Contacts of the helix formed by residues 124 - 145 (chain C) in PDB entry 4FJV
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 124 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LYS* 3.0 13.7 + - + +
121C VAL* 3.1 12.0 + - - +
123C ASN* 1.3 75.8 - - - +
125C GLN* 1.3 59.1 + - - +
126C SER* 3.2 8.3 + - - -
127C ALA* 3.1 31.7 + - + +
128C SER* 2.8 35.3 + - - -
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Residues in contact with GLN 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASN* 4.8 6.2 + - - -
8C LEU* 3.7 33.8 - - - +
46C LYS* 5.6 2.3 - - - +
48C ASP* 5.2 1.6 + - - -
54C ARG* 4.6 3.0 - - - +
123C ASN 3.5 4.4 + - - +
124C ASP* 1.3 71.6 + - - +
126C SER* 1.3 57.7 + - - +
128C SER* 4.1 0.3 - - - -
129C ASP* 2.9 71.3 + - - +
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ASP* 3.3 7.4 + - - -
125C GLN* 1.3 82.3 - - - +
127C ALA* 1.3 62.5 + - - +
129C ASP* 3.9 2.8 - - - +
130C HIS* 2.8 48.5 + - - -
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ALA* 4.6 4.7 - - + +
121C VAL* 3.9 24.5 - - + +
124C ASP* 3.1 20.5 + - + +
126C SER* 1.3 76.7 + - - +
128C SER* 1.3 62.4 + - - +
130C HIS* 3.4 7.5 + - - +
131C ILE* 3.1 29.9 + - + +
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Residues in contact with SER 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.9 5.4 - - - -
54C ARG* 2.8 35.4 + - - +
121C VAL 3.8 2.4 + - - -
122C PHE* 2.9 38.0 + - - -
124C ASP 2.8 20.4 + - - -
127C ALA* 1.3 70.7 - - - +
129C ASP* 1.3 65.2 + - - +
131C ILE* 3.2 12.3 + - - +
132C VAL* 3.0 22.7 + - - +
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASN* 5.0 0.8 + - - -
54C ARG* 3.1 27.7 + - - +
125C GLN* 2.9 47.3 + - - +
126C SER* 3.9 4.7 - - - +
128C SER* 1.3 76.2 - - - +
130C HIS* 1.3 58.3 + - - +
132C VAL* 3.3 0.8 + - - -
133C GLN* 2.8 27.9 + - - +
171C MET* 3.4 26.2 - - + +
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Residues in contact with HIS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASN* 3.9 28.2 + - + +
98C PHE* 3.8 37.1 - + - +
101C ALA* 3.5 20.6 - - + -
126C SER* 2.8 44.5 + - - +
127C ALA* 3.6 4.9 - - - +
128C SER 3.2 0.2 - - - -
129C ASP* 1.3 75.9 - - - +
131C ILE* 1.3 61.2 - - - +
133C GLN* 3.5 2.1 + - - +
134C PHE* 3.0 28.1 + - - +
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Residues in contact with ILE 131 (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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101C ALA* 4.2 17.0 - - + +
102C PHE* 3.8 20.4 - - + +
105C VAL* 3.8 27.8 - - + -
121C VAL* 3.9 22.2 - - + -
122C PHE* 3.9 32.8 - - + -
127C ALA* 3.1 17.9 + - + +
128C SER* 3.5 9.2 - - - +
130C HIS* 1.3 76.5 - - - +
132C VAL* 1.3 64.1 + - + +
134C PHE* 3.3 7.6 + - - +
135C LEU* 3.0 34.5 + - + +
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Residues in contact with VAL 132 (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 ASN* 3.5 29.8 - - + +
53C TYR* 4.0 9.6 - - + -
54C ARG* 3.7 50.0 - - + +
128C SER 3.0 17.6 + - - +
129C ASP 3.3 6.9 + - - +
131C ILE* 1.3 77.5 - - + +
133C GLN* 1.3 58.5 + - - +
135C LEU* 3.0 11.6 + - - +
136C ARG* 2.9 39.0 + - - +
171C MET* 3.6 9.4 - - + -
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Residues in contact with GLN 133 (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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98C PHE* 3.6 41.8 - - + -
