Contacts of the helix formed by residues 122 - 142 (chain C) in PDB entry 4WMJ
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 VAL 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 4.6 3.8 - - + -
106C ALA* 4.0 27.8 - - + -
115C ILE* 2.8 30.3 + - + +
117C VAL* 3.7 36.3 - - + -
120C LYS 4.1 2.2 - - - +
121C ASP* 1.3 72.4 - - - +
123C THR* 1.3 62.8 + - - +
124C PRO 3.4 0.4 - - - -
125C ASP* 2.9 31.5 + - + +
126C VAL* 3.0 17.7 + - + +
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Residues in contact with THR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ALA* 5.7 0.6 - - - +
109C ASN* 3.0 12.9 + - - +
112C ASN* 3.7 32.5 - - + +
113C ARG 2.9 19.6 + - - -
115C ILE* 4.0 5.7 + - - +
121C ASP* 3.0 17.1 + - - +
122C VAL* 1.3 77.5 - - - +
124C PRO* 1.3 67.2 - - + +
125C ASP 3.2 0.2 + - - -
126C VAL* 3.3 6.3 + - - +
127C ASN* 2.9 41.5 + - - +
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Residues in contact with PRO 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ASP* 3.5 30.7 - - + +
123C THR* 1.3 95.9 - - + +
125C ASP* 1.3 58.9 + - - +
127C ASN* 3.9 5.9 - - + +
128C ALA* 3.0 29.5 + - - +
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Residues in contact with ASP 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LYS* 5.5 5.7 + - - -
121C ASP 4.2 5.7 - - - +
122C VAL* 2.9 23.9 + - + +
124C PRO* 1.3 79.2 - - - +
126C VAL* 1.3 66.6 + - + +
128C ALA* 3.4 5.8 + - - +
129C VAL* 3.2 28.2 + - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ALA* 3.5 37.0 - - + +
107C LEU* 3.7 34.5 - - + +
109C ASN* 5.7 0.4 - - + +
122C VAL* 3.0 23.2 + - + +
123C THR* 3.7 8.7 - - + +
125C ASP* 1.3 75.5 - - + +
127C ASN* 1.3 64.9 + - - +
129C VAL* 3.3 6.1 + - - +
130C LEU* 3.0 36.5 + - + +
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Residues in contact with ASN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASN 5.3 1.0 - - - +
110C ARG* 5.1 4.0 + - - -
112C ASN* 2.9 33.3 + - - +
123C THR* 2.9 29.5 + - - +
124C PRO* 3.9 6.2 - - + +
126C VAL* 1.3 82.5 - - - +
128C ALA* 1.3 51.8 + - - +
130C LEU* 3.3 20.4 + - - +
131C ALA* 2.8 34.0 + - - +
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Residues in contact with ALA 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PRO 3.0 18.1 + - - +
125C ASP* 3.8 6.7 - - - +
126C VAL 3.3 0.4 - - - -
127C ASN* 1.3 75.0 - - - +
129C VAL* 1.3 60.8 + - + +
131C ALA* 3.4 6.9 + - - +
132C HIS* 3.1 28.2 + - - +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ASP 3.2 13.1 + - - +
126C VAL* 3.7 7.4 - - - +
128C ALA* 1.3 76.2 - - + +
130C LEU* 1.3 61.5 + - + +
132C HIS* 3.1 12.9 + - + +
133C MET* 2.8 46.1 + - + +
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU 4.1 11.2 - - - +
110C ARG* 4.0 24.5 - - - +
126C VAL* 3.0 28.4 + - + +
127C ASN* 3.6 23.6 - - - +
129C VAL* 1.3 76.0 - - + +
131C ALA* 1.3 57.8 + - - +
133C MET* 3.3 25.6 + - + +
134C LYS* 2.9 29.2 + - - +
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Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ASN 2.8 20.7 + - - +
128C ALA* 3.6 9.0 - - - +
129C VAL 3.2 0.2 - - - -
130C LEU* 1.3 72.6 - - - +
132C HIS* 1.3 57.4 + - - +
134C LYS* 3.3 10.4 + - - +
135C GLU* 3.0 29.3 + - - +
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Residues in contact with HIS 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ALA 3.1 17.1 + - - +
129C VAL* 3.5 11.8 - - - +
131C ALA* 1.3 75.3 - - - +
133C MET* 1.4 60.8 + - + +
135C GLU* 3.4 7.4 + - + +
136C PHE* 3.0 38.7 + - + +
