Contacts of the helix formed by residues 120 - 137 (chain B) in PDB entry 2PKG
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 SER 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B PRO* 4.7 4.6 + - - +
118B GLU 3.9 1.8 + - - -
119B HIS* 1.3 74.2 - - - +
121B PRO* 1.3 76.5 - - - +
122B SER* 3.3 11.4 + - - -
123B ASP* 2.7 48.8 + - - +
124B LEU* 2.8 11.0 + - - +
157B ARG* 4.3 0.7 - - - +
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Residues in contact with PRO 121 (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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119B HIS 3.9 0.8 - - - -
120B SER* 1.3 86.2 - - - +
122B SER* 1.3 74.0 + - - +
124B LEU* 3.0 25.4 + - + +
125B GLU* 3.1 26.3 + - - +
157B ARG* 4.0 34.9 - - + +
158B VAL* 5.5 0.2 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.0 9.9 + - - -
121B PRO* 1.3 86.6 - - - +
123B ASP* 1.3 57.9 + - - +
125B GLU* 4.7 4.9 - - - +
126B ALA* 3.2 24.4 + - - +
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO 3.8 18.2 - - - +
84B GLU* 4.4 3.3 - - - +
86B VAL* 5.5 0.9 - - - -
87B HIS* 3.5 28.8 - - + -
119B HIS* 4.0 15.8 + - + +
120B SER* 2.7 37.4 + - - +
122B SER* 1.3 72.7 - - - +
124B LEU* 1.3 56.9 + - - +
126B ALA* 3.1 3.3 + - - +
127B HIS* 2.7 44.4 + - - +
128B PHE 3.6 2.9 + - - -
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Residues in contact with LEU 124 (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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116B SER* 4.2 6.7 - - - +
119B HIS* 3.9 16.8 - - + -
120B SER 2.8 16.0 + - - +
121B PRO* 3.4 11.0 - - + +
123B ASP* 1.3 74.5 - - - +
125B GLU* 1.3 66.0 + - - +
126B ALA 2.9 1.2 + - - -
128B PHE* 3.1 46.8 + - + -
129B VAL* 3.2 12.4 + - - -
154B CYS* 3.8 29.4 - - + +
157B ARG* 3.4 46.0 - - + +
158B VAL* 3.6 11.9 - - + -
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Residues in contact with GLU 125 (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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121B PRO* 3.1 18.1 + - - +
122B SER* 4.7 4.1 - - - +
124B LEU* 1.3 79.6 - - - +
126B ALA* 1.3 59.6 + - - +
129B VAL* 4.2 10.8 - - - +
130B PRO* 3.5 14.9 - - - +
157B ARG 5.0 0.2 - - - +
158B VAL* 3.4 25.1 - - + +
159B SER* 3.3 39.5 + - - -
162B VAL* 3.7 14.6 - - + +
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Residues in contact with ALA 126 (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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122B SER 3.2 20.3 + - - +
123B ASP* 3.1 4.2 + - - +
124B LEU 2.9 2.6 + - - -
125B GLU* 1.3 80.7 - - - +
127B HIS* 1.3 83.2 + - + +
130B PRO* 4.0 9.3 - - - +
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Residues in contact with HIS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B HIS* 4.1 38.5 + + + +
90B LEU* 4.2 12.8 - - + +
119B HIS* 5.4 0.9 - - + -
123B ASP* 2.7 30.6 + - - +
124B LEU 3.2 0.4 + - - -
126B ALA* 1.3 94.7 + - + +
128B PHE* 1.3 65.9 + - - +
130B PRO* 3.5 8.0 - - - +
131B LEU* 3.4 15.6 + - - +
134B ARG* 4.3 5.7 + - - -
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Residues in contact with PHE 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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90B LEU* 3.9 17.0 - - + +
112B LEU* 3.6 48.9 - - + -
115B ILE* 4.9 0.2 - - + -
116B SER* 3.9 14.6 - - - -
119B HIS* 4.0 21.5 + + - +
123B ASP 3.6 1.8 + - - +
124B LEU* 3.1 25.4 + - + +
127B HIS* 1.3 73.9 - - - +
129B VAL* 1.3 59.6 + - - +
130B PRO 3.1 1.1 - - - -
131B LEU* 2.5 36.0 + - + +
132B VAL* 3.0 19.2 + - + +
150B LEU* 4.3 12.6 - - + -
153B VAL* 4.0 21.8 - - + -
154B CYS* 3.8 19.7 - - + -
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU 3.2 11.5 + - - +
125B GLU* 4.2 5.6 - - - +
128B PHE* 1.3 78.3 - - - +
130B PRO* 1.3 64.5 - - + +
