Contacts of the helix formed by residues 105 - 126 (chain C) in PDB entry 4D2W
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 SER 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 6.1 0.2 - - - +
104C LEU* 1.3 73.1 - - - +
106C GLU* 1.3 57.5 + - - +
107C GLU* 3.6 14.7 + - - +
108C GLU* 2.9 29.5 + - - +
109C THR* 2.8 30.5 + - - -
203C MET* 4.9 0.2 - - - -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU 3.9 0.2 + - - -
105C SER* 1.3 71.8 - - - +
107C GLU* 1.3 71.5 + - - +
109C THR* 3.4 3.0 + - - -
110C ARG* 2.9 53.1 + - - +
203C MET* 4.2 14.5 - - - +
233C SER* 2.9 32.6 + - - -
235C SER* 3.6 1.9 + - - -
236C SER* 3.7 9.5 + - - +
262C TRP* 3.6 18.0 + - + +
265C GLN* 3.3 19.4 + - - +
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C SER* 3.2 12.1 - - - +
106C GLU* 1.3 92.4 + - - +
108C GLU* 1.3 64.7 + - - +
110C ARG* 3.3 15.3 + - - +
111C VAL* 3.3 24.4 + - - +
265C GLN* 5.7 0.5 - - - +
266C ASP* 4.5 17.0 - - - +
267C TYR* 4.7 0.7 + - - -
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Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TYR* 2.6 40.2 + - - -
101C GLN* 4.4 6.6 - - - +
104C LEU* 3.7 29.0 - - + +
105C SER* 2.9 21.5 + - - +
107C GLU* 1.3 73.4 - - - +
109C THR* 1.3 66.4 + - - +
111C VAL* 3.3 12.3 + - + +
112C VAL* 3.3 25.0 + - + +
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Residues in contact with THR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 3.4 22.3 - - - +
105C SER 2.8 21.0 + - - -
106C GLU 3.6 5.6 - - - -
108C GLU* 1.3 74.8 - - - +
110C ARG* 1.4 52.0 + - - +
112C VAL* 3.3 3.6 + - - +
113C PHE* 2.7 37.0 + - + +
199C LEU* 4.0 20.2 - - + -
202C LEU* 3.6 28.2 + - + +
203C MET* 3.3 29.3 - - + +
262C TRP* 4.2 2.5 - - + -
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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
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106C GLU* 2.9 45.4 + - - +
107C GLU* 3.6 17.5 + - - +
108C GLU 3.2 0.4 - - - -
109C THR* 1.4 72.0 - - - +
111C VAL* 1.4 65.5 + - - +
113C PHE 4.3 0.4 - - - +
114C ARG* 3.0 34.3 + - + +
262C TRP* 2.7 58.6 + - + +
263C ILE 3.7 9.9 - - - +
265C GLN* 3.5 23.6 + - - +
266C ASP* 2.8 28.7 + - - -
267C TYR* 3.5 29.4 - - + -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLU 3.3 14.1 + - - +
108C GLU* 3.3 14.5 + - + +
110C ARG* 1.4 77.9 - - - +
112C VAL* 1.3 63.6 + - + +
114C ARG* 4.0 3.3 + - - +
115C GLN* 3.1 35.0 + - - +
267C TYR* 3.0 24.8 + - + +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 4.0 13.2 - - + -
97C TYR* 5.2 4.0 - - + -
104C LEU* 4.8 9.4 - - + -
108C GLU* 3.3 14.2 + - + +
109C THR* 3.7 7.2 - - - +
110C ARG 3.3 0.2 - - - -
111C VAL* 1.3 80.8 - - + +
113C PHE* 1.3 65.8 + - - +
115C GLN* 3.2 23.6 + - - +
116C ILE* 3.2 18.0 + - + +
140C PHE* 4.3 25.1 - - + -
144C HIS* 5.6 2.0 - - + +
146C LEU* 3.7 18.4 - - + +
202C LEU* 3.9 25.6 - - + -
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Residues in contact with PHE 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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109C THR* 2.7 24.6 + - + +
110C ARG 3.3 2.2 + - - +
112C VAL* 1.3 74.3 - - - +
114C ARG* 1.3 56.0 + - - +
