Contacts of the helix formed by residues 47 - 60 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLY 3.2 14.4 + - - -
46A SER* 1.3 80.8 - - - +
48A PHE* 1.3 57.2 + - - -
49A LEU 3.4 2.0 - - - -
50A GLY 3.7 2.2 - - - -
51A GLN* 2.4 37.9 + - - +
68A ASP* 3.5 3.9 + - - -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY* 1.3 71.9 - - - +
49A LEU* 1.3 66.3 + - + +
51A GLN* 3.3 10.0 - - + +
52A HIS* 3.1 49.4 - + - -
202A GLY 6.0 1.6 - - - -
203A ILE* 5.8 10.8 - - + -
240A VAL* 3.5 35.9 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 1.3 81.3 - - + +
50A GLY* 1.3 64.7 + - - +
52A HIS* 3.1 7.6 + - - +
53A MET* 3.0 24.3 + - + +
104A CYS* 4.1 23.8 - - + -
143A THR* 4.3 17.0 - - + -
200A PRO* 5.3 3.6 - - + -
203A ILE* 4.5 29.3 - - + +
240A VAL* 4.3 17.9 - - + -
243A VAL* 4.1 21.1 - - + -
244A VAL* 4.0 19.5 - - + -
247A HIS* 4.4 8.1 - - + -
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.2 4.7 - - - -
44A GLY 3.6 19.8 + - - -
45A GLY* 3.2 10.5 - - - -
47A GLY* 3.2 6.7 + - - -
49A LEU* 1.3 75.2 - - - +
51A GLN* 1.3 68.0 + - - +
53A MET* 3.1 16.3 + - - +
54A VAL* 3.2 18.9 + - - +
104A CYS* 4.2 6.0 - - - -
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Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 3.2 10.1 + - - -
46A SER* 3.9 13.0 + - - +
47A GLY 2.4 32.4 + - - +
48A PHE* 3.3 12.1 - - + +
50A GLY* 1.3 70.1 - - - +
52A HIS* 1.3 68.6 + - + +
54A VAL* 3.0 24.9 + - - +
55A GLU* 3.0 31.9 + - - +
73A PHE* 2.7 61.3 + - + +
80A PHE* 5.5 2.4 - - - -
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.1 51.2 - + - -
49A LEU 3.1 6.7 + - - +
51A GLN* 1.3 84.0 - - + +
53A MET* 1.3 63.6 + - - +
55A GLU* 3.8 19.2 + - - +
56A GLN* 3.0 30.9 + - - +
238A THR* 5.3 1.8 - - - -
240A VAL* 3.7 21.3 - - + +
241A GLU* 4.4 22.7 + - + +
244A VAL* 3.8 15.2 - - + +
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.0 12.1 - - + -
49A LEU* 3.0 20.3 + - + +
50A GLY* 3.1 13.2 + - - +
52A HIS* 1.3 76.6 - - - +
54A VAL* 1.3 57.1 + - - +
56A GLN* 4.1 1.6 - - - +
57A LEU* 3.1 49.4 + - + +
102A PHE* 4.3 19.5 - - + -
104A CYS* 3.4 31.9 - - - -
143A THR* 4.0 20.4 - - + -
244A VAL* 3.5 26.7 - - + +
247A HIS* 4.1 24.7 - - + -
248A ILE* 5.8 1.6 - - - -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.6 25.8 - - + -
45A GLY 4.2 3.8 - - - +
50A GLY 3.2 14.4 - - - +
51A GLN* 3.0 20.9 + - - +
53A MET* 1.3 74.4 - - - +
55A GLU* 1.3 70.6 + - + +
57A LEU* 3.7 5.1 - - - +
58A LEU* 2.9 38.8 + - + +
64A VAL* 3.8 13.2 - - + +
66A VAL* 3.8 23.8 - - + -
75A ASN* 5.7 1.8 - - - +
78A VAL* 4.9 13.2 - - + -
80A PHE* 5.8 4.7 - - + -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLN* 3.0 42.4 + - - +
52A HIS* 3.2 21.6 + - - +
54A VAL* 1.3 88.2 - - + +
56A GLN* 1.3 60.7 + - - +
58A LEU* 3.6 9.0 + - - +
59A ALA* 3.4 18.0 + - - +
75A ASN* 5.4 8.5 - - + +
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Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A HIS* 3.0 10.9 + - - +
55A GLU* 1.3 74.2 - - - +
57A LEU* 1.3 60.5 + - - +
59A ALA* 3.1 22.5 + - + +
60A ARG* 3.3 24.4 - - + +
237A PHE* 3.8 18.7 - - + -
241A GLU* 3.3 28.1 + - - +
244A VAL* 3.2 32.6 - - + +
245A HIS* 3.3 37.8 + - - +
248A ILE* 4.1 9.1 - - + +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A CYS* 4.4 5.8 - - - -
42A VAL* 4.1 10.1 - - + -
53A MET* 3.1 37.7 + - + +
54A VAL* 3.9 3.4 - - - +
56A GLN* 1.3 74.6 - - - +
58A LEU* 1.3 63.1 + - - +
61A GLY 3.6 1.0 + - - -
62A TYR* 3.0 73.8 + - + +
64A VAL* 4.1 11.7 - - + -
102A PHE* 3.5 38.1 - - + -
248A ILE* 3.6 24.5 - - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 2.9 25.5 + - + +
55A GLU* 3.8 7.6 - - - +
56A GLN 3.2 0.2 - - - -
57A LEU* 1.3 76.3 - - - +
59A ALA* 1.3 64.5 + - - +
61A GLY* 3.0 13.9 + - - -
62A TYR 3.4 20.0 - - - +
63A ALA* 5.3 0.4 - - - -
64A VAL* 4.2 13.2 - - + +
75A ASN* 3.3 30.3 - - - +
77A GLN* 4.1 42.7 + - + +
78A VAL* 3.9 15.3 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU 3.4 10.5 + - - +
56A GLN* 3.1 16.2 + - + +
58A LEU* 1.3 80.6 - - - +
60A ARG* 1.3 61.7 + - + +
61A GLY 3.5 0.7 + - - -
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 5.7 3.5 + - - +
56A GLN* 3.3 17.9 + - + +
57A LEU 3.7 1.3 + - - -
58A LEU 3.2 0.6 - - - -
59A ALA* 1.3 78.9 - - + +
61A GLY* 1.3 63.3 + - - +
62A TYR* 3.7 20.6 - - + -
245A HIS* 4.1 22.8 + - - -
248A ILE* 3.5 36.4 - - - +
249A LEU* 4.7 4.0 - - - +
252A GLU* 2.8 37.7 + - - -
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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