129C ASP 2.8 19.6 + - - +
131C ILE 3.4 0.2 - - - -
132C VAL* 1.3 73.0 - - - +
134C PHE* 1.3 62.0 + - - +
136C ARG* 3.3 7.8 + - - +
137C LEU* 3.1 38.5 + - + +
169C GLU 2.8 27.3 + - - +
170C PRO* 5.0 0.3 - - - +
171C MET* 3.4 29.5 + - - +
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Residues in contact with PHE 134 (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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78C VAL* 5.2 0.9 - - + -
81C THR* 3.5 22.9 - - + -
85C LEU* 4.3 18.6 - - + -
95C PHE* 5.4 0.4 - - + -
98C PHE* 3.4 27.0 - - + +
99C PHE* 3.6 40.4 - + + -
102C PHE* 3.5 45.5 - + + -
130C HIS 3.0 9.2 + - - +
131C ILE 3.5 6.5 - - - +
132C VAL 3.2 0.2 - - - -
133C GLN* 1.3 76.7 - - - +
135C LEU* 1.3 71.3 + - + +
137C LEU* 3.2 7.5 + - + +
138C LEU* 3.0 44.2 + - + +
187C LEU* 5.4 0.7 - - + -
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Residues in contact with LEU 135 (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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53C TYR* 3.5 36.1 - - + +
56C LEU* 5.7 0.9 - - + -
57C GLY* 4.1 17.7 - - - +
102C PHE* 4.0 15.7 - - + -
131C ILE* 3.0 31.3 + - + +
132C VAL* 3.0 7.6 + - - +
134C PHE* 1.3 83.9 - - + +
136C ARG* 1.3 56.1 + - - +
138C LEU* 3.4 4.9 + - + +
139C THR* 2.8 33.5 + - - -
183C LEU* 4.0 21.1 - - + +
187C LEU* 3.7 29.2 - - + -
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Residues in contact with ARG 136 (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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49C GLY 3.3 12.3 + - - -
50C ASN* 3.2 27.3 + - - -
53C TYR* 3.3 34.9 + - + -
132C VAL* 2.9 19.9 + - + +
133C GLN* 3.5 13.7 - - - +
134C PHE 3.2 0.2 - - - -
135C LEU* 1.3 77.8 - - - +
137C LEU* 1.3 57.3 + - - +
139C THR* 3.3 7.9 + - - -
140C SER* 3.0 24.6 + - - -
167C GLU 4.7 0.4 + - - -
168C VAL* 2.8 45.9 + - - +
169C GLU* 3.6 9.4 - - - +
170C PRO 3.2 17.9 + - - -
171C MET* 3.6 14.8 - - - +
173C THR* 2.8 43.9 + - - +
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Residues in contact with LEU 137 (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 LEU* 3.7 14.7 - - + +
90C PHE* 3.8 29.4 - - + -
94C LYS 5.2 0.7 - - - +
95C PHE* 4.0 26.7 - - + -
98C PHE* 4.1 24.9 - - + -
133C GLN* 3.1 36.6 + - + +
134C PHE* 3.7 6.7 - - + +
136C ARG* 1.3 72.4 - - - +
138C LEU* 1.3 60.2 + - - +
140C SER* 3.3 5.4 + - - -
141C ALA* 2.8 30.5 + - - +
169C GLU* 4.2 13.2 - - + -
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Residues in contact with LEU 138 (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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81C THR* 3.8 33.9 - - + +
84C ASP* 4.3 12.8 - - + +
85C LEU* 3.9 19.0 - - + +
134C PHE* 3.0 31.4 + - + +
135C LEU* 3.7 7.0 - - + +
137C LEU* 1.3 78.0 - - - +
139C THR* 1.3 56.7 + - - +
141C ALA* 3.5 2.2 + - + +
142C PHE* 3.0 28.6 + - - +
183C LEU* 4.7 2.5 - - + -
186C ALA* 4.2 17.2 - - + +
187C LEU* 3.5 38.8 - - + -
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Residues in contact with THR 139 (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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53C TYR* 3.8 5.6 - - - +
135C LEU 2.8 19.9 + - - -
136C ARG* 3.5 9.2 - - - -
