Contacts of the helix formed by residues 101 - 119 (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 GLU 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASP* 3.0 45.1 - - + +
99B VAL* 3.2 5.4 - - + +
100B GLU* 1.3 76.5 - - - +
102B THR* 1.3 82.4 + - - +
103B VAL* 3.0 27.5 + - + +
104B VAL* 2.8 25.5 + - + +
105B ARG* 3.3 4.0 + - - -
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Residues in contact with THR 102 (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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100B GLU 2.9 5.8 + - - -
101B GLU* 1.3 78.1 + - - +
103B VAL* 1.3 69.0 + - + +
104B VAL 2.8 0.9 + - - -
105B ARG* 3.0 32.7 + - - +
106B ASP* 2.6 53.4 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.6 38.2 - - + +
101B GLU* 3.0 18.2 + - + +
102B THR* 1.3 75.7 - - + +
104B VAL* 1.3 65.1 + - + +
106B ASP* 3.3 9.1 - - + +
107B LYS* 3.3 14.0 + - - +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASP* 3.3 45.8 - - + +
66B LEU* 3.9 21.1 - - + -
67B LEU* 4.1 11.0 - - + +
70B ALA* 4.3 2.6 - - + +
96B LEU* 4.0 14.4 - - + +
99B VAL* 3.6 28.3 - - + -
101B GLU* 2.8 18.1 + - + +
103B VAL* 1.3 75.5 - - + +
105B ARG* 1.3 64.1 - - - +
106B ASP 3.1 1.2 + - - -
107B LYS* 3.2 12.0 + - - +
108B ALA* 3.2 10.7 + - - +
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU 3.4 14.1 - - - +
97B ALA 3.2 20.6 - - - +
99B VAL 3.3 12.8 - - - +
100B GLU 2.4 34.1 + - - -
101B GLU 3.3 0.6 + - - -
102B THR* 3.0 33.8 + - - +
104B VAL* 1.3 77.0 - - - +
106B ASP* 1.3 65.2 + - - +
108B ALA* 3.8 5.5 - - - +
109B VAL* 2.9 31.7 + - - +
141B PHE* 4.5 10.1 - - - -
142B THR* 3.1 39.2 + - - +
145B THR* 4.7 15.4 - - - +
146B SER* 3.5 15.5 + - - +
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 2.6 48.3 + - - +
103B VAL* 3.3 9.9 - - - +
105B ARG* 1.3 75.1 + - - +
107B LYS* 1.3 63.1 + - - +
109B VAL* 3.2 9.9 + - - +
110B GLU* 3.1 18.3 + - - +
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Residues in contact with LYS 107 (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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67B LEU* 3.4 30.3 - - + +
70B ALA* 3.9 11.7 - - + -
71B GLU* 3.8 41.1 - - - -
103B VAL 3.3 3.9 + - - +
104B VAL 3.2 9.3 + - - +
106B ASP* 1.3 76.1 - - - +
108B ALA* 1.3 59.2 + - - +
110B GLU* 2.6 62.9 + - - +
111B SER* 2.8 17.4 + - - +
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Residues in contact with ALA 108 (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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70B ALA* 4.0 3.5 - - - +
93B LEU* 4.1 13.0 - - + +
96B LEU* 3.6 18.4 - - + -
97B ALA* 3.4 36.8 - - + +
104B VAL 3.2 6.1 + - - +
105B ARG 3.8 4.7 - - - +
107B LYS* 1.3 78.5 - - - +
109B VAL* 1.3 58.1 + - - +
111B SER* 3.3 8.1 + - - -
112B LEU* 2.8 35.0 + - - +
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Residues in contact with VAL 109 (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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97B ALA* 4.8 4.7 - - + -
105B ARG 2.9 17.9 - - - +
106B ASP* 3.2 8.7 + - - +
107B LYS 3.0 0.8 - - - -
108B ALA* 1.3 74.3 - - + +
110B GLU* 1.3 61.1 + - - +
112B LEU* 3.1 9.5 + - + +
113B ARG* 2.8 42.8 + - + +
146B SER* 3.6 35.2 - - - +
149B GLY* 4.4 9.4 - - - -
150B LEU* 3.4 23.1 - - + -
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Residues in contact with GLU 110 (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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398A ARG* 5.1 12.8 + - - -
106B ASP 3.1 11.9 + - - +
107B LYS* 2.6 58.7 + - - +
109B VAL* 1.3 70.5 - - - +
111B SER* 1.3 63.4 + - - +
113B ARG* 3.1 15.7 + - - +
114B ALA* 3.0 22.4 + - + +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA 2.8 26.7 + - - -
71B GLU* 4.5 2.9 + - - -
73B LEU 4.8 0.2 - - - -
74B GLY* 4.0 20.9 - - - -
93B LEU* 4.1 14.8 - - - -
