Contacts of the helix formed by residues 62 - 73 (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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 4.4 28.4 - - + +
28B ARG* 5.4 1.6 - - - +
61B ASP* 1.3 78.0 - - - +
63B ASP* 1.3 55.4 + - - +
64B GLU* 2.8 18.1 + - + +
65B VAL* 2.7 32.3 + - + +
66B LEU* 3.2 8.7 + - - +
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Residues in contact with ASP 63 (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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61B ASP 3.7 1.0 + - - -
62B GLU* 1.3 71.8 - - - +
64B GLU* 1.3 56.8 + - - +
66B LEU* 3.5 19.5 - - - +
67B LEU* 3.0 28.9 + - - +
99B VAL* 3.9 6.6 - - - +
101B GLU* 3.0 42.9 - - + +
104B VAL* 3.3 9.9 - - + +
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Residues in contact with GLU 64 (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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25B VAL* 6.1 1.0 - - - +
26B GLN* 4.7 7.6 - - - +
29B LEU* 4.0 30.7 - - + +
62B GLU* 2.8 14.2 + - + +
63B ASP* 1.3 77.4 - - - +
65B VAL* 1.3 66.5 + - + +
67B LEU* 3.4 13.7 - - + +
68B ALA* 3.2 18.7 + - - +
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Residues in contact with VAL 65 (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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25B VAL* 4.2 21.1 - - + +
28B ARG* 4.9 13.0 - - + +
29B LEU* 5.6 10.3 - - + +
32B ILE* 4.3 22.6 - - + +
59B ILE* 4.6 7.4 - - + -
61B ASP* 3.4 40.4 - - + +
62B GLU* 2.7 20.6 + - + +
64B GLU* 1.3 70.1 - - + +
66B LEU* 1.3 68.1 + - - +
68B ALA* 2.8 19.8 + - - +
69B LEU* 3.0 10.4 + - + +
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Residues in contact with LEU 66 (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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59B ILE* 4.0 31.2 - - + +
60B TYR* 4.7 4.0 - - - +
61B ASP 3.6 18.2 - - - +
62B GLU 3.5 4.7 - - - +
63B ASP* 3.5 35.2 - - - +
65B VAL* 1.3 75.7 - - - +
67B LEU* 1.3 64.5 + - - +
69B LEU* 2.7 21.0 + - + +
70B ALA* 2.8 16.4 + - - +
96B LEU* 3.9 20.3 - - + +
99B VAL* 4.4 15.9 - - + -
104B VAL* 3.9 17.0 - - + -
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Residues in contact with LEU 67 (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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63B ASP 3.0 15.8 + - - +
64B GLU* 3.4 13.9 - - + +
66B LEU* 1.3 78.1 - - - +
68B ALA* 1.3 60.7 + - - +
70B ALA* 4.0 4.6 - - - +
71B GLU* 3.1 22.7 + - + +
103B VAL* 3.6 40.6 - - + +
104B VAL* 4.1 6.9 - - + +
107B LYS* 3.4 29.4 - - + +
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Residues in contact with ALA 68 (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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29B LEU* 5.5 7.0 - - + -
32B ILE* 4.2 16.6 - - + -
33B LYS* 4.6 24.5 - - + +
64B GLU 3.2 8.1 + - - +
65B VAL* 2.8 12.2 + - - +
66B LEU 2.8 0.8 + - - -
67B LEU* 1.3 77.4 - - - +
69B LEU* 1.3 54.5 + - - +
71B GLU* 3.0 11.0 + - - +
72B GLN* 2.6 39.8 + - - +
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Residues in contact with LEU 69 (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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32B ILE* 3.8 12.5 - - + +
35B LEU* 4.0 24.0 - - + -
55B LEU* 4.1 18.2 - - + +
59B ILE* 3.3 41.7 - - + -
65B VAL* 3.0 10.2 + - + +
66B LEU* 2.7 14.1 + - - +
68B ALA* 1.3 71.4 - - - +
70B ALA* 1.3 55.6 + - - +
72B GLN* 2.9 4.2 + - + +
73B LEU* 2.6 66.1 + - + +
92B PRO* 5.8 2.0 - - + +
96B LEU* 4.4 14.8 - - + -
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Residues in contact with ALA 70 (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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66B LEU 2.8 17.6 + - - +
67B LEU* 4.0 2.7 - - - +
69B LEU* 1.3 75.1 - - - +
71B GLU* 1.3 61.9 + - - +
73B LEU* 3.5 10.8 + - - +
74B GLY 3.6 2.1 + - - -
93B LEU* 4.5 0.9 - - - -
96B LEU* 3.4 28.2 - - + +
104B VAL 4.3 5.8 - - - +
107B LYS* 3.9 21.3 - - + -
108B ALA* 4.0 10.5 - - - +
111B SER* 2.8 21.7 + - - -
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Residues in contact with GLU 71 (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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33B LYS* 3.2 28.9 + - - +
67B LEU* 3.1 17.2 + - + +
68B ALA* 3.0 7.8 + - - +
70B ALA* 1.3 75.3 - - - +
72B GLN* 1.3 70.7 + - - +
74B GLY* 2.9 15.6 + - - -
75B THR* 4.2 1.9 + - - -
107B LYS* 3.8 33.7 - - - +
111B SER* 4.5 1.0 + - - -
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Residues in contact with GLN 72 (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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32B ILE* 3.4 18.9 + - + +
33B LYS* 3.2 29.5 + - - +
35B LEU* 4.0 23.0 - - + +
36B SER* 4.3 19.0 - - - +
68B ALA 2.6 20.5 + - - +
69B LEU* 3.3 8.5 - - + +
71B GLU* 1.3 72.6 - - - +
73B LEU* 1.3 54.2 + - - +
74B GLY 2.6 17.4 + - - -
75B THR* 2.9 38.2 + - - +
76B PHE* 4.8 7.3 - - + -
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Residues in contact with LEU 73 (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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35B LEU* 6.1 0.7 - - + -
52B LEU* 4.5 7.0 - - + -
55B LEU* 5.2 3.4 - - + -
69B LEU* 2.6 48.0 + - + +
70B ALA 3.7 7.4 - - - +
71B GLU 3.3 0.2 - - - -
72B GLN* 1.3 70.9 - - - +
74B GLY* 1.3 62.5 + - - +
75B THR 4.2 3.1 - - - -
76B PHE* 3.8 23.1 - - + +
89B LEU* 3.4 37.9 - - + +
92B PRO* 3.9 35.0 - - + -
93B LEU* 4.1 21.8 - - + +
96B LEU* 4.6 3.1 - - + -
111B SER* 4.7 1.6 - - - -
115B ILE* 4.5 7.4 - - - +
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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