Contacts of the helix formed by residues 67 - 78 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R LYS 3.6 0.6 + - - -
66R LYS* 1.3 68.9 - - - +
68R ALA* 1.3 56.9 + - - +
70R ILE* 2.9 12.9 + - - +
71R VAL* 2.8 39.1 + - - +
87R TYR* 3.6 17.7 - - - -
90R MET* 3.5 16.2 - - - +
121R MET* 3.5 8.5 - - - -
124R THR* 2.6 41.5 + - - -
125R GLU* 3.7 7.3 + - - -
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Residues in contact with ALA 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R LYS* 3.3 5.1 - - + +
67R SER* 1.3 76.7 - - - +
69R ARG* 1.3 55.9 + - - +
71R VAL* 4.2 0.3 - - - +
72R GLY* 3.1 22.5 + - - -
121R MET* 3.4 38.6 + - + +
68T ALA 4.3 1.0 - - - +
72T GLY* 3.3 13.5 - - - -
75T MET* 3.3 39.3 - - + -
83T ASP* 5.7 0.2 - - + -
121T MET* 6.1 2.0 - - + -
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Residues in contact with ARG 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R GLN* 5.4 7.5 + - - +
58R MET* 3.9 16.7 - - + +
65R LYS* 3.4 41.5 - - - +
66R LYS* 3.2 19.1 + - + +
67R SER 3.1 0.4 - - - -
68R ALA* 1.3 78.2 - - - +
70R ILE* 1.3 56.2 + - - +
72R GLY* 3.9 0.9 - - - -
73R ASP* 3.1 28.9 + - + +
69T ARG 5.3 0.9 - - - +
72T GLY* 3.5 23.8 + - - +
73T ASP* 4.3 9.3 + - + +
76T GLY* 3.9 21.3 - - - -
77T LYS* 3.0 41.8 - - - +
154T GLU* 4.8 4.2 + - - -
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Residues in contact with ILE 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49R ILE* 4.9 4.7 - - + +
52R GLY 5.9 1.1 - - - -
53R LEU* 3.7 33.7 - - + +
58R MET* 3.6 26.2 - - + -
65R LYS* 3.9 10.1 - - + +
66R LYS 3.6 8.3 - - - +
67R SER* 2.9 10.1 + - - +
69R ARG* 1.3 73.5 - - - +
71R VAL* 1.3 60.2 + - + +
73R ASP* 3.3 7.7 + - - +
74R VAL* 3.0 40.6 + - + +
86R ILE* 6.4 0.7 - - + -
90R MET* 4.1 16.6 - - - -
126R ALA* 3.8 36.3 - - + +
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Residues in contact with VAL 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R SER* 2.8 23.0 + - - +
68R ALA 4.2 0.7 - - - +
70R ILE* 1.3 70.5 - - + +
72R GLY* 1.3 59.3 + - - +
74R VAL* 3.8 1.4 - - - +
75R MET* 2.9 34.1 + - + +
83R ASP* 3.8 38.6 - - + +
86R ILE* 3.9 20.5 - - + +
87R TYR* 4.0 34.5 - - + -
90R MET* 5.2 5.8 - - - -
121R MET* 4.0 17.0 - - - -
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Residues in contact with GLY 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R ALA 3.1 14.5 + - - -
69R ARG 3.9 1.1 - - - -
70R ILE 3.3 0.2 - - - -
71R VAL* 1.3 76.8 - - - +
73R ASP* 1.3 51.8 + - - +
75R MET* 3.4 1.6 + - - +
76R GLY 2.9 29.1 + - - -
68T ALA* 3.3 34.5 - - - -
69T ARG* 3.4 18.3 + - - +
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Residues in contact with ASP 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52R GLY* 3.8 18.4 - - - +
56R GLN* 3.5 30.7 + - + +
58R MET* 5.4 1.1 - - + +
69R ARG* 3.1 18.1 + - + +
70R ILE* 3.6 8.2 - - - +
72R GLY* 1.3 73.9 - - - +
74R VAL* 1.3 63.8 + - - +
76R GLY* 3.5 0.5 + - - -
77R LYS* 2.8 68.8 + - - +
78R TYR* 4.5 2.6 - - - -
69T ARG* 4.4 11.7 + - + +
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Residues in contact with VAL 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45R VAL* 5.2 0.4 - - + +
48R ARG* 3.9 31.0 - - + +
49R ILE* 3.9 22.7 - - + +
52R GLY* 4.4 10.3 - - - -
70R ILE* 3.0 28.4 + - + +
71R VAL* 3.9 3.1 - - - +
73R ASP* 1.3 76.5 - - - +
75R MET* 1.3 58.8 + - - +
78R TYR* 3.0 20.1 + - + -
79R HIS* 3.0 41.3 + - + -
86R ILE* 4.2 19.7 - - + -
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Residues in contact with MET 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71R VAL* 2.9 24.0 + - + +
72R GLY 3.8 2.2 - - - +
74R VAL* 1.3 75.9 - - - +
76R GLY* 1.3 63.7 + - - +
79R HIS 3.3 24.2 + - - +
80R PRO* 4.0 3.4 - - + +
81R HIS 3.7 21.8 - - - +
83R ASP* 3.5 35.7 - - + -
86R ILE* 3.7 7.2 - - + -
150R TYR* 3.8 7.6 + - - -
66T LYS* 4.3 18.0 - - + +
68T ALA* 3.3 33.7 - - + -
122T ARG* 3.9 22.0 - - + +
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Residues in contact with GLY 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72R GLY 2.9 17.3 + - - -
73R ASP 3.8 1.6 - - - -
74R VAL 3.3 0.2 - - - -
75R MET* 1.3 76.7 - - - +
77R LYS* 1.3 58.2 + - - +
150R TYR* 2.6 24.7 + - - -
151R ASP* 4.5 4.0 - - - +
66T LYS* 4.1 21.4 - - - +
69T ARG* 4.5 11.9 - - - -
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Residues in contact with LYS 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R GLN* 3.4 18.4 + - - +
73R ASP* 2.8 39.9 + - - +
76R GLY* 1.3 79.4 - - - +
78R TYR* 1.3 91.7 + - + +
149R ASN* 2.9 32.0 + - - +
150R TYR* 3.9 2.0 - - - -
154R GLU* 3.7 32.0 - - + +
69T ARG* 5.0 14.8 - - - +
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Residues in contact with TYR 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48R ARG* 3.3 56.7 + - + -
51R TYR* 3.6 22.2 - + - -
52R GLY* 4.0 20.6 - - - -
55R GLU* 3.6 26.9 - - - +
56R GLN* 5.3 0.2 + - - -
73R ASP* 4.5 6.9 + - - -
74R VAL* 3.0 14.6 + - - +
76R GLY 3.8 0.4 - - - -
77R LYS* 1.3 116.9 - - + +
79R HIS* 1.3 58.5 + - - +
80R PRO* 3.4 9.9 - - - +
149R ASN* 4.6 2.5 - - + -
150R TYR* 3.8 11.3 - - - +
154R GLU* 4.6 9.1 + - + -
155R ARG 4.0 10.5 - - - -
156R GLU* 4.0 23.7 - - + +
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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