Contacts of the helix formed by residues 120 - 135 (chain C) in PDB entry 2PWZ
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 PRO 120 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C PHE* 4.1 25.8 - - + -
94C ASN* 5.3 3.1 - - + -
119C ASN* 1.4 84.7 - - + +
121C VAL* 1.3 56.2 + - - +
122C ASN* 3.3 5.2 - - + +
123C THR* 3.0 22.5 + - - +
124C THR* 2.8 37.9 + - + -
178C SER* 5.5 8.5 - - - +
302C ASP* 6.3 1.3 - - - -
305C LEU* 5.9 0.9 - - + -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE 3.8 12.3 - - - +
117C ILE 3.5 13.9 - - - +
118C THR 3.4 12.6 - - - +
119C ASN* 2.9 22.2 + - - +
120C PRO* 1.3 68.0 - - - +
122C ASN* 1.3 66.7 + - - +
123C THR 3.0 0.9 + - - -
124C THR* 3.4 7.9 - - - +
125C VAL* 3.1 21.3 + - + +
145C GLY* 3.6 31.9 - - - -
146C VAL 4.3 4.0 - - - +
147C THR* 4.8 0.2 - - + -
177C HIS* 3.8 29.8 - - + +
253C TYR* 3.5 15.2 - - + -
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Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C PRO* 3.2 4.4 + - + +
121C VAL* 1.3 76.4 - - - +
123C THR* 1.3 59.1 + - - +
126C ALA* 4.3 5.4 + - - +
176C GLY* 3.3 5.7 - - - -
177C HIS* 2.8 26.0 + - - +
178C SER* 3.6 11.3 + - - +
181C THR* 3.1 24.0 + - - -
253C TYR* 2.7 31.7 + - - +
263C PHE* 5.1 0.2 - - - -
299C LEU* 3.4 15.9 - - + +
302C ASP* 2.8 39.9 + - + +
303C ILE* 3.9 12.3 - - - +
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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
----------------------------------------------------------
91C PHE* 3.4 35.9 - - + -
120C PRO* 3.0 18.4 + - - +
122C ASN* 1.3 77.7 - - - +
124C THR* 1.3 65.7 + - + +
125C VAL 3.4 0.4 - - - -
126C ALA* 3.2 7.4 + - - +
127C ILE* 3.2 23.5 + - + +
302C ASP* 2.8 33.4 + - - +
305C LEU* 4.1 8.9 - - + +
306C GLY* 3.7 20.1 - - - +
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Residues in contact with THR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 5.6 0.7 - - + -
94C ASN 5.0 0.7 - - - +
95C ALA* 5.0 7.4 - - + +
98C VAL* 3.7 27.5 - - + +
116C ILE* 3.4 13.2 - - - +
118C THR* 2.7 29.2 + - + +
119C ASN 4.3 2.9 - - - +
120C PRO* 2.8 35.7 + - + +
121C VAL* 3.4 7.3 + - - -
123C THR* 1.3 76.2 - - + +
125C VAL* 1.3 56.2 + - - +
127C ILE* 3.4 15.7 + - + +
128C ALA* 3.0 26.9 + - - +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 4.0 26.2 - - + -
121C VAL* 3.1 14.8 + - + +
124C THR* 1.3 73.9 - - - +
126C ALA* 1.3 58.0 + - - +
128C ALA* 3.3 2.1 - - - +
129C ALA* 2.8 35.0 + - - +
143C LEU* 3.5 10.0 - - + +
145C GLY* 3.3 36.1 - - - +
253C TYR* 3.0 38.1 - - + +
263C PHE* 3.8 17.5 - - + -
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Residues in contact with ALA 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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122C ASN 4.3 6.7 - - - +
123C THR 3.3 13.0 - - - +
125C VAL* 1.3 78.7 - - - +
127C ILE* 1.3 65.0 + - - +
129C ALA* 3.3 2.1 + - - +
130C GLU* 3.0 29.5 + - - +
262C ARG* 4.7 0.3 + - - -
263C PHE* 3.8 26.2 - - + -
303C ILE* 3.6 26.9 - - + +
306C GLY* 4.1 5.4 - - - -
307C GLU* 4.1 4.9 - - + +
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Residues in contact with ILE 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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95C ALA* 3.5 36.3 - - + +
98C VAL* 4.3 4.3 - - + -
99C LYS* 3.9 33.2 - - + +
123C THR* 3.2 23.0 + - + +
124C THR* 3.5 15.7 - - + +
125C VAL 3.4 0.2 - - - -
126C ALA* 1.3 74.9 - - - +
128C ALA* 1.3 63.1 + - - +
130C GLU* 3.2 4.7 + - - +
131C VAL* 3.0 26.4 + - - +
306C GLY* 3.5 23.8 + - - +
309C PHE* 4.0 12.6 - - + -
