Contacts of the helix formed by residues 104 - 122 (chain C) in PDB entry 5D0A
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLY 3.4 1.2 + - - -
103C LYS* 1.3 69.9 - - - +
105C TYR* 1.3 66.8 + - - +
106C HIS* 2.5 41.7 + - - +
107C ASP* 2.9 33.7 + - - +
108C VAL* 3.2 8.0 + - - +
289C HIS* 2.9 21.3 + - - +
290C VAL 4.1 2.2 - - - +
291C SER* 3.3 33.2 - - - +
294C TRP* 6.0 1.7 - - - +
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Residues in contact with TYR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA* 4.0 14.3 + - + -
103C LYS 3.1 6.7 + - - -
104C ASP* 1.3 78.2 + - - +
106C HIS* 1.3 78.6 + + - +
108C VAL* 3.7 9.4 - - - -
109C LEU* 2.8 35.8 + - + +
133C VAL* 3.8 25.1 - - + -
134C ASP* 3.0 31.5 + - + +
168C TYR* 3.4 60.7 + + + -
261C MET* 6.0 0.2 - - - -
291C SER* 4.0 10.5 - - - -
503C B12 3.9 24.0 - - + +
504C GOL 4.0 4.7 + - - -
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Residues in contact with HIS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ASP* 2.5 38.7 + - - +
105C TYR* 1.3 106.0 + + - +
107C ASP* 1.3 60.0 + - - +
110C ARG* 3.1 30.7 + - - +
133C VAL* 3.6 35.2 - - + +
134C ASP* 2.9 26.3 + - + -
135C THR* 4.0 15.1 - - + +
291C SER* 4.5 7.4 - - - -
294C TRP* 5.9 8.7 - + + -
504C GOL 5.3 3.1 - - - -
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Residues in contact with ASP 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 3.6 35.0 + - - +
104C ASP* 2.9 28.2 + - - +
106C HIS* 1.3 78.9 - - - +
108C VAL* 1.3 63.7 + - - +
110C ARG* 3.9 4.3 - - - +
111C GLU* 3.1 24.3 + - - +
289C HIS* 5.2 2.3 + - - +
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 4.2 17.7 - - + -
103C LYS* 3.7 30.3 - - + +
104C ASP 3.2 13.8 + - - +
105C TYR* 3.9 8.5 - - - +
107C ASP* 1.3 76.8 - - - +
109C LEU* 1.3 65.2 + - + +
111C GLU* 3.3 9.4 + - - +
112C LYS* 3.3 22.7 + - - +
260C GLU* 3.4 32.1 - - + +
261C MET* 4.3 13.5 - - + -
505C PO4 4.0 9.6 - - - +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 4.5 5.5 - - + +
75C LEU* 4.1 29.2 - - + -
105C TYR* 2.8 22.3 + - + +
108C VAL* 1.3 85.4 - - + +
110C ARG* 1.3 61.2 + - - +
112C LYS* 3.3 6.7 + - - +
113C LEU* 2.9 35.0 + - - +
133C VAL* 4.2 9.0 - - + -
168C TYR* 3.7 40.4 - - + +
169C LEU 3.6 17.5 - - - +
170C ALA* 3.5 31.2 - - + +
261C MET* 4.7 0.2 - - + -
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C HIS 3.1 22.5 + - - +
107C ASP* 3.9 5.4 - - - +
109C LEU* 1.3 76.0 - - - +
111C GLU* 1.3 58.8 + - - +
113C LEU* 3.3 14.3 + - - -
114C ASP* 2.9 61.0 + - - +
117C GLU* 4.8 5.5 + - - -
131C SER* 3.5 37.4 + - - +
132C MET* 4.6 4.2 - - - +
133C VAL* 4.3 9.3 - - + +
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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
----------------------------------------------------------
107C ASP 3.1 18.8 + - - +
108C VAL* 3.4 6.0 - - - +
109C LEU 3.2 0.2 - - - -
110C ARG* 1.3 77.9 - - - +
112C LYS* 1.3 91.0 + - - +
114C ASP* 3.5 9.1 + - - +
115C LEU* 3.3 37.9 + - + +
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ILE* 2.8 47.7 + - + +
18C GLY* 5.0 0.2 - - - -
19C VAL* 4.5 5.8 - - + -
73C ILE* 4.4 13.9 - - + -
75C LEU* 4.4 22.7 - - + -
108C VAL* 3.3 15.0 + - - +
109C LEU* 3.3 7.8 + - - +
110C ARG 3.2 0.4 - - - -
111C GLU* 1.3 95.6 + - - +
113C LEU* 1.3 65.0 + - - +
115C LEU* 3.3 7.3 + - + +
116C LEU* 3.0 27.1 + - - +
260C GLU* 5.2 0.6 + - - -
505C PO4 2.6 41.1 + - - -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 3.7 26.2 - - + -
109C LEU 2.9 21.8 + - - +
110C ARG* 3.6 16.4 - - - +
112C LYS* 1.3 71.7 - - - +
114C ASP* 1.3 56.6 - - - +
116C LEU* 3.0 9.1 + - + +
117C GLU* 2.7 37.3 + - - +
