Contacts of the helix formed by residues 110 - 128 (chain C) in PDB entry 3SF4
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 ASN 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 3.0 27.6 + - + +
108C LEU* 3.3 6.2 + - + +
109C GLY* 1.3 74.5 - - - +
111C PHE* 1.3 60.7 + - - +
112C ASP* 3.8 4.5 + - - +
113C GLU* 3.0 51.4 + - - +
114C ALA* 3.1 18.7 + - - +
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Residues in contact with PHE 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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106C LYS* 3.7 25.4 - - + -
109C GLY* 3.1 33.5 + - - -
110C ASN* 1.3 68.3 - - - +
112C ASP* 1.3 64.3 + - - +
114C ALA* 3.0 5.4 + - - +
115C ILE* 2.7 36.4 + - + +
144C VAL* 3.9 11.7 - - + -
147C ALA* 3.5 37.5 - - + -
148C LYS* 3.7 34.8 - - + -
151C SER* 3.3 31.0 - - - -
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Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASN* 3.4 4.2 - - - +
111C PHE* 1.3 78.3 - - - +
113C GLU* 1.3 64.7 + - + +
115C ILE* 3.3 8.9 + - - +
116C VAL* 3.2 24.9 + - - +
148C LYS* 4.3 19.9 + - - -
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Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 3.8 20.3 - - + +
110C ASN* 3.0 39.5 + - - +
112C ASP* 1.3 76.3 - - + +
114C ALA* 1.3 64.2 + - - +
116C VAL* 3.2 12.3 + - + +
117C CYS* 3.0 27.3 + - - -
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLY* 3.5 23.6 - - - +
105C LEU* 3.8 9.8 - - + +
106C LYS* 3.8 10.5 - - + +
110C ASN 3.1 16.0 + - - +
111C PHE* 3.0 10.4 + - - +
113C GLU* 1.3 75.3 - - - +
115C ILE* 1.3 64.6 + - - +
117C CYS* 3.4 1.4 + - - +
118C CYS* 3.1 29.1 + - - -
144C VAL* 3.9 16.8 - - + -
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Residues in contact with ILE 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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111C PHE* 2.7 32.6 + - + +
112C ASP* 3.5 11.7 - - - +
114C ALA* 1.3 71.6 - - - +
116C VAL* 1.3 67.2 + - + +
118C CYS* 3.8 0.3 - - - -
119C GLN* 2.8 33.9 + - + +
141C LEU* 4.0 9.3 - - + +
144C VAL* 3.4 24.2 - - + -
145C TYR* 3.4 56.8 - - + +
148C LYS* 5.0 8.1 - - + +
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASP 3.3 14.6 - - - +
113C GLU* 3.2 14.6 + - + +
115C ILE* 1.3 81.5 - - + +
117C CYS* 1.3 62.2 + - - +
119C GLN* 3.3 5.3 + - - +
120C ARG* 2.9 29.3 + - + +
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Residues in contact with CYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 4.9 7.4 - - - -
98C SER* 3.2 28.8 - - - +
101C LEU* 4.0 21.1 - - - -
102C GLY* 3.7 9.9 - - - -
105C LEU* 3.8 20.2 - - - -
113C GLU* 3.0 19.3 + - - +
114C ALA 3.9 0.2 - - - +
115C ILE 3.3 0.2 - - - -
116C VAL* 1.3 80.8 - - - +
118C CYS* 1.3 58.4 + - - +
120C ARG* 2.9 11.9 + - - +
121C HIS 2.9 23.9 + - - -
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Residues in contact with CYS 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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98C SER 4.8 0.9 - - - -
99C GLY* 4.3 8.5 - - - -
102C GLY* 4.0 19.1 - - - -
103C ASN* 4.4 1.3 - - - -
114C ALA 3.1 17.0 + - - +
117C CYS* 1.3 79.5 - - - +
119C GLN* 1.3 62.4 + - - +
121C HIS* 3.3 10.3 + - - +
122C LEU* 3.0 21.3 + - - +
137C ALA* 4.1 3.4 - - - +
140C ASN* 3.9 22.0 - - + -
141C LEU* 3.5 28.6 - - + +
144C VAL* 3.9 21.1 - - + -
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Residues in contact with GLN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE* 2.8 26.3 + - + +
116C VAL* 3.5 6.1 - - - +
118C CYS* 1.3 73.6 - - - +
120C ARG* 1.3 66.3 + - - +
122C LEU* 3.1 19.6 + - - +
123C ASP* 2.8 61.3 + - - +
