Contacts of the helix formed by residues 120 - 135 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G PHE* 4.1 31.4 - - + -
94G ASN* 5.6 1.1 - - + -
119G ASN* 1.4 84.5 - - + +
121G VAL* 1.3 61.8 + - - +
122G ASN* 3.3 4.9 - - + +
123G THR* 3.1 18.3 + - - +
124G THR* 2.8 34.8 + - + +
178G SER* 5.5 9.4 - - - +
302G ASP* 6.4 1.1 - - - -
305G LEU* 6.2 0.4 - - + -
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Residues in contact with VAL 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ILE 3.8 11.7 - - - +
117G ILE 3.7 11.2 - - - +
118G THR 3.6 12.3 - - - +
119G ASN* 3.0 22.7 + - - +
120G PRO* 1.3 70.6 - - - +
122G ASN* 1.3 63.2 + - - +
123G THR 2.9 1.7 + - - -
124G THR* 3.2 7.2 - - - +
125G VAL* 3.1 26.9 + - + +
145G GLY* 3.6 33.0 - - - -
146G VAL 4.3 4.7 - - - +
147G THR* 4.7 1.3 - - + -
177G HIS* 3.7 29.3 - - + +
253G TYR* 3.6 10.5 - - + -
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Residues in contact with ASN 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G PRO* 3.3 3.3 - - + -
121G VAL* 1.3 75.5 - - - +
123G THR* 1.3 58.7 + - - +
126G ALA* 4.5 3.5 + - - +
176G GLY* 3.1 7.1 - - - -
177G HIS* 2.8 25.5 + - - +
178G SER* 3.4 13.6 + - - +
181G THR* 2.8 25.7 + - - -
253G TYR* 2.8 33.7 + - - +
299G LEU* 3.6 13.9 - - + +
302G ASP* 3.2 35.1 + - + +
303G ILE* 3.8 14.2 - - - +
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Residues in contact with THR 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G PHE* 3.7 26.5 - - + -
120G PRO* 3.1 19.8 + - - +
121G VAL 3.0 0.2 - - - -
122G ASN* 1.3 77.8 - - - +
124G THR* 1.3 59.7 + - - +
125G VAL 3.3 1.3 - - - -
126G ALA* 3.1 8.3 + - - +
127G ILE* 3.0 27.4 + - + +
302G ASP* 2.7 31.0 + - - +
305G LEU* 4.0 8.8 - - + +
306G GLY* 3.4 28.2 - - - +
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Residues in contact with THR 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G PHE* 5.6 1.1 - - + -
94G ASN 5.1 0.9 - - - +
95G ALA* 5.1 5.8 - - + +
98G VAL* 3.8 27.4 - - + +
116G ILE* 3.3 14.3 - - - +
118G THR* 2.9 27.5 + - + +
119G ASN 4.3 4.7 - - - +
120G PRO* 2.8 35.4 + - + +
121G VAL* 3.2 8.3 - - - -
123G THR* 1.3 71.7 - - + +
125G VAL* 1.3 58.8 + - - +
127G ILE* 3.2 18.7 + - + +
128G ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ILE* 4.1 20.0 - - + -
121G VAL* 3.1 19.8 + - + +
124G THR* 1.3 76.2 - - - +
126G ALA* 1.3 56.2 + - - +
128G ALA* 3.2 3.1 + - - +
129G ALA* 2.8 27.4 + - - +
143G LEU* 3.7 18.1 - - + +
145G GLY* 3.3 32.8 - - - +
253G TYR* 3.7 21.8 - - + +
254G VAL* 5.5 0.7 - - - -
263G PHE* 3.8 26.5 - - + -
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Residues in contact with ALA 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G ASN 4.5 3.2 + - - +
123G THR 3.1 12.9 + - - +
125G VAL* 1.3 79.1 - - - +
127G ILE* 1.3 62.5 + - - +
129G ALA* 3.4 1.7 + - - +
130G GLU* 3.1 28.6 + - - +
262G ARG* 4.5 0.2 + - - -
263G PHE* 3.6 32.4 - - + -
303G ILE* 3.6 28.3 - - + +
306G GLY* 4.1 2.5 - - - -
307G GLU* 4.1 9.6 - - + +
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Residues in contact with ILE 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G PHE* 4.7 1.8 - - + -
95G ALA* 3.6 37.0 - - + +
98G VAL* 4.3 6.5 - - + -
99G LYS* 4.1 29.2 - - + -
123G THR* 3.0 25.1 + - + +
124G THR* 3.2 18.1 + - + +
126G ALA* 1.3 76.6 - - - +
128G ALA* 1.3 62.4 + - - +
