.0 12.0 - + + +
87A SER 2.7 21.8 + - - +
88A THR* 3.7 10.1 - - + +
90A SER* 1.3 72.6 - - - +
92A ILE* 1.3 88.3 + - + +
94A MET* 3.3 17.7 + - - +
95A MET* 3.4 39.1 + - + +
338A ILE* 3.6 38.2 + - + +
339A SER* 3.6 19.9 + - - +
342A ARG* 3.5 46.9 - - - +
346A GLU* 3.5 30.5 - - - -
347A LEU* 3.9 14.4 - - + -
350A GLY* 4.4 4.5 - - - -
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Residues in contact with ILE 92 (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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88A THR* 2.8 28.5 + - - +
89A ALA* 4.1 4.0 - - - +
91A TRP* 1.3 86.1 - - + +
93A PHE* 1.3 59.9 + - - +
95A MET* 3.0 13.5 + - - +
96A PHE* 2.9 27.8 + - + +
350A GLY* 3.3 40.4 - - - +
353A SER* 4.6 3.4 - - - +
354A GLY* 4.2 15.2 - - - -
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Residues in contact with PHE 93 (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 ALA 3.1 17.9 + - - +
90A SER* 3.1 12.1 + - - +
92A ILE* 1.3 80.2 - - - +
94A MET* 1.3 64.3 + - + +
96A PHE* 3.2 19.7 + + - +
97A ALA* 2.8 33.6 + - + +
260A ASP* 5.5 4.7 - - - -
263A THR* 4.0 17.9 - - + -
264A TYR* 3.9 31.4 - + - -
267A PHE* 3.9 26.2 - + - -
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Residues in contact with MET 94 (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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86A PHE* 3.3 44.4 - - + -
90A SER* 2.8 24.1 + - - +
91A TRP* 3.5 10.3 - - - +
92A ILE 3.2 0.4 - - - -
93A PHE* 1.3 84.3 - - + +
95A MET* 1.3 60.0 + - - +
97A ALA* 3.9 6.4 - - - +
98A SER* 3.4 19.2 + - - -
334A PHE* 4.4 19.5 - - + -
338A ILE* 3.7 34.5 - - + -
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Residues in contact with MET 95 (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 TRP* 3.4 53.6 - - + +
92A ILE* 3.0 12.8 + - - +
94A MET* 1.3 74.5 - - - +
96A PHE* 1.3 65.1 + - - +
97A ALA 3.1 1.8 - - - -
98A SER* 2.5 26.6 + - - -
99A CYS* 3.6 4.5 - - - -
334A PHE* 5.4 1.8 - - - -
335A LEU* 4.1 24.0 - - + -
338A ILE* 4.5 6.5 - - + -
339A SER* 4.6 1.8 - - - +
347A LEU* 4.5 3.4 - - + -
350A GLY 3.8 10.1 - - - +
351A MET* 3.6 38.4 - - + +
354A GLY* 4.6 0.9 - - - -
355A LEU* 3.5 26.5 - - + +
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Residues in contact with PHE 96 (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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92A ILE* 2.9 16.9 + - + +
93A PHE* 3.3 22.0 - + + +
95A MET* 1.3 76.4 - - - +
97A ALA* 1.3 59.8 + - - +
99A CYS* 3.8 14.0 + - - +
100A THR* 4.9 2.8 - - - +
267A PHE* 4.0 37.9 - + - -
354A GLY 3.9 11.3 + - - +
357A ALA* 3.7 14.1 - - + -
358A GLY* 3.4 35.1 - - - -
361A LEU* 4.3 22.4 - - + -
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Residues in contact with ALA 97 (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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93A PHE* 2.8 24.7 + - + +
94A MET* 4.0 8.3 - - - +
95A MET 3.1 0.2 - - - -
96A PHE* 1.3 74.1 - - - +
98A SER* 1.3 59.6 + - - +
99A CYS 3.1 10.8 + - - -
100A THR* 3.3 23.4 + - - +
263A THR* 3.6 37.2 + - + +
267A PHE* 5.2 0.9 - - - -
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Residues in contact with SER 98 (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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94A MET 3.4 10.2 + - - -
95A MET* 2.5 26.6 + - - -
97A ALA* 1.3 77.2 - - - +
99A CYS* 1.3 50.6 + - - +
100A THR 3.3 6.2 + - - +
331A MET* 3.7 28.3 - - - +
334A PHE* 4.3 14.3 - - - -
355A LEU* 4.1 2.9 - - - +
601A NM2 2.7 28.1 - - - +
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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