Contacts of the helix formed by residues 81 - 92 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78G ASP* 3.1 18.2 + - + +
79G GLY 3.4 0.2 - - - -
80G PHE* 1.3 73.2 - - + +
82G PHE* 1.3 65.0 + - - +
83G ARG 3.1 3.8 + - - -
84G TYR* 3.3 13.2 + - + -
85G ILE* 3.5 9.5 + - - +
100G PHE* 4.0 24.5 - - + -
102G GLU* 3.5 28.9 - - - +
105G ARG* 3.7 42.6 - - + +
106G LEU* 3.5 21.9 - - + +
109G GLU* 3.9 33.4 - - + +
83H ARG* 4.1 1.3 - - - +
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Residues in contact with PHE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G LEU* 4.0 28.7 - - + -
31G VAL* 3.8 20.4 - - + -
36G TYR* 3.5 39.7 - + + -
43G LEU* 5.3 0.4 - - + -
51G LEU* 4.4 14.6 - - + -
75G ILE* 5.2 2.5 - - + -
77G ARG* 5.9 0.4 - - + -
78G ASP 3.5 11.9 + - - +
79G GLY 3.8 3.6 - - - +
80G PHE 3.3 1.0 - - - -
81G LEU* 1.3 76.0 - - - +
83G ARG* 1.3 55.8 + - - +
85G ILE* 3.1 17.4 + - + +
86G LEU* 2.8 51.7 + - + +
89G LEU* 5.2 0.4 - - + -
109G GLU* 6.3 0.2 - - - -
113G PHE* 3.4 43.5 - + - -
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Residues in contact with ARG 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASP* 2.8 40.0 + - - +
80F PHE* 3.3 31.2 - - - +
81F LEU* 3.8 2.8 - - - +
102F GLU* 3.0 33.9 + - - -
105F ARG* 2.9 19.7 - - - +
36G TYR* 3.1 34.8 + - + +
80G PHE 3.5 11.2 - - - +
81G LEU 3.1 0.2 - - - -
82G PHE* 1.3 76.7 - - - +
84G TYR* 1.3 78.4 + - + +
86G LEU* 3.6 5.1 + - - +
87G ASP* 3.4 23.4 + - - +
90G ARG* 5.3 0.5 + - - -
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Residues in contact with TYR 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F GLU* 3.9 0.9 + - - -
105F ARG* 3.9 31.9 - - - -
80G PHE 3.9 17.0 - - - -
81G LEU* 3.9 12.3 - - + -
82G PHE 3.2 0.6 - - - -
83G ARG* 1.3 95.1 + - + +
85G ILE* 1.3 65.7 + - - +
86G LEU 3.2 0.2 - - - -
87G ASP* 3.9 4.5 - - - +
88G TYR* 3.3 3.1 + - - +
94G VAL* 3.1 33.4 - - + +
95G VAL 4.8 4.0 - - - -
96G LEU* 5.0 4.7 - - + -
97G PRO* 3.4 34.8 - - + +
100G PHE* 3.4 35.5 - + - -
106G LEU* 3.8 28.0 - - + -
118G LEU* 5.3 1.7 - - - +
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Residues in contact with ILE 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LEU* 4.8 1.1 - - + -
81G LEU 3.5 13.4 + - - +
82G PHE* 3.1 25.2 + - + +
84G TYR* 1.3 79.5 - - - +
86G LEU* 1.3 61.1 + - - +
88G TYR* 3.3 7.7 + - - +
89G LEU* 3.2 28.2 + - + +
106G LEU* 3.9 14.6 - - + -
109G GLU* 4.1 7.0 - - + -
110G ALA* 3.9 24.0 - - - +
113G PHE* 3.9 31.2 - - + -
115G LEU* 4.5 10.5 - - + -
118G LEU* 3.7 24.2 - - + -
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Residues in contact with LEU 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F GLY 5.6 0.2 - - - +
36G TYR* 3.9 31.0 - - + -
37G PHE 4.1 9.0 - - - +
38G THR* 3.7 30.7 - - + +
42G THR* 4.6 2.7 - - + -
43G LEU* 5.3 0.4 - - + -
82G PHE* 2.8 29.4 + - + +
