Contacts of the helix formed by residues 81 - 92 (chain M) in PDB entry 5A15
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 LEU 81 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M ASP* 3.0 23.6 + - + +
80M PHE* 1.3 71.9 - - + +
82M PHE* 1.3 64.9 + - - +
83M ARG 3.0 2.7 - - - -
84M TYR* 3.1 17.1 + - + -
85M ILE* 3.2 14.4 + - - +
100M PHE* 3.7 34.1 - - + -
102M GLU* 3.9 16.4 - - - +
105M ARG* 3.7 36.8 - - + +
106M LEU* 3.7 18.0 - - + +
109M GLU* 3.7 32.1 - - + +
83N ARG* 4.1 4.3 - - - +
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Residues in contact with PHE 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M LEU* 4.2 24.9 - - + -
31M VAL* 3.9 28.7 - - + -
36M TYR* 4.0 15.9 - + + -
43M LEU* 5.1 0.4 - - + -
51M LEU* 4.1 20.0 - - + -
75M ILE* 5.3 1.8 - - + -
78M ASP 3.5 12.1 + - - +
79M GLY 3.7 11.7 - - - +
80M PHE 3.2 0.8 - - - -
81M LEU* 1.3 77.2 - - - +
83M ARG* 1.3 55.8 + - - +
85M ILE* 3.6 18.2 - - + -
86M LEU* 2.7 59.2 + - + +
89M LEU* 5.0 0.2 - - + -
113M PHE* 3.6 41.7 - + - -
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Residues in contact with ARG 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L ASP* 2.5 39.6 + - - +
80L PHE* 3.8 31.3 - - + +
81L LEU* 4.0 3.0 - - - +
102L GLU* 2.8 34.4 + - - -
105L ARG* 2.9 16.4 - - - +
36M TYR* 3.5 28.1 + - + +
80M PHE 3.4 15.1 + - - +
82M PHE* 1.3 78.7 - - - +
84M TYR* 1.3 85.0 + - + +
86M LEU* 3.6 4.5 + - - +
87M ASP* 3.2 34.7 + - - +
90M ARG* 4.9 1.6 + - - +
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Residues in contact with TYR 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L GLU* 4.4 0.3 + - - -
105L ARG* 3.9 21.1 - - - -
80M PHE* 3.8 16.6 - - + -
81M LEU* 3.1 19.8 + - + +
83M ARG* 1.3 105.6 + - - +
85M ILE* 1.3 65.4 + - - +
86M LEU 3.3 0.4 - - - -
87M ASP* 3.6 2.2 + - - -
88M TYR* 3.4 15.9 + - - +
94M VAL* 3.7 28.4 - - + +
95M VAL 4.9 0.4 - - - -
96M LEU* 5.2 2.2 - - + -
97M PRO* 3.6 32.7 - - + +
100M PHE* 3.7 36.0 - + - -
106M LEU* 3.9 22.4 - - + +
118M LEU* 5.3 1.1 - - - +
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Residues in contact with ILE 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU* 5.2 0.4 - - + -
81M LEU 3.2 13.9 + - - +
82M PHE* 3.5 27.1 - - + +
84M TYR* 1.3 78.1 - - - +
86M LEU* 1.3 61.5 + - - +
88M TYR* 3.2 16.7 + - - +
89M LEU* 3.3 19.7 + - + +
106M LEU* 3.7 17.0 - - + -
109M GLU* 4.1 7.9 - - + -
110M ALA* 3.9 21.5 - - - +
113M PHE* 4.0 27.1 - - + -
115M LEU* 4.3 11.9 - - + -
118M LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M TYR* 4.0 28.7 - - + -
37M PHE 4.3 8.1 - - - +
38M THR* 3.9 28.5 - - + +
42M THR* 4.5 4.9 - - + -
43M LEU* 5.0 1.3 - - + -
82M PHE* 2.7 38.9 + - + +
83M ARG* 3.8 5.2 - - - +
85M ILE* 1.3 76.0 - - - +
87M ASP* 1.3 61.2 + - - +
89M LEU* 3.3 21.7 + - + +
90M ARG* 3.1 60.2 + - - +
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Residues in contact with ASP 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L ARG* 5.3 2.4 + - - -
78L ASP* 4.5 5.4 + - - +
105L ARG* 2.2 36.8 + - - +
109L GLU* 4.5 11.9 - - - +
83M ARG* 3.2 19.1 + - - +
84M TYR* 3.9 7.1 - - - +
85M ILE 3.3 0.6 - - - -
86M LEU* 1.3 77.3 - - - +
88M TYR* 1.3 59.1 + - - +
90M ARG* 3.0 30.3 + - - +
91M ASP* 2.9 31.2 + - - +
93M GLN 3.5 9.9 - - - +
94M VAL* 4.6 8.3 - - + -
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Residues in contact with TYR 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M ILE* 3.4 30.9 - - + +
84M TYR 3.4 5.2 + - - +
85M ILE 3.2 9.8 + - - +
87M ASP* 1.3 75.5 - - - +
89M LEU* 1.3 63.5 + - - +
92M ARG* 2.5 72.4 + - + +
93M GLN* 3.7 5.2 - - - -
94M VAL* 3.4 23.1 - - + +
115M LEU* 4.0 22.8 - - + +
117M ASP* 3.4 28.1 + - + +
118M LEU* 4.1 34.0 + - + -
121M LEU* 4.3 12.1 - - + -
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Residues in contact with LEU 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M THR* 3.7 28.2 - - + +
43M LEU* 4.8 8.7 - - + +
45M SER* 3.7 22.6 + - - +
46M ILE* 3.8 27.8 - - + -
49M SER* 5.6 2.7 - - - +
51M LEU* 3.6 31.6 - - + -
82M PHE* 5.0 0.4 - - + -
85M ILE* 3.3 18.6 + - + +
86M LEU* 3.3 25.0 + - + +
88M TYR* 1.3 79.6 - - + +
90M ARG* 1.3 61.7 + - - +
92M ARG* 4.4 9.4 + - - +
115M LEU* 4.2 17.5 - - + -
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Residues in contact with ARG 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L GLY* 4.2 4.0 + - - -
76L ASP* 3.0 39.9 + - - +
77L ARG* 3.8 28.6 + - - +
78L ASP* 3.6 18.0 - - - +
37M PHE 3.7 10.7 + - - -
42M THR* 4.1 14.8 - - + +
83M ARG* 4.9 1.4 + - - +
86M LEU* 3.1 49.9 + - - +
87M ASP* 3.0 32.4 + - - +
88M TYR 3.1 0.4 - - - -
89M LEU* 1.3 81.2 - - - +
91M ASP* 1.3 71.6 + - - +
92M ARG* 4.8 6.3 + - - -
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Residues in contact with ASP 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L ARG* 2.7 44.7 + - - -
108L ARG* 3.3 27.9 + - - +
112L TYR* 5.0 0.7 - - - -
87M ASP* 2.9 20.3 + - - +
90M ARG* 1.3 78.4 - - - +
92M ARG* 1.3 72.6 + - - +
93M GLN* 3.1 34.6 + - + +
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Residues in contact with ARG 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M SER* 3.1 43.9 + - - -
46M ILE* 4.2 11.7 - - + +
88M TYR* 2.5 56.2 + - + +
89M LEU 4.4 10.6 + - - +
90M ARG 4.8 5.5 + - - -
91M ASP* 1.3 74.8 - - - +
93M GLN* 1.3 57.8 + - - +
121M LEU* 4.8 3.6 - - - +
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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