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Residues in contact with MET 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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129C VAL* 2.8 38.6 + - + +
130C LEU* 3.5 28.0 - - + +
132C HIS* 1.4 72.7 - - + +
134C LYS* 1.3 55.8 + - - +
136C PHE* 3.9 4.9 - - - +
137C SER* 2.7 41.4 + - - +
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Residues in contact with LYS 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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130C LEU 2.9 12.7 + - - +
131C ALA* 3.4 13.2 - - - +
132C HIS 3.3 0.2 - - - -
133C MET* 1.3 74.6 - - - +
135C GLU* 1.3 64.8 + - - +
137C SER* 3.3 5.4 + - - -
138C THR* 3.0 33.6 + - - +
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Residues in contact with GLU 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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131C ALA 3.0 17.4 + - - +
132C HIS* 3.7 10.3 - - + +
133C MET 3.4 0.2 - - - -
134C LYS* 1.3 78.1 - - - +
136C PHE* 1.3 62.7 + - - +
138C THR* 3.3 11.5 + - - +
139C GLN* 2.9 56.9 + - - +
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Residues in contact with PHE 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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132C HIS* 3.0 28.4 + - + +
133C MET* 4.0 4.3 - - - +
135C GLU* 1.3 77.0 - - - +
137C SER* 1.3 62.7 + - - +
139C GLN* 3.1 10.7 + - - +
140C VAL* 2.9 49.4 + - + +
145C TRP* 3.5 48.5 - + - -
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Residues in contact with SER 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C MET* 2.7 27.5 + - - +
134C LYS* 3.7 6.3 - - - -
136C PHE* 1.3 80.1 - - - +
138C THR* 1.3 59.0 + - - +
140C VAL* 3.8 2.8 - - - +
141C ILE* 2.9 50.6 + - - +
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Residues in contact with THR 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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134C LYS* 3.0 20.7 + - - +
135C GLU* 3.5 15.5 - - - +
137C SER* 1.3 76.7 - - - +
139C GLN* 1.3 63.7 + - + +
141C ILE* 4.8 4.0 - - - -
142C SER* 2.7 42.3 + - - +
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Residues in contact with GLN 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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135C GLU* 2.9 49.2 + - - +
136C PHE* 3.1 13.8 + - - +
138C THR* 1.3 80.4 - - + +
140C VAL* 1.3 62.7 + - - +
142C SER* 3.4 3.9 + - - -
144C ALA* 3.0 22.3 + - + -
145C TRP* 3.0 56.4 + - + +
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PHE* 2.9 54.3 + - + +
137C SER* 4.0 3.4 - - - +
139C GLN* 1.3 73.8 - - - +
141C ILE* 1.3 68.9 + - + +
143C GLY* 3.1 13.9 + - - -
145C TRP* 3.9 24.7 - - + +
153C ILE* 3.9 40.3 + - + +
156C VAL* 5.0 10.5 - - + -
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Residues in contact with ILE 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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137C SER* 2.9 38.4 + - - +
138C THR* 4.3 3.1 - - - +
140C VAL* 1.3 75.7 - - + +
142C SER* 1.3 62.7 + - - +
143C GLY 3.0 1.4 + - - -
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Residues in contact with SER 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C THR* 2.7 34.1 + - - +
139C GLN 3.4 1.0 + - - -
141C ILE* 1.3 77.7 - - - +
143C GLY* 1.3 59.6 + - - +
144C ALA* 3.4 18.7 + - - +
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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