131C SER* 3.8 28.3 - - - +
132C MET 3.8 23.6 - - - +
133C VAL* 4.6 1.1 - - + -
170C ALA* 4.0 8.3 - - + -
171C GLU* 4.0 23.3 - - - +
172C MET* 4.2 13.4 - - + +
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Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 2.9 55.9 + - - +
111C GLU* 3.7 8.8 - - - +
113C LEU* 1.3 74.5 - - - +
115C LEU* 1.3 58.8 + - + +
117C GLU* 3.5 15.9 - - - +
118C ASP* 2.9 28.8 + - - +
131C SER* 5.6 0.2 - - - -
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 3.7 22.6 + - - +
17C ILE* 4.0 34.8 - - + -
111C GLU* 3.3 39.3 + - + +
112C LYS* 3.6 8.5 - - + +
113C LEU 3.2 0.4 - - - -
114C ASP* 1.3 77.3 - - + +
116C LEU* 1.3 60.5 + - - +
118C ASP* 3.3 6.5 + - + +
119C PHE* 2.9 28.9 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.1 13.4 - - + +
13C TYR* 4.0 13.9 - - + -
14C ALA* 3.9 34.5 - - + -
17C ILE* 3.9 13.0 - - + -
19C VAL* 4.7 4.9 - - + -
22C ILE* 4.6 6.5 - - + -
71C VAL* 4.9 5.4 - - + -
73C ILE* 4.0 31.0 - - + -
112C LYS 3.0 17.5 + - - +
113C LEU* 3.0 11.2 + - + +
115C LEU* 1.3 75.5 - - - +
117C GLU* 1.3 62.6 + - - +
119C PHE* 3.2 7.5 - - - +
120C LEU* 3.2 25.5 + - - +
172C MET* 4.2 16.2 - - + -
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Residues in contact with GLU 117 (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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110C ARG* 4.8 6.8 + - - -
113C LEU 2.7 18.5 + - - +
114C ASP* 3.5 19.8 - - - +
116C LEU* 1.3 73.3 - - - +
118C ASP* 1.3 59.0 + - - +
120C LEU* 2.9 7.7 + - - +
121C LYS* 2.9 57.3 + - + +
129C THR* 3.5 20.1 + - - +
131C SER* 4.2 11.4 + - - -
172C MET* 4.0 16.2 - - - -
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Residues in contact with ASP 118 (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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114C ASP 2.9 18.4 + - - +
115C LEU* 3.3 8.7 + - + +
117C GLU* 1.3 74.5 - - - +
119C PHE* 1.3 60.1 + - - +
121C LYS* 4.3 9.8 - - - +
122C SER* 2.9 38.1 + - - -
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Residues in contact with PHE 119 (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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6C LEU* 4.0 17.3 - - + -
9C GLU* 3.7 28.0 - - + -
10C LEU* 3.7 41.1 - - + -
13C TYR* 3.7 37.9 - + + -
115C LEU 2.9 14.2 + - - +
116C LEU 3.2 8.7 - - - +
118C ASP* 1.3 77.6 - - - +
120C LEU* 1.3 65.2 + - + +
122C SER* 2.9 21.6 + - - -
123C LYS* 3.4 35.7 - - - +
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Residues in contact with LEU 120 (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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6C LEU* 4.2 15.9 - - + -
10C LEU* 4.5 9.2 - - + -
116C LEU 3.4 9.9 - - - +
117C GLU* 2.9 7.9 + - - +
119C PHE* 1.3 96.4 - - + +
121C LYS* 1.3 66.4 + - + +
122C SER 3.1 1.6 - - - -
123C LYS* 3.1 19.7 + - - +
124C HIS 3.6 5.0 + - - -
127C ILE* 3.6 23.0 - - + +
129C THR* 4.0 14.8 - - + -
172C MET* 3.6 30.5 - - + -
174C THR* 4.1 3.4 - - + -
176C ILE* 3.8 31.6 - - + -
178C PHE* 4.7 3.6 - - + -
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU* 2.9 46.8 + - + +
118C ASP* 3.9 11.9 - - - +
120C LEU* 1.3 80.0 - - + +
122C SER* 1.3 61.0 + - - +
123C LYS 3.2 7.8 + - - +
124C HIS 4.0 9.2 + - - -
127C ILE* 3.6 26.9 - - - +
128C ARG* 4.6 0.7 - - - +
129C THR* 3.6 25.0 + - + +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ASP* 2.9 23.1 + - - -
119C PHE* 2.9 19.0 + - - -
120C LEU 3.1 0.4 - - - -
121C LYS* 1.3 76.4 - - - +
123C LYS* 1.3 68.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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