Contacts of the helix formed by residues 83 - 94 (chain C) in PDB entry 5BXD
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 MET 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ARG* 3.5 13.0 - - - +
80C ASP* 3.0 23.1 + - + +
81C GLY 3.3 0.2 - - - -
82C GLN* 1.3 82.9 - - + +
84C PHE* 1.3 63.9 + - - +
85C ARG 3.1 0.2 - - - -
86C TYR* 3.2 29.0 + - + +
87C ILE* 3.4 13.1 + - - +
102C PHE* 4.2 4.5 - - + -
104C ASP* 3.4 37.5 - - + +
107C LEU* 4.1 14.8 - - + +
108C LEU* 3.6 41.4 - - + +
111C GLU* 3.8 21.5 - - + -
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 4.6 14.1 - - + -
36C VAL* 3.7 42.6 - - + -
41C TYR* 3.7 20.6 - + + -
48C LEU* 4.8 5.4 - - + -
56C ILE* 4.3 20.6 - - + -
77C ILE* 4.5 2.5 - - + -
80C ASP 3.6 4.8 + - - +
81C GLY 3.3 12.3 + - - +
82C GLN 3.2 1.2 - - - -
83C MET* 1.3 76.7 - - - +
85C ARG* 1.3 55.0 + - - +
87C ILE* 3.7 17.7 - - + -
88C LEU* 2.8 59.0 + - + +
91C LEU* 5.4 0.2 - - + -
111C GLU* 5.7 0.2 - - - +
115C PHE* 3.9 36.1 - + - -
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Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR* 3.3 32.9 + - + +
82C GLN 3.7 9.4 - - - +
83C MET 3.1 1.0 - - - -
84C PHE* 1.3 76.5 - - - +
86C TYR* 1.3 79.2 + - + +
88C LEU* 3.5 3.9 + - - +
89C ASN* 2.9 28.2 + - + +
92C ARG* 5.6 2.8 + - - +
80D ASP* 2.9 42.8 + - - +
82D GLN* 3.5 42.5 + - - +
83D MET* 3.9 11.7 - - - +
104D ASP* 4.6 10.3 + - - -
107D LEU* 4.1 17.0 - - - +
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Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLN 4.4 6.5 - - - -
83C MET* 3.2 30.6 + - + +
85C ARG* 1.3 96.6 + - + +
87C ILE* 1.3 65.9 + - - +
89C ASN* 3.9 6.3 - - + +
90C PHE* 3.0 23.0 + - - +
95C LYS 5.2 0.2 - - - +
96C LEU* 5.5 1.6 - - + +
97C LEU 3.6 21.5 + - - +
98C ILE* 3.8 9.0 - - + -
99C PRO* 3.6 34.4 - - + +
102C PHE* 3.5 31.7 - + - -
108C LEU* 3.7 19.7 - - + -
120C MET* 3.7 6.9 - - + +
107D LEU* 4.8 8.5 - - + -
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ILE* 5.4 1.6 - - + -
83C MET 3.6 13.5 - - - +
84C PHE* 3.2 25.3 + - + +
86C TYR* 1.3 78.4 - - - +
88C LEU* 1.3 57.4 + - - +
90C PHE* 3.1 5.7 + - - +
91C LEU* 3.0 34.1 + - + +
108C LEU* 4.1 6.5 - - + -
111C GLU* 3.9 7.6 - - + -
112C ALA* 3.7 35.9 - - - +
115C PHE* 4.0 25.1 - - + -
117C LEU* 3.9 17.4 - - + +
120C MET* 3.8 20.6 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR* 4.0 35.2 - - + -
42C THR 4.6 0.2 - - - +
43C SER* 3.5 30.1 - - - +
47C THR* 4.2 8.3 - - + -
48C LEU* 4.1 16.8 - - + -
84C PHE* 2.8 33.0 + - + +
85C ARG* 3.8 4.5 - - - +
87C ILE* 1.3 73.0 - - - +
89C ASN* 1.3 58.1 + - - +
91C LEU* 3.2 10.1 + - + +
92C ARG* 2.9 64.8 + - - +
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ARG* 2.9 19.4 + - + +
86C TYR* 4.0 7.6 - - + +
87C ILE 3.3 0.4 - - - -
88C LEU* 1.3 74.0 - - - +
90C PHE* 1.3 55.7 + - - +
92C ARG* 4.1 14.4 + - - +
93C THR* 2.7 49.5 + - - +
95C LYS 4.4 1.1 - - - +
97C LEU* 3.4 42.6 + - - +
80D ASP* 3.9 26.5 - - - +
107D LEU* 4.1 16.6 - - + +
111D GLU* 4.3 6.0 + - - +
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Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 3.8 31.7 - + - -
86C TYR 3.0 14.1 + - - +
87C ILE 3.1 8.9 + - - +
89C ASN* 1.3 75.4 - - - +
91C LEU* 1.3 61.8 + - - +
94C SER* 2.6 50.3 + - - -
95C LYS* 3.3 30.9 + - - +
96C LEU* 4.0 3.1 - - - -
117C LEU* 4.1 20.0 - - + -
119C PRO* 3.7 17.7 - - + -
120C MET* 3.3 61.2 - - + -
123C GLU* 4.6 5.2 - - + -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C THR* 3.6 28.3 - - + +
48C LEU* 4.2 20.9 - - + +
50C LYS* 2.9 33.3 + - - +
51C TYR* 3.7 28.7 - - + +
56C ILE* 4.0 31.9 - - + -
84C PHE* 5.4 1.3 - - + -
87C ILE* 3.0 21.5 + - + +
88C LEU* 3.2 14.6 + - + +
90C PHE* 1.3 76.9 - - + +
92C ARG* 1.3 57.3 + - - +
117C LEU* 3.9 24.0 - - + -
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR* 6.1 0.2 - - - -
42C THR 2.9 28.1 + - - -
47C THR* 3.7 19.3 - - + +
50C LYS* 3.1 16.3 + - - +
85C ARG* 5.6 2.8 + - - +
88C LEU* 2.9 46.1 + - - +
89C ASN* 3.7 16.5 + - - +
90C PHE 3.2 0.2 - - - -
91C LEU* 1.3 77.7 - - - +
93C THR* 1.3 65.4 + - + +
37D GLY* 3.6 17.0 + - - -
78D ASP* 2.9 34.3 + - - +
79D ARG* 3.5 43.3 + - - +
80D ASP* 3.7 15.0 + - - +
81D GLY 4.9 0.4 - - - +
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LYS* 5.2 0.2 - - - -
89C ASN* 2.7 33.9 + - - +
92C ARG* 1.3 79.3 - - + +
94C SER* 1.3 69.8 + - - +
95C LYS* 3.0 32.7 + - - +
97C LEU* 3.7 10.7 - - + +
79D ARG* 3.6 28.5 - - - +
110D GLU* 3.7 29.8 - - + +
111D GLU* 4.1 1.3 - - - +
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LYS* 4.0 15.2 + - - +
51C TYR* 2.7 27.5 + - - -
90C PHE* 2.6 36.3 + - - -
91C LEU 4.4 0.2 - - - -
92C ARG 3.7 0.6 - - - -
93C THR* 1.3 74.9 - - - +
95C LYS* 1.3 59.8 + - - +
123C GLU* 5.2 3.5 - - - +
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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