126C ARG* 5.0 2.2 - - - +
141C LEU* 3.9 18.8 - - + +
177C PHE* 4.5 8.8 - - - -
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 5.8 0.9 - - + -
86C ARG* 3.8 12.0 - - - +
94C GLU* 2.9 35.5 + - - +
98C SER* 3.4 17.9 - - - +
116C VAL* 2.9 16.6 + - + +
117C CYS* 3.0 15.5 - - - +
119C GLN* 1.3 76.9 - - - +
121C HIS* 1.3 58.9 + - - +
123C ASP* 3.3 16.0 + - - +
124C ILE* 3.1 42.7 + - + +
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Residues in contact with HIS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ALA* 3.4 34.7 + - + +
96C LYS* 5.0 0.4 + - - +
98C SER* 3.9 1.5 - - - -
99C GLY* 3.7 22.6 - - - +
117C CYS 2.9 10.4 + - - +
118C CYS* 3.4 11.7 - - - +
119C GLN 3.2 0.2 - - - -
120C ARG* 1.3 78.0 - - - +
122C LEU* 1.3 61.2 + - - +
124C ILE* 3.5 1.4 + - - +
125C SER* 2.9 41.0 + - - -
133C GLY* 3.4 22.6 + - - -
136C ARG* 4.5 2.5 - - + -
137C ALA* 3.7 12.8 - - + +
140C ASN* 3.8 17.2 + - - -
48F GLN* 3.1 29.3 + - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C CYS 3.0 11.3 + - - +
119C GLN* 3.1 20.8 + - - +
121C HIS* 1.3 76.5 - - - +
123C ASP* 1.3 63.6 + - - +
125C SER* 3.3 4.6 + - - -
126C ARG* 3.0 51.4 + - - +
134C GLU* 3.6 32.1 - - + +
137C ALA* 3.5 13.6 - - + +
138C LEU* 3.6 34.5 - - + -
141C LEU* 3.7 17.9 - - + -
177C PHE* 4.4 5.4 - - + -
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Residues in contact with ASP 123 (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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119C GLN* 2.8 51.7 + - - +
120C ARG* 3.3 16.9 + - - +
122C LEU* 1.3 77.1 - - - +
124C ILE* 1.3 64.4 + - + +
126C ARG* 3.3 12.5 + - - +
127C GLU* 3.0 22.6 + - - +
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Residues in contact with ILE 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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91C GLN* 3.6 27.4 - - + +
94C GLU* 3.5 39.9 - - + +
95C ALA* 3.9 20.4 - - + +
120C ARG* 3.1 38.3 + - + +
123C ASP* 1.3 76.1 - - + +
125C SER* 1.3 63.4 + - - +
127C GLU* 3.0 16.1 + - - +
128C LEU* 2.9 40.2 + - + +
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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
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95C ALA* 4.7 3.3 - - - +
121C HIS* 2.9 39.1 + - - -
122C LEU 3.5 4.7 - - - -
124C ILE* 1.3 78.8 - - - +
126C ARG* 1.3 56.0 + - - +
128C LEU* 3.2 4.0 + - - -
129C ASN 3.0 8.0 + - - -
130C ASP* 2.9 39.3 + - - -
133C GLY* 3.3 11.2 - - - -
134C GLU* 3.4 27.8 - - - -
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Residues in contact with ARG 126 (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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119C GLN* 5.0 1.6 - - - +
122C LEU* 3.0 44.4 + - - +
123C ASP* 3.7 12.7 + - - +
125C SER* 1.3 76.4 - - - +
127C GLU* 1.3 62.1 + - - +
129C ASN* 3.4 16.5 + - - +
134C GLU* 2.8 37.3 + - + +
138C LEU* 4.0 14.3 - - - +
180C GLU* 3.1 26.9 + - - -
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Residues in contact with GLU 127 (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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91C GLN* 3.0 29.3 + - - +
123C ASP 3.0 13.9 + - - +
124C ILE* 3.0 17.6 + - - +
126C ARG* 1.3 79.4 - - - +
128C LEU* 1.3 61.2 + - + +
129C ASN* 3.2 7.4 + - - +
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN* 3.8 28.3 - - + +
92C LEU* 3.5 40.8 - - + +
95C ALA* 5.5 1.1 - - + -
124C ILE* 2.9 36.4 + - + +
125C SER* 3.2 6.3 + - - +
127C GLU* 1.3 80.5 - - + +
129C ASN* 1.3 71.1 + - - +
130C ASP* 3.1 8.4 + - + +
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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