Contacts of the helix formed by residues 58 - 70 (chain B) in PDB entry 1GKU
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 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B GLU 5.0 4.7 - - - -
57B PRO* 1.3 76.3 - - - +
59B ALA* 1.3 66.1 + - - +
60B ILE* 4.0 12.3 - - + -
61B GLN* 2.8 35.7 + - - +
62B LYS* 3.2 9.5 + - - +
81B GLY 2.8 30.4 + - - -
82B VAL* 4.3 13.4 - - + +
83B GLY 5.2 1.5 - - - +
441B ALA* 4.0 1.2 - - - +
498B ARG 2.9 23.4 + - - -
499B GLN* 2.7 29.0 + - - +
500B GLU 4.6 0.8 - - - -
501B PHE 3.1 20.2 + - - +
502B ASP* 3.0 33.8 + - - +
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Residues in contact with ALA 59 (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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57B PRO 3.9 1.2 + - - -
58B ARG* 1.3 71.0 - - - +
60B ILE* 1.3 62.4 + - - +
62B LYS* 3.2 14.6 + - - +
63B MET* 3.1 20.4 + - - +
502B ASP* 3.0 9.7 + - - +
505B LYS* 3.7 26.4 - - + +
506B PRO* 3.6 22.9 - - + +
622B ASP 5.4 0.3 - - - +
623B ALA 6.1 0.4 - - - +
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Residues in contact with ILE 60 (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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58B ARG* 4.0 7.2 - - + -
59B ALA* 1.3 79.2 - - - +
61B GLN* 1.3 64.5 + - + +
63B MET* 3.4 12.2 + - + +
64B TRP* 3.1 40.7 + - + +
78B ALA* 3.3 33.0 - - + -
79B PRO* 4.6 2.5 - - + -
82B VAL* 3.5 36.3 - - + -
502B ASP* 5.0 2.8 + - - +
504B ILE 5.2 6.5 + - - +
505B LYS* 5.6 0.2 - - - +
506B PRO* 4.0 16.7 - - + +
546B VAL* 4.5 22.7 - - + -
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Residues in contact with GLN 61 (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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50B PHE* 4.1 14.1 - - - -
56B GLU 4.8 0.6 + - - -
57B PRO* 3.5 17.2 - - + +
58B ARG* 2.8 41.5 + - - +
60B ILE* 1.3 79.5 - - - +
62B LYS* 1.3 65.5 + - - +
64B TRP* 3.3 29.3 + - + +
65B ALA* 3.1 17.7 + - - +
82B VAL* 4.1 4.7 - - + -
83B GLY* 2.9 30.9 + - - +
86B SER* 4.7 1.7 + - - -
87B PHE* 3.6 29.8 - - + +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.2 9.8 - - + +
46B PHE* 6.5 0.2 - - - -
47B VAL* 4.9 12.3 - - + +
51B ARG* 5.0 6.5 - - - +
56B GLU* 4.0 12.3 + - - -
57B PRO* 3.5 41.0 + - + -
58B ARG 3.2 7.5 + - - +
59B ALA* 3.2 13.8 + - - +
61B GLN* 1.3 76.2 - - - +
63B MET* 1.3 62.8 + - - +
65B ALA* 3.0 10.5 + - - +
66B LYS* 3.0 37.0 + - - +
624B GLU* 5.6 6.3 - - - +
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Residues in contact with MET 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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59B ALA 3.1 11.9 + - - +
60B ILE* 3.6 14.8 - - + +
61B GLN 3.2 0.2 - - - -
62B LYS* 1.3 75.7 - - - +
64B TRP* 1.3 77.7 + - + +
66B LYS* 3.1 15.0 + - - +
67B ARG* 3.1 57.5 + - - +
506B PRO* 3.9 18.2 - - + -
539B GLU* 5.3 3.1 - - - +
546B VAL* 5.9 6.1 - - + -
548B MET* 3.8 32.8 - - + +
622B ASP* 3.5 31.9 - - + +
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Residues in contact with TRP 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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60B ILE* 3.1 24.2 + - + +
61B GLN* 3.5 29.4 - - + +
62B LYS 3.3 0.2 - - - -
63B MET* 1.3 82.9 - - + +
