Contacts of the helix formed by residues 47 - 60 (chain B) in PDB entry 6JKG
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 GLY 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B GLY* 2.8 15.9 + - - -
46B SER* 1.3 81.0 - - - +
48B PHE* 1.3 67.6 + - - -
49B LEU 3.3 2.7 - - - -
50B GLY 3.9 0.9 - - - -
51B GLN* 3.1 24.1 + - - +
68B ASP* 3.7 1.4 + - - -
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Residues in contact with PHE 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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47B GLY* 1.3 73.9 - - - +
49B LEU* 1.3 62.4 + - - +
51B GLN* 3.5 5.9 - - + +
52B HIS* 2.9 46.9 - + - -
203B ILE* 4.5 34.3 - - + -
240B VAL* 3.5 34.1 - - + -
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Residues in contact with LEU 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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47B GLY* 3.3 0.4 - - - -
48B PHE* 1.3 80.8 - - + +
50B GLY* 1.3 56.1 + - - +
51B GLN 3.2 0.2 - - - -
52B HIS* 3.1 4.9 + - - -
53B MET* 2.7 54.4 + - + +
104B CYS* 4.1 16.8 - - + +
143B THR* 4.4 13.2 - - + +
200B PRO* 5.5 3.4 - - + -
203B ILE* 4.9 21.5 - - + +
240B VAL* 4.2 13.7 - - + -
243B VAL* 4.0 20.2 - - + -
244B VAL* 3.9 23.6 - - + -
247B HIS* 4.6 5.4 - - + +
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Residues in contact with GLY 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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42B VAL* 4.1 4.5 - - - -
44B GLY 3.3 24.2 + - - -
45B GLY* 3.5 11.7 - - - -
47B GLY* 3.6 3.2 + - - -
49B LEU* 1.3 75.3 - - - +
51B GLN* 1.3 67.0 + - - +
53B MET* 3.0 9.0 + - - +
54B VAL* 2.8 28.2 + - - +
104B CYS* 4.9 6.0 - - - +
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Residues in contact with GLN 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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45B GLY 3.0 18.0 + - - +
46B SER* 4.9 3.8 - - - +
47B GLY 3.1 15.6 + - - +
48B PHE* 3.5 8.3 - - - +
50B GLY* 1.3 76.5 - - - +
52B HIS* 1.3 67.3 + - + +
54B VAL* 3.4 5.4 + - - +
55B GLU* 3.1 41.7 + - - +
72B GLY* 4.9 1.9 - - - -
73B PHE* 2.9 51.5 + - - +
75B ASN* 5.3 10.1 + - - +
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Residues in contact with HIS 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 PHE* 2.9 46.0 - + - -
49B LEU 3.1 7.0 + - - +
51B GLN* 1.3 82.4 - - + +
53B MET* 1.3 68.1 + - - +
55B GLU* 3.0 22.3 + - - -
56B GLN* 2.7 38.5 + - - +
238B THR* 5.9 0.7 - - - -
240B VAL* 3.7 25.8 - - + +
241B GLU* 4.7 16.2 + - + +
244B VAL* 4.0 14.1 - - + -
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Residues in contact with MET 53 (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 VAL* 4.1 13.2 - - + -
49B LEU* 2.7 32.0 + - + +
50B GLY* 3.3 12.6 - - - +
52B HIS* 1.3 72.3 - - - +
54B VAL* 1.3 63.3 + - - +
56B GLN* 3.5 2.3 + - - +
57B LEU* 2.9 44.3 + - + +
102B PHE* 4.2 11.7 - - + -
104B CYS* 2.7 40.8 - - - -
143B THR* 3.9 1.6 - - + -
244B VAL* 3.6 29.5 - - - +
247B HIS* 3.6 39.7 - - + +
248B ILE* 5.2 0.9 - - - -
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Residues in contact with VAL 54 (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 VAL* 4.3 11.7 - - + -
45B GLY* 4.5 3.4 - - - +
50B GLY 2.8 26.4 + - - +
51B GLN* 3.6 7.4 - - - +
53B MET* 1.3 71.1 - - - +
55B GLU* 1.3 66.9 + - - +
57B LEU* 2.7 17.9 + - - +
58B LEU* 2.8 31.5 + - + +
64B VAL* 3.6 24.9 - - + -
66B VAL* 3.6 24.2 - - + -
75B ASN* 4.5 12.8 - - - +
78B VAL* 4.1 10.1 - - + -
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Residues in contact with GLU 55 (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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51B GLN* 3.1 40.7 + - - +
52B HIS* 3.0 30.8 + - - +
54B VAL* 1.3 82.8 - - - +
56B GLN* 1.3 72.7 + - - +
58B LEU* 3.2 14.5 + - - +
59B ALA* 3.4 11.1 + - - +
75B ASN* 4.9 11.5 + - - +
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Residues in contact with GLN 56 (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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52B HIS* 2.7 46.6 + - - +
55B GLU* 1.3 80.9 + - - +
57B LEU* 1.3 61.1 + - - +
59B ALA* 3.4 8.4 + - - +
60B ARG* 3.4 24.1 + - + +
237B PHE* 4.8 20.0 - - + -
241B GLU* 4.1 29.5 + - - +
244B VAL* 3.7 31.7 - - + +
245B HIS* 5.3 0.9 - - - +
248B ILE* 3.9 10.1 - - + -
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Residues in contact with LEU 57 (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 CYS* 4.1 10.3 - - - -
42B VAL* 3.9 11.9 - - + -
53B MET* 2.9 34.7 + - + +
54B VAL 2.7 12.4 + - - +
56B GLN* 1.3 70.1 - - - +
58B LEU* 1.3 65.7 + - - +
60B ARG* 3.1 13.4 + - + +
62B TYR* 3.2 45.4 + - + +
64B VAL* 3.6 12.6 - - + -
102B PHE* 3.6 42.6 - - + -
248B ILE* 3.8 24.9 - - + -
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Residues in contact with LEU 58 (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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54B VAL* 2.8 36.6 + - + +
55B GLU* 3.9 5.4 - - - +
57B LEU* 1.3 71.8 - - - +
59B ALA* 1.3 65.3 + - - +
61B GLY* 2.8 16.6 + - - -
62B TYR 3.3 22.3 + - - +
64B VAL* 3.8 13.9 - - + +
75B ASN* 5.0 11.2 - - - +
76B PRO* 4.0 20.0 - - + +
77B GLN* 3.6 30.5 - - + +
78B VAL* 4.7 3.6 - - + -
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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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55B GLU 3.4 9.0 + - - +
56B GLN* 3.7 11.2 - - - +
57B LEU 3.3 0.6 - - - -
58B LEU* 1.3 78.6 - - - +
60B ARG* 1.3 63.0 + - + +
61B GLY* 3.1 1.9 + - - -
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Residues in contact with ARG 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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56B GLN* 3.4 13.7 + - + +
57B LEU* 3.1 12.3 + - - +
58B LEU 3.0 0.4 - - - -
59B ALA* 1.3 77.4 - - + +
61B GLY* 1.3 59.0 + - - +
62B TYR* 3.8 26.6 + - + -
233B ASN* 6.0 0.8 - - - +
245B HIS* 3.6 18.0 + - - -
248B ILE* 4.5 17.6 - - + +
249B LEU* 3.3 30.1 - - - +
252B GLU* 2.8 23.3 + - - -
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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