130G GLU 3.4 0.3 + - - -
131G VAL* 3.1 27.3 + - + +
306G GLY* 3.4 22.2 - - - +
309G PHE* 4.1 13.9 - - + -
310G VAL* 3.5 19.3 - - + +
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Residues in contact with ALA 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G VAL* 4.7 0.6 - - + +
102G VAL* 3.8 27.1 - - + -
116G ILE* 3.5 30.7 - - + -
124G THR 2.9 9.4 + - - +
125G VAL 3.4 8.1 - - - +
127G ILE* 1.3 76.6 - - - +
129G ALA* 1.3 63.8 + - - +
131G VAL* 3.3 2.9 + - - +
132G LEU* 3.0 29.7 + - + +
143G LEU* 3.8 9.9 - - + -
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G VAL 2.8 19.2 + - - +
126G ALA 3.4 3.1 + - - +
128G ALA* 1.3 71.9 - - - +
130G GLU* 1.3 57.5 + - - +
132G LEU* 3.3 3.1 + - - +
133G LYS* 3.0 34.9 + - - +
138G TYR* 3.6 27.4 - - + +
143G LEU* 3.5 9.8 - - + +
262G ARG* 4.5 6.3 - - - +
263G PHE* 3.6 26.0 - - + -
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Residues in contact with GLU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G ALA 3.1 20.1 + - - +
128G ALA 3.2 0.2 - - - -
129G ALA* 1.3 72.3 - - - +
131G VAL* 1.3 63.1 + - - +
133G LYS* 3.0 32.6 + - - +
134G LYS* 3.2 24.1 + - - +
262G ARG* 2.7 27.1 + - - +
307G GLU* 3.9 20.3 - - - +
310G VAL* 3.7 27.1 - - + +
311G ASN* 3.3 29.8 + - - +
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Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G LYS* 3.8 36.6 - - + -
102G VAL* 3.7 21.1 - - + +
103G GLN* 3.5 36.1 - - + +
106G ALA* 5.3 2.0 - - + -
127G ILE 3.1 16.9 + - - +
128G ALA* 3.6 7.2 - - - +
130G GLU* 1.3 74.1 - - - +
132G LEU* 1.3 66.6 + - - +
134G LYS* 3.5 5.9 + - - +
135G ALA* 3.3 20.4 + - - +
310G VAL* 4.1 12.3 - - + -
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Residues in contact with LEU 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G VAL* 3.8 15.9 - - + +
105G VAL* 5.2 1.6 - - + -
106G ALA* 4.0 17.5 - - + +
110G PRO* 5.5 3.4 - - + +
114G ILE* 3.9 30.5 - - + -
128G ALA 3.0 26.3 + - - +
129G ALA 3.3 0.2 + - - -
131G VAL* 1.3 75.6 - - - +
133G LYS* 1.3 62.8 + - - +
135G ALA* 3.3 4.5 + - - +
136G GLY 3.1 16.3 + - - -
137G VAL* 3.1 32.9 + - + +
138G TYR* 3.4 37.4 + - + -
139G ASP 5.7 0.4 - - - +
143G LEU* 4.1 13.5 - - + -
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Residues in contact with LYS 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G ALA 3.0 28.5 + - - +
130G GLU* 3.0 38.0 + - - +
131G VAL 3.4 0.2 - - - -
132G LEU* 1.3 76.8 - - - +
134G LYS* 1.3 56.3 + - - +
136G GLY* 3.0 19.1 + - - +
138G TYR* 3.5 31.9 - - + +
262G ARG* 3.3 18.6 - - - +
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Residues in contact with LYS 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G LYS* 5.7 4.8 - - - +
130G GLU 3.2 17.6 + - - +
131G VAL* 3.8 7.0 - - - +
132G LEU 3.3 0.2 - - - -
133G LYS* 1.3 78.5 - - - +
135G ALA* 1.3 59.0 + - - +
310G VAL* 4.3 25.8 + - + +
311G ASN* 5.2 9.4 - - - +
312G LYS* 5.0 14.8 - - - +
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Residues in contact with ALA 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G ALA* 3.8 26.5 - - + -
131G VAL* 3.3 12.4 + - + +
132G LEU 3.3 9.1 + - - +
133G LYS 3.2 0.4 - - - -
134G LYS* 1.3 76.3 - - - +
136G GLY* 1.3 61.6 + - - +
137G VAL* 3.8 13.0 - - + +
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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