132B VAL* 3.1 12.7 + - - +
133B LYS* 2.8 51.6 + - - +
154B CYS* 4.1 22.2 - - + -
158B VAL* 4.1 14.4 - - + -
162B VAL* 3.8 30.1 - - + -
166B LEU* 4.1 10.5 - - + -
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Residues in contact with PRO 130 (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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125B GLU 3.5 17.0 - - - +
126B ALA 4.0 11.4 - - - +
127B HIS* 3.5 13.5 - - - +
128B PHE 3.3 4.0 - - - -
129B VAL* 1.3 95.2 - - + +
131B LEU* 1.3 54.8 + - - +
133B LYS* 3.3 12.5 + - + +
134B ARG* 2.6 57.9 + - - +
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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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90B LEU* 3.5 35.7 - - + +
94B GLU* 2.9 47.3 - - + +
112B LEU* 3.7 31.0 - - + -
127B HIS 3.4 9.6 + - - +
128B PHE* 2.5 23.1 + - + +
130B PRO* 1.3 70.5 - - - +
132B VAL* 1.3 66.2 + - + +
134B ARG* 3.1 15.6 + - - +
135B LEU* 3.0 34.4 + - + +
150B LEU* 4.4 6.7 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 3.8 24.0 - - + +
129B VAL* 3.2 14.4 - - - +
131B LEU* 1.3 79.0 - - + +
133B LYS* 1.3 65.3 + - + +
135B LEU* 3.0 3.5 + - - +
136B ALA* 2.9 22.9 + - - +
147B ALA* 4.2 2.8 - - + +
150B LEU* 4.0 35.9 - - + +
151B PHE* 3.4 47.1 - - + -
154B CYS* 4.3 4.7 - - - -
166B LEU* 4.5 7.2 - - + -
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Residues in contact with LYS 133 (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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129B VAL* 2.8 42.4 + - + +
130B PRO* 3.6 12.4 - - + +
132B VAL* 1.3 77.2 - - + +
134B ARG* 1.3 62.5 + - + +
136B ALA* 3.8 6.8 - - - +
137B GLY* 3.0 21.8 + - - -
162B VAL* 5.5 0.2 - - - +
165B GLU* 2.9 44.6 + - - -
166B LEU* 5.3 3.4 - - + -
169B TYR* 3.3 51.9 + - + +
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Residues in contact with ARG 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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90B LEU* 6.0 1.4 - - - +
94B GLU* 2.7 41.2 + - - +
127B HIS 4.3 6.1 + - - -
130B PRO* 2.6 41.9 + - - +
131B LEU* 3.1 22.4 + - - +
133B LYS* 1.3 73.5 - - - +
135B LEU* 1.3 62.0 + - - +
137B GLY* 3.7 2.8 + - - -
138B GLY* 3.7 13.5 + - - -
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Residues in contact with LEU 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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94B GLU* 3.9 20.4 - - + +
97B ALA* 4.2 20.6 - - + -
98B THR* 3.7 23.1 - - - +
112B LEU* 5.1 0.2 - - + -
131B LEU* 3.0 28.5 + - + +
132B VAL 3.0 6.3 + - - +
134B ARG* 1.3 74.4 - - - +
136B ALA* 1.3 66.0 + - - +
137B GLY 3.1 1.8 - - - -
138B GLY 3.1 11.1 + - - -
143B SER* 3.4 37.7 - - - +
144B ARG 3.4 6.2 + - - -
146B SER* 4.8 1.1 - - - -
147B ALA* 3.8 13.2 - - + +
150B LEU* 4.1 24.9 - - + -
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Residues in contact with ALA 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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132B VAL 2.9 15.8 + - - +
133B LYS* 3.9 3.8 - - - +
135B LEU* 1.3 77.8 - - - +
137B GLY* 1.3 56.4 + - - +
138B GLY 3.3 0.7 - - - -
144B ARG* 3.4 20.7 - - - +
147B ALA* 3.6 18.3 - - + +
151B PHE* 4.2 8.3 - - + -
169B TYR* 4.2 18.1 - - + -
173B LEU* 4.1 23.3 - - + +
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Residues in contact with GLY 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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133B LYS 3.0 15.3 + - - -
134B ARG 4.0 4.0 - - - -
135B LEU 3.1 0.4 - - - -
136B ALA* 1.3 77.4 - - - +
138B GLY* 1.3 61.8 + - - +
139B ASP* 3.9 2.8 + - - +
144B ARG* 5.0 0.4 - - - -
169B TYR* 5.4 5.6 - - - -
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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