Contacts of the helix formed by residues 104 - 115 (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 ASP 104 (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 22.2 + - - -
99B PRO* 3.2 28.8 - - - +
83C MET* 3.4 27.0 - - + +
102C PHE* 3.4 24.6 - - + -
103C LYS* 1.3 83.6 - - - +
105C TYR* 1.3 63.0 + - - +
106C THR* 3.4 2.7 - - - -
107C LEU* 3.2 13.8 + - + +
108C LEU* 2.9 18.4 + - - +
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Residues in contact with TYR 105 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ASP* 5.2 8.5 + - - +
96C LEU* 5.8 0.4 - - + -
98C ILE* 5.6 1.6 - - + -
102C PHE* 3.4 14.4 - + + +
103C LYS 3.5 5.4 + - - -
104C ASP* 1.3 75.3 - - - +
106C THR* 1.3 69.6 + - + +
108C LEU 3.2 0.9 + - - -
109C TYR* 2.8 54.9 + + + +
124C MET* 3.1 61.5 + - + +
125C GLU* 3.6 8.1 + - - +
127C TRP* 3.8 26.9 - + + -
128C LYS* 3.4 45.0 - - + +
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Residues in contact with THR 106 (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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97B LEU* 4.0 20.5 - - - +
98B ILE 3.7 11.1 + - - +
99B PRO* 5.4 0.3 - - - +
100B ASP* 5.0 10.7 + - - +
103C LYS 5.6 0.2 + - - -
105C TYR* 1.3 88.9 - - + +
107C LEU* 1.3 77.2 + - - +
109C TYR* 3.9 4.7 - - - +
110C GLU* 3.4 20.8 + - - +
128C LYS* 6.1 1.1 - - - -
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Residues in contact with LEU 107 (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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85B ARG* 3.6 35.4 - - - +
86B TYR* 4.3 8.1 - - + -
89B ASN* 4.7 8.7 - - - +
97B LEU* 3.6 31.6 - - + +
98B ILE 3.5 26.0 - - - -
99B PRO* 3.7 8.3 - - + -
80C ASP* 5.3 0.4 - - - +
83C MET* 4.1 12.1 - - + +
104C ASP* 3.2 18.8 + - + +
105C TYR 3.2 0.4 - - - -
106C THR* 1.3 93.6 + - - +
108C LEU* 1.3 65.0 + - - +
110C GLU* 3.4 5.2 + - - +
111C GLU* 3.3 24.8 + - - +
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Residues in contact with LEU 108 (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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83C MET* 3.6 41.7 - - + +
86C TYR* 3.7 24.5 - - + -
87C ILE* 4.1 7.4 - - + -
96C LEU* 4.1 18.8 - - + -
98C ILE* 4.1 5.2 - - + -
102C PHE* 4.0 17.5 - - + -
104C ASP 2.9 16.2 + - - +
105C TYR 3.8 2.9 - - - +
107C LEU* 1.3 73.9 - - - +
109C TYR* 1.3 61.1 + - - +
111C GLU* 3.1 2.6 + - + +
112C ALA* 2.9 26.5 + - - +
120C MET* 3.9 11.0 - - + -
124C MET* 3.8 20.6 - - + -
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Residues in contact with TYR 109 (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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105C TYR* 2.8 50.8 + + + +
106C THR* 3.9 7.4 - - - +
108C LEU* 1.3 77.6 - - - +
110C GLU* 1.3 59.9 + - - +
112C ALA* 3.3 1.9 + - - +
113C LYS* 2.8 44.9 + - + +
121C LEU* 3.8 38.4 - - + +
124C MET* 3.6 17.2 - - + +
125C GLU* 2.8 30.2 + - + -
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Residues in contact with GLU 110 (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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93B THR* 4.0 12.8 - - + +
95B LYS* 3.0 45.6 + - - +
97B LEU* 3.6 29.5 - - + +
79C ARG* 3.8 14.9 + - - +
106C THR 3.4 6.8 + - - +
107C LEU 3.6 6.5 - - - +
108C LEU 3.2 0.6 - - - -
109C TYR* 1.3 81.8 - - - +
111C GLU* 1.3 58.6 + - - +
113C LYS* 3.4 12.0 + - - +
114C TYR* 2.8 28.4 + - - +
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Residues in contact with GLU 111 (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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89B ASN* 4.7 3.5 - - - +
93B THR* 4.6 4.3 - - - +
97B LEU* 5.7 0.7 - - - +
79C ARG* 2.8 54.3 + - - +
80C ASP* 3.8 20.7 + - + +
83C MET* 3.8 23.3 - - + -
84C PHE 5.7 0.2 - - - +
87C ILE* 3.9 17.7 - - + -
107C LEU 3.3 15.0 + - - +
108C LEU 3.1 7.0 + - - +
110C GLU* 1.3 77.8 - - - +
112C ALA* 1.3 59.5 + - - +
114C TYR* 3.2 2.1 + - - +
115C PHE* 2.9 44.3 + - + -
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Residues in contact with ALA 112 (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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87C ILE* 3.7 8.9 - - + +
108C LEU 2.9 16.5 + - - +
109C TYR 3.8 0.9 - - - +
111C GLU* 1.3 76.4 - - - +
113C LYS* 1.3 57.9 + - - +
115C PHE* 3.6 1.6 + - - -
116C GLN 3.0 5.7 + - - -
117C LEU* 3.0 31.0 + - + -
120C MET* 3.9 32.8 - - + -
121C LEU* 3.7 21.9 - - + +
124C MET* 4.3 6.1 - - - -
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Residues in contact with LYS 113 (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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95B LYS* 6.1 1.1 - - - +
109C TYR* 2.8 31.9 + - + +
110C GLU* 3.5 16.2 - - - +
112C ALA* 1.3 74.9 - - - +
114C TYR* 1.3 66.1 + - - +
116C GLN* 3.0 18.9 + - - +
118C GLN* 5.2 3.6 + - - -
121C LEU* 3.7 27.8 - - + +
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Residues in contact with TYR 114 (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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55C ARG* 3.6 51.2 + - + -
59C LEU* 5.6 4.7 - - + +
77C ILE* 5.2 2.5 - - + +
79C ARG* 3.4 62.4 - - + +
110C GLU* 2.8 22.5 + - - +
111C GLU 3.2 3.8 + - - +
113C LYS* 1.3 73.8 - - - +
115C PHE* 1.3 79.7 + + - +
116C GLN* 3.0 15.6 + - - +
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Residues in contact with PHE 115 (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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54C SER* 3.5 5.5 - - - -
55C ARG* 2.9 25.0 + - + -
56C ILE* 3.5 41.5 + - + -
59C LEU* 4.6 5.6 - - + -
77C ILE* 4.0 17.0 - - + -
79C ARG* 3.9 19.7 - - + -
80C ASP 6.1 0.2 - - - -
84C PHE* 3.9 29.8 - + + -
87C ILE* 4.0 19.1 - - + -
111C GLU* 2.9 44.3 + - + +
112C ALA 4.3 2.0 - - - +
114C TYR* 1.3 90.8 - + - +
116C GLN* 1.3 66.6 + - - +
117C LEU* 3.3 11.5 + - + +
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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