116C ILE* 3.1 22.1 + - + +
117C VAL* 2.9 48.4 + - + +
195C MET* 3.3 37.5 - - + -
198C LEU* 4.6 3.6 - - + -
199C LEU* 3.8 28.3 - - + -
202C LEU* 4.3 9.4 - - + -
239C LEU* 4.6 3.8 - - + -
243C MET* 3.9 26.2 - - + -
257C LEU* 4.7 1.3 - - + -
262C TRP* 3.9 15.0 - + + -
263C ILE* 3.7 23.3 - - + -
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Residues in contact with ARG 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 3.0 18.9 + - + +
111C VAL* 4.1 4.7 - - - +
113C PHE* 1.3 76.0 - - - +
115C GLN* 1.4 56.9 + - + +
117C VAL* 4.5 1.6 - - - -
118C SER* 3.1 27.2 + - - -
263C ILE* 2.9 46.2 + - + +
267C TYR* 3.4 47.7 + - + +
269C TYR* 3.1 53.7 + - - -
270C PRO 3.4 10.7 + - - -
271C VAL* 3.7 30.1 - - + +
272C GLU 4.7 1.0 - - - +
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Residues in contact with GLN 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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68C HIS* 3.3 40.4 - - + +
111C VAL* 3.1 35.2 + - - +
112C VAL* 3.2 16.3 + - - +
114C ARG* 1.4 75.7 - - + +
116C ILE* 1.3 64.1 + - - +
118C SER* 3.4 3.3 + - - -
119C ALA* 3.2 23.0 + - - +
140C PHE* 5.5 0.8 - - - -
144C HIS 4.7 8.1 + - - -
145C LYS* 3.5 14.0 - - + +
146C LEU* 2.8 41.6 + - + +
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Residues in contact with ILE 116 (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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94C LEU* 4.0 7.4 - - + -
112C VAL* 3.6 30.5 - - + +
113C PHE* 3.1 25.7 + - + +
115C GLN* 1.3 75.4 - - - +
117C VAL* 1.4 62.0 + - - +
119C ALA* 3.5 4.4 + - - +
120C VAL* 3.1 30.1 + - + +
133C LEU* 5.6 2.0 - - + -
138C LEU* 3.8 37.0 - - + -
146C LEU* 3.9 8.3 - - + -
195C MET* 4.2 25.1 - - + -
198C LEU* 4.3 17.9 - - + -
202C LEU* 4.4 4.9 - - + -
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Residues in contact with VAL 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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113C PHE* 2.9 49.0 + - + +
114C ARG 4.0 4.3 - - - +
115C GLN 3.3 0.2 - - - -
116C ILE* 1.4 74.8 - - - +
118C SER* 1.4 54.1 + - - +
120C VAL* 3.4 0.3 + - - +
121C ALA* 2.8 34.1 + - - +
195C MET* 4.4 9.2 - - - -
254C MET* 4.4 4.6 - - - +
257C LEU* 3.9 30.3 - - + +
258C LEU* 3.8 26.5 - - + -
263C ILE* 4.2 7.4 - - + -
271C VAL* 4.1 13.5 - - + -
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C HIS* 3.2 25.6 + - - -
67C GLN* 4.2 1.0 + - - -
68C HIS* 3.7 12.3 - - - -
114C ARG 3.1 19.4 + - - -
115C GLN* 3.4 7.2 - - - -
117C VAL* 1.4 73.8 - - - +
119C ALA* 1.3 61.8 + - - +
122C TYR 3.2 17.7 + - - -
271C VAL* 3.6 12.7 - - - +
272C GLU 3.0 23.6 + - - -
273C TRP* 3.6 8.6 - - - +
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Residues in contact with ALA 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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66C HIS* 3.7 13.1 - - - -
68C HIS* 3.5 27.4 - - + +
69C ILE* 4.5 3.1 - - + +
115C GLN 3.2 9.5 + - - +
116C ILE* 3.7 9.6 - - - +
117C VAL 3.4 0.2 - - - -
118C SER* 1.3 77.9 + - - +
120C VAL* 1.3 58.3 + - - +
122C TYR* 3.2 6.2 + - - +
123C VAL* 2.9 31.6 + - - +
138C LEU* 5.9 2.0 - - + -
148C LEU* 4.3 17.9 - - + -