310C VAL* 3.7 16.6 - - + +
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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
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98C VAL* 4.4 0.4 - - + +
102C VAL* 3.6 25.7 - - + +
116C ILE* 3.2 35.7 - - + -
124C THR 3.0 8.1 + - - +
125C VAL 3.3 7.0 - - - +
127C ILE* 1.3 77.4 - - - +
129C ALA* 1.3 63.6 + - - +
131C VAL* 3.2 5.0 + - - +
132C LEU* 2.9 28.2 + - - +
143C LEU* 3.8 8.1 - - + -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C VAL 2.8 21.2 + - - +
126C ALA 3.6 5.6 - - - +
128C ALA* 1.3 73.4 - - - +
130C GLU* 1.3 56.9 + - - +
132C LEU* 3.3 2.9 + - - +
133C LYS* 2.9 42.3 + - - +
138C TYR* 3.8 19.7 - - + -
143C LEU* 3.7 15.2 - - + +
262C ARG* 4.4 1.3 - - - +
263C PHE* 3.6 21.8 - - + -
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Residues in contact with GLU 130 (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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126C ALA 3.0 19.3 + - - +
127C ILE 3.6 3.8 - - - +
129C ALA* 1.3 73.0 - - - +
131C VAL* 1.3 59.6 + - - +
133C LYS* 3.1 29.1 + - - +
134C LYS* 3.0 35.3 + - - +
262C ARG* 2.8 27.1 + - - +
307C GLU* 4.0 18.4 - - - +
310C VAL* 3.8 22.2 - - + -
311C ASN* 3.1 29.8 + - - +
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LYS* 3.8 38.8 - - + +
102C VAL* 4.0 9.4 - - + +
103C GLN* 3.6 52.3 + - - +
106C ALA* 5.1 1.6 - - + -
127C ILE 3.0 19.1 + - - +
128C ALA* 3.6 8.1 - - - +
130C GLU* 1.3 76.6 - - - +
132C LEU* 1.3 61.7 + - - +
134C LYS* 3.4 6.5 + - - +
135C ALA* 3.2 20.8 + - - +
310C VAL* 4.3 11.4 - - + +
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Residues in contact with LEU 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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102C VAL* 3.8 14.6 - - + +
105C VAL* 4.9 0.4 - - + -
106C ALA* 4.1 21.8 - - + +
110C PRO 5.4 4.5 - - - +
114C ILE* 3.8 32.8 - - + -
128C ALA 2.9 25.3 + - - +
129C ALA 3.7 3.4 - - - +
131C VAL* 1.3 75.5 - - - +
133C LYS* 1.3 56.8 + - - +
135C ALA* 3.4 6.1 + - - +
136C GLY 3.0 7.3 + - - -
137C VAL* 3.0 38.8 + - + +
138C TYR* 3.3 34.3 + - + -
139C ASP 5.4 1.1 - - - +
143C LEU* 4.2 15.9 - - + -
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Residues in contact with LYS 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 ALA 2.9 18.1 + - - +
130C GLU* 3.1 41.6 + - - +
131C VAL 3.3 0.2 - - - -
132C LEU* 1.3 73.4 - - - +
134C LYS* 1.3 60.8 + - + +
136C GLY* 3.0 19.1 + - - +
138C TYR* 3.6 30.3 - - + +
255C GLU* 5.9 0.2 - - - -
262C ARG* 3.2 22.9 - - - +
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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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99C LYS* 6.2 0.2 - - - +
103C GLN* 5.9 2.5 - - - +
130C GLU* 3.0 16.1 + - - +
131C VAL* 3.8 6.1 - - - +
133C LYS* 1.3 77.6 - - + +
135C ALA* 1.3 57.2 + - - +
136C GLY 3.8 0.2 + - - -
310C VAL* 3.8 40.4 + - + +
311C ASN* 3.9 19.0 - - - +
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Residues in contact with ALA 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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103C GLN* 4.3 11.6 - - - +
106C ALA* 3.8 27.4 - - + +
131C VAL 3.2 13.1 + - - +
132C LEU 3.7 8.3 - - - +
133C LYS 3.2 0.4 - - - -
134C LYS* 1.3 75.5 - - - +
136C GLY* 1.3 60.5 + - - +
137C VAL* 3.5 10.2 + - + +
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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
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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