137C LEU 3.2 0.2 - - - -
138C LEU* 1.3 76.8 - - - +
140C SER* 1.3 61.2 + - - +
142C PHE* 3.3 7.0 + - - +
143C ILE* 3.2 25.6 + - + +
168C VAL* 3.7 17.0 - - + -
179C GLN* 3.5 38.1 - - + +
182C ALA* 4.0 8.1 - - + -
183C LEU* 3.5 27.0 - - - +
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Residues in contact with SER 140 (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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90C PHE* 3.8 2.7 - - - -
136C ARG 3.0 10.0 + - - -
137C LEU 3.3 7.6 + - - -
139C THR* 1.3 76.5 - - - +
141C ALA* 1.3 56.7 + - - +
143C ILE* 3.3 2.6 + - - +
144C ARG* 2.9 39.7 + - - +
164C CYS* 3.1 22.5 - - - +
168C VAL* 3.6 10.2 - - - +
169C GLU* 2.7 42.9 + - - -
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Residues in contact with ALA 141 (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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84C ASP* 3.9 13.7 - - + +
85C LEU* 3.8 19.5 - - + -
88C ALA* 3.7 24.5 - - + -
90C PHE* 3.8 4.1 - - + -
137C LEU 2.8 21.1 + - - +
138C LEU* 3.6 8.3 - - + +
139C THR 3.4 0.2 - - - -
140C SER* 1.3 72.2 - - - +
142C PHE* 1.3 62.0 + - - +
144C ARG* 3.8 0.3 - - - +
145C ASN* 2.9 32.6 + - - +
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Residues in contact with PHE 142 (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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84C ASP* 6.5 0.2 - - - -
138C LEU 3.0 15.3 + - - +
139C THR* 3.3 9.8 + - - +
141C ALA* 1.3 75.8 - - - +
143C ILE* 1.3 61.8 + - - +
145C ASN* 4.8 0.9 - - - +
146C ARG* 3.0 78.8 + - - +
150C PHE* 4.0 13.7 - + - -
182C ALA* 3.7 26.7 - - + +
185C GLN* 3.4 42.2 - - + -
186C ALA* 3.7 30.3 - - + -
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Residues in contact with ILE 143 (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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139C THR* 3.2 23.0 + - + +
140C SER 3.6 6.1 - - - +
142C PHE* 1.3 74.5 - - - +
144C ARG* 1.3 66.7 + - - +
146C ARG 2.9 14.2 + - - +
147C ALA* 3.0 12.8 + - - -
150C PHE* 4.0 18.8 - - + -
160C ILE* 3.9 24.7 - - + -
163C PHE* 4.3 4.3 - - + -
164C CYS* 3.6 17.7 - - - -
168C VAL* 4.3 18.8 - - + -
178C ILE* 3.6 28.5 - - + +
179C GLN* 4.7 0.4 - - - -
182C ALA* 3.8 19.7 - - + -
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Residues in contact with ARG 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA* 3.9 31.5 + - + +
90C PHE* 4.0 7.5 - - - -
140C SER* 2.9 35.7 + - - +
141C ALA 3.9 2.5 - - - +
143C ILE* 1.3 72.7 - - - +
145C ASN* 1.3 62.0 + - - +
146C ARG 3.2 1.0 + - - -
147C ALA* 3.4 19.5 + - - +
160C ILE* 4.8 5.6 - - + -
161C LYS* 3.6 34.8 + - + +
164C CYS* 3.9 14.8 - - - -
165C THR* 2.9 29.1 + - - +
169C GLU* 2.9 21.2 + - - -
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Residues in contact with ASN 145 (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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84C ASP* 3.2 34.4 + - - +
87C ALA* 3.5 16.0 - - - +
88C ALA* 3.4 22.6 + - - +
141C ALA* 2.9 23.0 + - - +
142C PHE* 4.9 0.4 - - - +
144C ARG* 1.3 76.4 - - - +
146C ARG* 1.3 78.9 + - - +
147C ALA 3.7 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
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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