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Residues in contact with VAL 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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116C ILE* 3.1 22.4 + - + +
117C VAL 4.2 0.9 - - - +
119C ALA* 1.3 72.4 - - + +
121C ALA* 1.3 65.6 + - - +
123C VAL* 3.3 7.6 + - + +
124C HIS* 3.0 53.0 + - + +
130C HIS* 5.8 1.1 - - + -
133C LEU* 3.8 30.3 - - + -
148C LEU* 4.5 8.5 - - + -
191C ASP* 4.2 10.8 - - + +
195C MET* 3.9 21.3 - - + -
254C MET* 3.7 9.4 - - + -
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Residues in contact with ALA 121 (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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117C VAL 2.8 18.7 + - - +
120C VAL* 1.3 76.6 - - - +
122C TYR* 1.3 55.5 + - - +
124C HIS* 3.5 3.3 + - - +
125C SER* 3.0 27.7 + - - -
254C MET* 3.8 33.0 - - + +
258C LEU* 3.8 11.0 - - + -
273C TRP* 3.6 26.8 - - + -
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Residues in contact with TYR 122 (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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63C ASN 3.9 3.6 + - - -
64C LEU* 3.7 24.5 - - + -
65C ARG 3.0 37.2 + - - -
66C HIS* 3.3 39.5 - + + -
69C ILE* 3.8 10.8 - - + -
118C SER 3.2 7.1 + - - +
119C ALA 3.2 4.9 + - - +
121C ALA* 1.3 73.5 - - - +
123C VAL* 1.3 68.6 + - - +
125C SER* 2.6 28.2 + - - -
126C GLN* 3.2 32.9 + - + +
273C TRP* 3.5 17.0 - + - +
275C SER* 3.8 23.8 - - - -
279C PHE* 4.4 6.4 - - - -
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 4.4 7.0 - - + -
69C ILE* 3.7 23.6 - - + -
119C ALA 2.9 21.9 + - - +
120C VAL* 3.6 10.8 - - + +
122C TYR* 1.3 75.7 - - - +
124C HIS* 1.3 66.4 + - + +
126C GLN* 3.2 14.2 + - - +
127C GLY 3.6 0.2 + - - -
128C TYR* 3.2 45.2 + - + +
129C ALA 4.4 0.2 - - - -
130C HIS* 4.2 15.7 - - + +
148C LEU* 4.3 8.1 - - + -
151C PHE* 3.9 22.4 - - + -
191C ASP* 5.0 0.2 - - - +
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Residues in contact with HIS 124 (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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120C VAL* 3.0 29.7 + - + +
121C ALA* 3.8 5.6 - - - +
123C VAL* 1.3 78.2 - - + +
125C SER* 1.3 62.5 + - - +
127C GLY* 3.1 14.7 + - - -
128C TYR 3.2 20.2 - - - -
129C ALA* 4.3 0.4 - - - -
188C SER* 3.3 45.0 + - - -
191C ASP* 2.7 34.4 + - + +
192C VAL* 4.8 2.4 - - + +
254C MET* 3.6 25.9 - - + +
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Residues in contact with SER 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ALA 3.0 14.7 + - - -
122C TYR* 2.6 24.3 + - - -
124C HIS* 1.3 74.6 - - - +
126C GLN* 1.3 65.8 + - - +
127C GLY 3.3 1.4 + - - -
273C TRP* 3.3 33.4 - - - -
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Residues in contact with GLN 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ASN* 4.4 11.3 + - - +
64C LEU* 3.8 17.0 - - + -
122C TYR* 3.6 42.2 - - + +
123C VAL 3.2 9.4 + - - +
124C HIS 3.1 1.0 - - - -
125C SER* 1.3 84.6 + - - +
127C GLY* 1.3 60.4 + - - +
128C TYR* 3.4 17.5 - - + -
279C PHE* 6.2 0.4 - - - -
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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