65B ALA* 1.3 63.6 + - - +
67B ARG* 3.2 17.5 + - - +
68B ILE* 3.0 28.0 + - - +
74B PHE* 3.4 33.2 - + + -
76B ALA* 3.7 27.9 - - + +
78B ALA* 3.9 20.0 - - + -
82B VAL* 3.7 17.3 - - + -
83B GLY 3.6 21.1 - - - -
84B LYS* 4.3 15.0 - - + -
87B PHE* 3.8 24.0 - + + -
221B MET* 3.9 12.3 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.7 18.4 - - + -
46B PHE* 4.3 12.8 - - + -
61B GLN 3.1 12.6 + - - +
62B LYS* 3.0 16.3 + - - +
64B TRP* 1.3 76.2 - - - +
66B LYS* 1.3 62.1 + - - +
68B ILE* 2.9 12.6 + - - +
69B LEU* 2.9 21.4 + - + +
87B PHE* 4.0 2.0 - - + -
91B MET* 4.0 25.4 - - + -
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Residues in contact with LYS 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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39B GLU* 5.4 1.4 - - - +
40B ASP* 5.1 0.7 - - - +
43B LEU* 4.0 30.4 - - + +
62B LYS* 3.0 30.4 + - - +
63B MET* 3.1 8.3 + - - +
65B ALA* 1.3 74.8 - - - +
67B ARG* 1.3 62.8 + - - +
68B ILE 3.3 0.3 + - - -
69B LEU* 3.6 6.5 + - - +
70B ARG* 3.3 32.0 + - - +
621B HIS* 2.9 41.0 + - + +
622B ASP* 3.3 39.0 - - - +
624B GLU* 3.3 23.8 + - - -
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Residues in contact with ARG 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 MET* 3.1 49.8 + - - +
64B TRP* 3.5 11.0 - - - +
66B LYS* 1.3 77.3 - - - +
68B ILE* 1.3 52.8 + - - +
70B ARG* 3.6 7.6 + - - +
71B LYS 3.3 4.3 + - - -
72B GLU* 2.6 62.6 + - + +
74B PHE* 3.3 51.9 - - + +
75B ALA 5.0 3.0 + - - -
76B ALA* 6.1 0.2 - - - +
539B GLU* 3.3 30.5 + - - -
548B MET* 4.4 6.1 - - - -
619B LEU* 6.3 0.4 - - - +
622B ASP* 3.6 21.9 + - - +
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Residues in contact with ILE 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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64B TRP 3.0 14.8 + - - +
65B ALA 2.9 7.8 + - - +
67B ARG* 1.3 74.5 - - - +
69B LEU* 1.3 57.4 + - + +
70B ARG 2.9 5.2 - - - -
71B LYS* 2.7 22.6 + - - +
72B GLU 4.6 0.2 - - - -
74B PHE* 3.9 13.7 - - + -
87B PHE* 3.9 29.4 - - + -
91B MET* 4.3 14.8 - - + -
95B LEU* 4.3 24.5 - - + -
178B PHE* 3.9 27.1 - - + -
219B CYS* 4.0 21.1 - - - -
221B MET* 4.2 7.9 - - + -
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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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39B GLU* 3.7 38.2 - - + +
42B LEU* 3.9 21.8 - - + +
43B LEU* 3.4 48.5 - - + +
46B PHE* 5.3 1.8 - - + -
65B ALA* 2.9 21.2 + - + +
66B LYS* 4.2 5.4 - - - +
68B ILE* 1.3 76.1 - - - +
70B ARG* 1.3 57.0 + - - +
71B LYS* 3.3 1.2 - - - +
91B MET* 4.5 11.0 - - + -
94B PHE* 4.4 9.2 - - + -
95B LEU* 4.4 22.7 - - + -
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Residues in contact with ARG 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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37B PHE* 3.6 16.8 - - - -
39B GLU* 4.6 18.4 + - + +
66B LYS* 3.3 25.8 + - - +
67B ARG* 3.7 7.3 - - - +
68B ILE 2.9 0.2 - - - -
69B LEU* 1.3 79.4 - - - +
71B LYS* 1.3 68.2 + - - +
72B GLU* 2.8 43.6 + - + +
618B LYS* 3.3 35.1 - - - +
621B HIS* 3.5 20.2 + - - -
622B ASP* 2.7 37.2 + - - -
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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