83G ARG 3.7 6.7 - - - +
84G TYR 3.2 0.2 - - - -
85G ILE* 1.3 79.1 - - - +
87G ASP* 1.3 61.8 + - - +
89G LEU* 3.3 22.2 + - + +
90G ARG* 3.1 59.6 + - - +
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Residues in contact with ASP 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F ARG* 5.2 3.0 + - - -
78F ASP* 3.9 13.2 + - - +
105F ARG* 2.2 38.1 + - - +
109F GLU* 4.4 6.8 - - - +
83G ARG 3.4 14.5 + - - +
84G TYR* 4.1 1.1 - - - +
85G ILE 3.3 0.6 - - - -
86G LEU* 1.3 74.6 - - - +
88G TYR* 1.3 60.7 + - - +
90G ARG* 3.1 30.9 + - - +
91G ASP* 2.9 31.0 + - - +
93G GLN 3.4 7.1 - - - +
94G VAL* 3.7 17.3 - - + -
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Residues in contact with TYR 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ILE* 3.5 25.0 - - + +
84G TYR 3.8 2.9 - - - +
85G ILE 3.3 8.9 + - - +
86G LEU 3.2 0.2 - - - -
87G ASP* 1.3 74.9 - - - +
89G LEU* 1.3 63.6 + - - +
92G ARG* 2.7 71.2 + - - -
93G GLN* 3.7 8.7 - - - -
94G VAL* 3.1 21.3 - - + +
115G LEU* 3.7 27.1 - - + +
117G ASP* 3.3 29.0 + - + +
118G LEU* 3.5 44.0 + - + -
121G LEU* 4.2 8.7 - - + -
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Residues in contact with LEU 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G THR* 3.5 34.9 - - + +
43G LEU* 4.6 9.2 - - + +
45G SER* 3.9 16.2 + - - +
46G ILE* 4.1 18.2 - - + -
49G SER* 6.0 0.7 - - - +
51G LEU* 3.5 30.7 - - + -
82G PHE* 5.2 0.7 - - + -
85G ILE* 3.2 17.0 + - + +
86G LEU* 3.3 24.7 + - + +
88G TYR* 1.3 79.1 - - + +
90G ARG* 1.3 61.7 + - - +
92G ARG* 4.6 6.5 + - - +
115G LEU* 3.8 29.8 - - + -
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Residues in contact with ARG 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F GLY* 3.9 3.8 - - - -
76F ASP* 2.5 44.7 + - - +
77F ARG* 3.2 42.0 + - - +
78F ASP* 3.2 4.8 - - - +
37G PHE 3.3 11.7 + - - -
38G THR* 4.4 0.2 + - - -
42G THR* 4.2 14.1 - - + +
83G ARG 5.3 0.6 + - - -
86G LEU* 3.1 46.0 + - - +
87G ASP* 3.1 30.9 + - - +
88G TYR 3.1 0.6 - - - -
89G LEU* 1.3 81.2 - - - +
91G ASP* 1.3 72.6 + - - +
92G ARG* 5.3 1.4 - - - +
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Residues in contact with ASP 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F ARG* 2.6 46.5 + - - -
108F ARG* 3.3 26.2 + - - +
112F TYR* 5.2 0.2 - - - -
87G ASP* 2.9 19.3 + - - +
90G ARG* 1.3 80.3 - - - +
92G ARG* 1.3 73.1 + - - +
93G GLN* 3.1 33.4 + - + +
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Residues in contact with ARG 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G SER* 5.1 7.1 + - - -
46G ILE* 4.2 29.0 - - - +
88G TYR* 2.7 58.5 + - - -
89G LEU 4.7 7.9 - - - +
90G ARG 5.3 1.3 - - - +
91G ASP* 1.3 74.3 - - - +
93G GLN* 1.3 58.9 + - - +
117G ASP* 3.6 23.0 + - - +
121G LEU* 4.8 4.9 - - - +
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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