107B LYS* 2.8 18.6 + - - +
108B ALA* 3.4 7.4 - - - -
110B GLU* 1.3 73.4 + - - +
112B LEU* 1.3 65.0 + - - +
114B ALA* 2.9 16.8 + - - +
115B ILE* 2.9 19.9 + - - +
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Residues in contact with LEU 112 (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* 4.2 9.2 - - + -
93B LEU* 3.9 32.3 - - + +
94B GLU 4.8 0.9 - - - +
97B ALA* 4.5 16.2 - - + -
108B ALA 2.8 25.6 + - - +
109B VAL* 3.2 13.9 - - + +
111B SER* 1.3 74.0 - - - +
113B ARG* 1.3 62.5 + - - +
115B ILE* 3.6 6.3 + - + +
116B SER* 2.9 23.2 + - - -
128B PHE* 3.6 23.0 - - + -
131B LEU* 3.7 33.2 - - + -
135B LEU* 5.1 0.2 - - + -
150B LEU* 4.1 18.2 - - + -
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 2.8 31.1 + - - +
110B GLU* 3.1 13.4 + - - +
112B LEU* 1.3 72.8 - - - +
114B ALA* 1.3 57.1 + - - +
116B SER* 2.7 25.0 - - - -
117B HIS* 3.0 17.3 - - + -
149B GLY* 3.5 16.7 + - - +
150B LEU* 4.0 14.6 - - + -
152B SER* 4.2 7.3 + - - -
153B VAL* 4.2 21.5 - - + +
188B LYS* 4.8 9.6 - - - +
191B GLU* 3.0 38.4 + - - -
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Residues in contact with ALA 114 (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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74B GLY* 5.4 6.1 - - - +
110B GLU* 3.0 11.6 + - + +
111B SER* 2.9 12.6 + - - +
113B ARG* 1.3 72.5 - - - +
115B ILE* 1.3 65.1 + - + +
116B SER 2.9 4.7 + - - -
117B HIS* 3.3 19.7 + - - +
118B GLU* 4.1 7.6 + - - +
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Residues in contact with ILE 115 (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 LEU 4.5 5.4 - - - +
74B GLY 4.0 19.7 - - - +
77B THR* 3.5 25.6 - - + -
86B VAL* 3.9 1.3 - - + +
89B LEU* 3.7 29.8 - - + -
90B LEU* 3.5 28.3 - - + -
93B LEU* 4.2 12.3 - - + -
111B SER 2.9 21.4 + - - +
112B LEU* 3.9 8.3 - - + +
114B ALA* 1.3 73.0 - - + +
116B SER* 1.3 67.6 + - - +
117B HIS 3.3 0.2 - - - -
118B GLU* 2.9 14.4 + - - +
119B HIS* 2.8 25.7 - - - +
128B PHE* 4.9 0.9 - - + -
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Residues in contact with SER 116 (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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112B LEU 2.9 15.7 + - - -
113B ARG* 2.7 22.4 + - - -
114B ALA 2.9 1.2 - - - -
115B ILE* 1.3 75.7 - - - +
117B HIS* 1.3 64.8 + - - -
119B HIS* 2.9 35.9 + - - +
124B LEU* 4.2 5.0 - - - +
128B PHE* 3.9 20.4 - - - -
153B VAL* 3.6 23.0 + - - +
157B ARG* 3.3 7.2 + - - -
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Residues in contact with HIS 117 (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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113B ARG* 3.0 26.3 + - + -
114B ALA* 3.3 12.2 + - - +
115B ILE 3.3 0.4 - - - -
116B SER* 1.3 78.7 + - - +
118B GLU* 1.3 60.6 + - + +
119B HIS 2.8 18.8 + - - +
153B VAL* 4.4 18.6 - - + +
157B ARG* 3.4 19.7 + - - +
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Residues in contact with GLU 118 (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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77B THR* 3.2 39.2 + - + -
83B PRO* 3.0 51.9 - - + +
86B VAL* 3.5 18.1 - - + +
114B ALA 4.2 4.3 - - - +
115B ILE* 2.9 15.7 + - - +
117B HIS* 1.3 78.6 - - - +
119B HIS* 1.3 57.9 + - - +
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.8 13.9 - - + +
87B HIS* 3.6 21.0 - - + +
90B LEU* 3.5 26.6 - - + +
115B ILE* 2.8 49.2 - - - +
116B SER* 2.9 18.1 + - - +
117B HIS 2.8 3.2 - - - +
118B GLU* 1.3 79.6 - - - +
120B SER* 1.3 61.1 + - - +
123B ASP* 4.0 18.3 + - - +
124B LEU* 3.9 18.2 - - + -
128B PHE* 4.0 14.3 - + + +
157B ARG* 2.6 33.1 + - - -
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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
------------------------------------------------------------
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