Contacts of the helix formed by residues 39 - 52 (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 GLU 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.9 9.3 - - + +
38B PRO* 1.3 107.1 - - - +
40B ASP* 1.3 65.9 + - - +
41B PHE 3.0 3.6 - - - -
42B LEU* 3.0 31.7 + - + +
43B LEU 3.2 6.9 + - - -
66B LYS 5.4 1.3 - - - +
69B LEU* 3.7 44.0 - - + +
70B ARG* 4.5 19.4 - - + +
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Residues in contact with ASP 40 (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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36B LEU* 3.0 36.0 - - + +
37B PHE* 2.9 29.9 + - - +
39B GLU* 1.3 76.7 - - - +
41B PHE* 1.3 62.5 + - - +
43B LEU* 3.0 23.9 + - + +
44B LYS* 2.9 22.9 + - - +
66B LYS* 5.1 0.9 - - - +
621B HIS* 2.9 35.3 + - - -
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Residues in contact with PHE 41 (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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36B LEU* 5.1 1.8 - - - +
37B PHE 4.8 0.2 + - - -
38B PRO 4.4 9.7 + - - +
39B GLU 3.0 0.2 + - - -
40B ASP* 1.3 80.0 - - - +
42B LEU* 1.3 71.1 + - + +
44B LYS* 3.3 13.7 + - + +
45B GLU* 3.1 35.9 + - - +
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Residues in contact with LEU 42 (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* 3.0 27.6 + - + +
41B PHE* 1.3 83.4 - - + +
43B LEU* 1.3 56.1 + - - +
45B GLU* 3.1 13.8 + - - +
46B PHE* 2.6 35.9 + - - +
69B LEU* 3.9 25.6 - - + +
94B PHE* 3.7 9.8 - - + -
95B LEU* 6.4 0.4 - - + -
98B LYS* 4.5 19.5 - - + +
100B LYS* 6.6 0.2 - - - -
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Residues in contact with LEU 43 (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 3.2 2.6 + - - -
40B ASP* 3.0 30.9 + - + +
42B LEU* 1.3 74.8 - - - +
44B LYS* 1.3 69.2 + - - +
46B PHE* 2.9 14.5 + - + +
47B VAL* 2.9 23.2 + - + +
62B LYS* 4.2 15.5 - - + +
65B ALA* 3.7 29.2 - - + -
66B LYS* 4.0 32.8 - - + +
69B LEU* 3.4 18.1 - - + +
624B GLU* 5.5 1.1 - - - +
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Residues in contact with LYS 44 (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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40B ASP 2.9 10.9 + - - +
41B PHE* 3.5 17.3 - - + +
43B LEU* 1.3 76.8 - - - +
45B GLU* 1.3 61.6 + - - +
47B VAL* 2.7 27.6 - - + +
48B GLU* 3.1 33.0 + - + +
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Residues in contact with GLU 45 (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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41B PHE* 3.1 31.0 + - - +
42B LEU* 3.1 14.6 + - - +
44B LYS* 1.3 81.8 - - - +
46B PHE* 1.3 61.9 + - - +
48B GLU* 3.4 15.0 + - - +
49B PHE* 3.0 22.3 + - - +
94B PHE* 4.1 7.4 - - + -
98B LYS* 2.8 38.4 + - - -
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Residues in contact with PHE 46 (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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42B LEU 2.6 16.7 + - - +
43B LEU* 2.9 13.0 + - + +
45B GLU* 1.3 74.2 - - - +
47B VAL* 1.3 57.5 + - + +
49B PHE* 3.0 9.6 + + - +
50B PHE* 2.6 64.8 + + + +
57B PRO* 5.9 4.9 - - + -
61B GLN 5.6 0.7 - - - -
65B ALA* 4.3 11.2 - - + -
69B LEU* 5.3 2.0 - - + -
87B PHE* 3.9 23.6 - + - -
90B ALA 3.8 8.1 - - - -
91B MET* 3.5 51.1 - - + -
94B PHE* 3.5 37.2 - + + -
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Residues in contact with VAL 47 (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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43B LEU* 2.9 20.3 + - + +
44B LYS* 2.7 30.1 - - + +
46B PHE* 1.3 78.8 - - + +
48B GLU* 1.3 56.6 + - + +
50B PHE* 3.6 8.5 - - - +
51B ARG* 2.8 64.5 + - + +
56B GLU* 4.8 0.7 - - - +
57B PRO* 4.4 20.2 - - + +
62B LYS* 4.9 10.5 - - + +
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Residues in contact with GLU 48 (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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44B LYS* 3.1 41.3 + - + +
45B GLU* 3.5 13.6 - - - +
46B PHE 3.1 0.2 - - - -
47B VAL* 1.3 76.3 - - + +
49B PHE* 1.3 65.1 + - - +
51B ARG* 3.0 36.4 + - - +
52B LYS* 3.4 21.1 + - - +
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Residues in contact with PHE 49 (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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45B GLU 3.0 10.4 + - - +
46B PHE* 3.0 13.0 + + - +
48B GLU* 1.3 81.7 - - - +
50B PHE* 1.3 63.0 + - - +
51B ARG 3.3 0.7 + - - -
52B LYS* 3.5 15.8 - - + +
53B CYS* 2.9 41.2 + - + +
90B ALA* 3.1 27.6 - - + -
93B LEU* 3.4 34.5 - - + -
94B PHE* 3.4 31.2 - + + -
97B LEU* 3.9 20.4 - - + -
122B TYR 6.0 0.7 - - - -
126B ALA* 5.9 7.0 - - + -
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Residues in contact with PHE 50 (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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46B PHE* 2.6 41.5 + + + +
47B VAL* 3.6 7.4 - - - +
49B PHE* 1.3 74.6 - - - +
51B ARG* 1.3 56.4 + - - +
53B CYS* 3.9 4.3 - - - -
54B VAL* 2.7 60.0 + - + -
55B GLY 3.1 7.9 + - - -
56B GLU 4.2 6.5 - - - -
57B PRO* 3.8 39.7 - - + -
61B GLN* 4.1 20.9 - - - -
86B SER* 5.0 1.3 - - - -
87B PHE* 4.1 20.6 - + - -
90B ALA* 3.6 31.6 - - + -
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Residues in contact with ARG 51 (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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47B VAL* 2.8 39.7 + - + +
48B GLU* 3.0 26.3 + - - +
50B PHE* 1.3 75.6 - - - +
52B LYS* 1.3 58.5 + - - +
53B CYS 3.1 5.2 + - - -
54B VAL 4.5 0.3 - - - -
55B GLY* 3.7 15.1 + - - -
56B GLU* 2.6 54.4 + - + +
62B LYS* 5.0 5.1 - - - +
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Residues in contact with LYS 52 (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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48B GLU* 3.9 20.6 + - - +
49B PHE* 3.5 19.5 - - + +
51B ARG* 1.3 77.4 - - - +
53B CYS* 1.3 60.1 + - + +
125B LYS* 3.4 51.2 - - + +
126B ALA* 6.1 0.2 - - + -
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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