Contacts of the helix formed by residues 127 - 142 (chain B) in PDB entry 2PWY
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 ARG 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A SAH 3.5 19.5 - - - +
125B GLU* 2.9 13.2 + - - +
126B ALA* 1.3 83.9 - - + +
128B PRO* 1.3 71.9 - - + +
129B HIS* 3.3 4.2 - - + +
130B HIS* 3.0 53.4 + - + +
131B LEU* 3.0 10.6 + - - +
151B LEU* 4.1 1.3 - - - -
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Residues in contact with PRO 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA 3.6 8.5 - - - +
127B ARG* 1.3 82.5 - - + +
129B HIS* 1.3 57.5 + - - +
131B LEU* 3.3 3.3 + - + +
132B ALA* 3.0 29.8 + - - +
151B LEU* 3.7 28.9 - - + -
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER* 4.8 1.4 - - - -
127B ARG* 3.3 3.7 - - + +
128B PRO* 1.3 80.5 - - - +
130B HIS* 1.3 71.4 + - + +
132B ALA* 3.6 6.5 + - - +
133B GLN* 3.3 22.7 + - - +
136B ARG* 5.1 1.2 + - - -
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Residues in contact with HIS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A SAH 2.7 27.5 + - - -
73B SER* 3.6 25.9 + - - -
74B ALA* 4.1 19.3 + - + +
103B GLY 3.1 17.1 - - - +
125B GLU* 3.6 13.9 - - - -
127B ARG* 3.0 59.9 + - + +
129B HIS* 1.3 81.1 - - + +
131B LEU* 1.3 59.4 + - - +
133B GLN 3.3 1.9 + - - -
134B ALA 2.9 23.7 + - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B THR* 4.0 18.6 - - + +
125B GLU* 3.6 17.0 - - + +
127B ARG 3.0 8.2 + - - +
128B PRO* 3.3 8.7 + - + +
130B HIS* 1.3 77.0 - - - +
132B ALA* 1.3 55.5 + - - +
134B ALA* 3.1 3.3 + - - +
135B GLU* 2.8 58.3 + - + +
149B PHE* 3.7 25.4 - - + -
150B HIS* 3.9 7.9 - - - +
151B LEU* 3.7 42.2 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PRO 3.0 17.0 + - - +
129B HIS* 3.9 7.2 - - - +
130B HIS 3.3 0.2 - - - -
131B LEU* 1.3 77.5 - - - +
133B GLN* 1.3 61.7 + - - +
135B GLU* 3.4 7.6 + - - +
136B ARG* 3.1 45.9 + - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.2 48.5 - - + +
72B ARG 4.6 0.4 - - - -
73B SER* 3.9 22.4 - - - +
129B HIS 3.3 10.8 + - - +
130B HIS 3.7 6.3 - - - +
132B ALA* 1.3 75.3 - - - +
134B ALA* 1.3 60.9 + - - +
136B ARG* 2.8 40.3 + - - +
137B ASN* 2.8 66.0 + - - +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B THR* 3.5 29.6 - - + -
103B GLY 3.5 20.8 + - - +
104B SER 3.6 19.7 - - - -
105B GLY* 3.7 0.7 - - - +
130B HIS 2.9 11.3 + - - +
131B LEU* 3.5 5.8 - - - +
133B GLN* 1.3 76.1 - - - +
135B GLU* 1.3 57.0 + - - +
137B ASN* 3.1 2.6 + - - +
138B VAL* 2.8 35.2 + - - +
149B PHE* 4.8 0.2 - - - -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 2.8 35.9 + - + +
132B ALA* 3.8 6.1 - - - +
134B ALA* 1.3 74.9 - - - +
136B ARG* 1.3 58.7 + - + +
138B VAL* 3.4 0.7 + - - +
139B ARG* 2.9 66.6 + - - +
149B PHE* 3.3 52.6 - - + +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 5.2 2.0 - - - +
129B HIS 5.1 1.2 + - - -
132B ALA* 3.1 33.6 + - - +
133B GLN* 2.8 51.2 + - - +
135B GLU* 1.3 77.4 - - + +
137B ASN* 1.3 63.4 + - - +
139B ARG* 3.4 3.3 + - - +
140B ALA* 3.0 27.9 + - - +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 6.0 1.2 - - - -
66B TYR* 2.6 34.9 + - - -
70B MET* 3.8 23.2 - - - +
71B LYS* 2.7 30.9 + - - +
104B SER* 3.0 33.4 + - - +
105B GLY* 5.3 0.2 - - - -
109B LEU* 4.8 1.3 - - + -
133B GLN* 2.8 41.7 + - - +
134B ALA 3.6 2.0 - - - +
136B ARG* 1.3 73.0 - - - +
138B VAL* 1.3 63.8 + - + +
140B ALA* 3.7 3.3 + - - -
141B PHE* 3.7 1.7 + - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLY* 3.9 29.2 - - - +
108B THR* 4.1 10.3 - - + -
109B LEU* 4.1 18.3 - - + +
134B ALA 2.8 20.0 + - - +
135B GLU 3.9 3.6 - - - +
137B ASN* 1.3 76.6 - - - +
139B ARG* 1.3 61.4 + - + +
141B PHE* 3.2 2.6 + - - -
142B TRP* 2.9 44.7 + - + +
147B VAL* 4.6 10.5 - - + -
149B PHE* 3.9 28.0 - - + -
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLU* 2.9 61.6 + - - +
136B ARG* 4.1 3.8 - - - +
138B VAL* 1.3 81.3 - - + +
140B ALA* 1.3 61.6 + - - +
141B PHE 3.3 0.5 + - - -
142B TRP 3.8 17.0 + - - +
143B GLN* 5.3 1.2 - - - +
147B VAL 5.5 2.0 + - - -
149B PHE* 4.1 19.2 - - + -
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLY* 4.2 6.6 - - - -
6B PRO* 3.4 21.4 - - - +
20B PHE* 3.9 22.4 - - + -
66B TYR* 3.5 15.9 - - - +
136B ARG 3.0 18.2 + - - +
137B ASN* 4.7 0.2 - - - -
138B VAL 3.2 0.4 - - - -
139B ARG* 1.3 76.9 - - - +
141B PHE* 1.3 57.3 + - - +
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP* 5.6 0.2 - - - -
6B PRO* 4.5 11.4 - - + -
61B PRO* 3.6 32.1 - - + -
63B LEU* 3.6 41.1 - - + -
66B TYR* 3.5 50.0 - + + -
109B LEU* 4.2 11.9 - - + -
113B ARG* 3.5 26.5 - - - -
137B ASN 3.7 3.6 + - - +
138B VAL 3.2 2.5 + - - +
140B ALA* 1.3 80.0 - - - +
142B TRP* 1.3 63.5 + + + +
143B GLN 4.4 0.2 - - - -
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Residues in contact with TRP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA* 4.8 4.5 - - + -
93A PRO* 3.8 32.5 - - + -
109B LEU* 3.6 17.9 - - + -
112B ALA* 3.5 34.5 - - + +
113B ARG* 4.1 27.8 - - + -
116B GLY* 5.0 1.3 - - - -
117B GLU 5.8 0.2 - - - -
138B VAL* 2.9 31.2 + - + +
139B ARG* 3.8 15.8 + - - +
140B ALA 3.8 0.4 - - - -
141B PHE* 1.3 84.6 - + + +
143B GLN* 1.3 60.3 + - - +
144B VAL* 3.3 49.9 + - + +
146B ASN* 2.8 25.2 + - - -
147B VAL* 4.6 2.7 - - + -
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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
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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