Contacts of the helix formed by residues 67 - 78 (chain a) in PDB entry 6QX2
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 SER 67 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65a LYS 3.6 0.8 + - - -
66a LYS* 1.3 68.7 - - - +
68a ALA* 1.3 57.3 + - - +
70a ILE* 2.9 13.5 + - - +
71a VAL* 2.8 38.9 + - - +
87a TYR* 3.6 18.4 - - - -
90a MET* 3.5 16.2 - - - +
121a MET* 3.5 8.3 - - - -
124a THR* 2.6 41.0 + - - -
125a GLU* 3.7 7.3 + - - -
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Residues in contact with ALA 68 (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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66a LYS* 3.3 2.6 - - + -
67a SER* 1.3 77.3 - - - +
69a ARG* 1.3 56.8 + - - +
71a VAL* 4.2 0.5 - - - +
72a GLY* 3.1 22.2 + - - -
121a MET* 3.4 36.6 + - + +
68c ALA 4.5 0.2 - - - +
72c GLY* 3.4 12.0 - - - -
75c MET* 3.2 44.0 - - + -
83c ASP* 5.6 0.4 - - + -
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Residues in contact with ARG 69 (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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56a GLN* 5.8 3.2 + - - +
58a MET* 4.0 17.9 - - + +
65a LYS* 2.8 43.0 - - + +
66a LYS* 3.2 11.6 + - - +
67a SER 3.1 0.6 - - - -
68a ALA* 1.3 76.4 - - - +
70a ILE* 1.3 58.2 + - - +
72a GLY* 3.6 0.9 + - - -
73a ASP* 3.1 29.7 + - + +
69c ARG 5.4 0.7 - - - +
72c GLY* 3.5 29.5 + - - +
73c ASP* 4.6 6.8 + - + +
76c GLY* 4.3 16.2 + - - -
77c LYS* 3.3 37.1 - - - +
154c GLU* 4.6 6.2 + - - -
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Residues in contact with ILE 70 (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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49a ILE* 4.9 3.8 - - + -
52a GLY 5.8 0.9 - - - -
53a LEU* 3.7 38.4 - - + +
58a MET* 4.4 8.3 - - + -
65a LYS* 3.9 22.4 - - + +
66a LYS 3.6 7.4 - - - +
67a SER* 2.9 10.8 + - - +
69a ARG* 1.3 73.8 - - - +
71a VAL* 1.3 60.8 + - - +
73a ASP* 3.3 7.3 + - - +
74a VAL* 3.0 41.3 + - + +
86a ILE* 6.4 0.4 - - + -
90a MET* 4.1 16.8 - - - -
126a ALA* 3.8 35.0 - - + +
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Residues in contact with VAL 71 (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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67a SER* 2.8 23.2 + - - +
68a ALA 4.2 0.4 - - - +
70a ILE* 1.3 70.5 - - + +
72a GLY* 1.3 59.2 + - - +
74a VAL* 3.4 1.2 + - - +
75a MET* 2.9 34.2 + - + +
83a ASP* 3.9 38.8 - - + +
86a ILE* 3.9 20.3 - - + +
87a TYR* 4.0 35.7 - - + -
90a MET* 5.2 6.1 - - - -
121a MET* 4.0 15.9 - - - -
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Residues in contact with GLY 72 (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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68a ALA 3.1 15.0 + - - -
69a ARG 3.9 1.1 - - - -
71a VAL* 1.3 76.7 - - - +
73a ASP* 1.3 51.6 + - - +
75a MET* 3.8 2.6 - - - +
76a GLY* 2.9 29.8 + - - -
68c ALA* 3.2 33.0 - - - -
69c ARG* 3.6 18.1 + - - -
72c GLY* 5.1 0.2 - - - -
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Residues in contact with ASP 73 (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 GLY* 3.8 18.7 - - - +
56a GLN* 3.5 28.8 + - + +
69a ARG* 3.1 18.2 + - + +
70a ILE* 3.3 8.2 + - - +
72a GLY* 1.3 72.6 - - - +
74a VAL* 1.3 65.1 + - - +
76a GLY* 3.5 0.9 + - - -
77a LYS* 2.8 68.5 + - - +
78a TYR* 4.5 1.9 - - - -
69c ARG* 4.4 12.3 + - + +
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Residues in contact with VAL 74 (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 VAL 5.2 0.4 - - - +
48a ARG* 3.9 34.3 - - + +
49a ILE* 3.9 17.3 - - + -
52a GLY* 4.4 12.6 - - - -
70a ILE* 3.0 30.4 + - + +
71a VAL* 3.9 4.0 - - - +
73a ASP* 1.3 75.8 - - - +
75a MET* 1.3 57.8 + - - +
78a TYR* 3.0 19.3 + - + -
79a HIS* 3.0 40.5 + - + -
86a ILE* 4.2 19.5 - - + -
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Residues in contact with MET 75 (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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71a VAL* 2.9 22.9 + - + +
72a GLY* 3.8 2.9 - - - +
74a VAL* 1.3 74.7 - - - +
76a GLY* 1.3 66.4 + - - +
77a LYS 3.7 0.2 + - - -
79a HIS 3.3 23.8 + - - +
80a PRO* 4.0 0.7 - - - +
81a HIS 3.2 24.9 - - - +
83a ASP* 3.5 34.1 - - + -
86a ILE* 3.7 7.2 - - + -
150a TYR* 3.8 7.8 + - - -
66c LYS* 3.3 26.9 + - + -
68c ALA* 3.5 20.9 - - + -
121c MET* 5.8 0.4 - - + -
122c ARG* 3.7 26.7 - - + -
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Residues in contact with GLY 76 (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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72a GLY 2.9 18.1 + - - -
73a ASP 3.8 1.6 - - - -
74a VAL 3.3 0.2 - - - -
75a MET* 1.3 76.7 - - - +
77a LYS* 1.3 58.7 + - - +
150a TYR* 2.6 24.4 + - - -
151a ASP* 4.6 3.6 - - - +
66c LYS* 4.1 22.0 - - - +
69c ARG* 4.4 11.0 - - - -
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Residues in contact with LYS 77 (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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56a GLN* 3.4 19.8 + - - +
73a ASP* 2.8 39.9 + - - +
76a GLY* 1.3 77.9 - - - +
78a TYR* 1.3 90.5 + - + +
149a ASN* 2.9 30.8 + - - +
150a TYR* 3.9 2.0 - - - -
154a GLU* 3.7 32.5 - - + +
69c ARG* 4.4 19.5 - - - +
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Residues in contact with TYR 78 (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 ARG* 3.3 56.8 + - + -
51a TYR* 3.6 22.2 - + - -
52a GLY* 4.0 20.9 - - - -
55a GLU* 3.6 26.9 - - - +
56a GLN* 5.1 0.9 + - - -
73a ASP* 4.5 6.3 - - - -
74a VAL* 3.0 14.4 + - + +
76a GLY 3.8 0.6 - - - -
77a LYS* 1.3 116.4 + - + +
79a HIS* 1.3 59.6 + - - +
80a PRO* 3.4 9.1 - - - +
149a ASN* 4.6 3.8 - - + -
150a TYR* 3.8 10.8 + - - +
154a GLU* 4.6 8.5 + - + -
155a ARG 4.0 9.9 - - - -
156a GLU* 4.0 22.1 - - + +
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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