Contacts of the helix formed by residues 67 - 78 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65J LYS 3.6 0.6 + - - -
66J LYS* 1.3 67.3 - - - +
68J ALA* 1.3 56.3 + - - +
70J ILE* 2.9 12.9 + - - +
71J VAL* 2.8 38.9 + - - +
87J TYR* 3.6 17.7 - - - -
90J MET* 3.5 17.3 - - - +
121J MET* 3.5 9.0 - - - -
124J THR* 2.6 40.2 + - - -
125J GLU* 3.7 6.8 + - - -
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Residues in contact with ALA 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J LYS* 4.5 6.1 - - + -
67J SER* 1.3 77.9 - - - +
69J ARG* 1.3 55.9 + - - +
71J VAL* 4.3 0.7 - - - +
72J GLY* 3.1 21.8 + - - -
121J MET* 3.4 41.4 + - + +
68L ALA 4.5 0.5 - - - +
72L GLY* 3.6 15.5 - - - -
75L MET* 3.7 35.2 - - + -
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Residues in contact with ARG 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J MET* 4.6 12.7 - - + +
65J LYS* 3.7 31.0 - - + +
66J LYS* 3.2 19.7 + - + +
67J SER 3.1 0.6 - - - -
68J ALA* 1.3 77.5 - - - +
70J ILE* 1.3 57.2 + - - +
72J GLY* 3.9 0.7 - - - -
73J ASP* 3.1 28.7 + - + +
69L ARG 5.6 1.2 - - - +
72L GLY* 3.9 22.6 + - - +
73L ASP* 4.9 6.3 - - + +
76L GLY* 4.7 17.1 + - - -
77L LYS* 3.9 36.4 - - - +
154L GLU* 5.1 4.9 + - - -
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Residues in contact with ILE 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J ILE* 5.0 3.8 - - + -
52J GLY 5.8 0.7 - - - -
53J LEU* 3.7 38.1 - - + +
58J MET* 4.4 8.5 - - + -
65J LYS* 3.9 23.3 - - + +
66J LYS 3.3 8.5 + - - +
67J SER* 2.9 10.8 + - - +
69J ARG* 1.3 73.3 - - - +
71J VAL* 1.3 60.2 + - + +
73J ASP* 3.3 7.9 + - - +
74J VAL* 3.0 40.7 + - + +
86J ILE* 6.4 0.4 - - + -
90J MET* 4.1 16.6 - - - -
126J ALA* 3.7 34.5 - - + +
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Residues in contact with VAL 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67J SER* 2.8 23.1 + - - +
68J ALA 4.3 0.7 - - - +
70J ILE* 1.3 71.2 - - + +
72J GLY* 1.3 59.6 + - - +
74J VAL* 3.4 1.0 + - - +
75J MET* 2.9 34.2 + - + +
83J ASP* 3.9 38.8 - - + +
86J ILE* 3.9 21.8 - - + +
87J TYR* 4.1 27.8 - - + -
90J MET* 5.1 6.3 - - - -
121J MET* 4.0 21.8 - - + -
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Residues in contact with GLY 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J ALA 3.1 15.1 + - - -
69J ARG 3.9 1.6 - - - -
71J VAL* 1.3 77.6 - - - +
73J ASP* 1.3 50.1 + - - +
75J MET* 3.8 5.6 - - - +
76J GLY* 2.9 32.1 + - - -
68L ALA* 3.6 28.9 - - - -
69L ARG* 3.9 15.6 + - - +
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Residues in contact with ASP 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J GLY* 3.8 18.9 - - - +
56J GLN* 3.5 30.3 + - + +
69J ARG* 3.1 19.7 + - + +
70J ILE* 3.3 8.0 + - - +
72J GLY* 1.3 74.3 - - - +
74J VAL* 1.3 63.9 + - - +
76J GLY* 3.5 0.7 + - - -
77J LYS* 2.8 70.0 + - - +
78J TYR* 4.5 2.5 - - - -
69L ARG* 4.7 10.9 + - + +
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Residues in contact with VAL 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J VAL* 5.2 0.4 - - + +
48J ARG* 3.9 33.4 - - + +
49J ILE* 3.9 17.9 - - + +
52J GLY* 4.4 12.6 - - - -
70J ILE* 3.0 29.3 + - + +
71J VAL* 3.9 3.8 - - - +
73J ASP* 1.3 76.4 - - - +
75J MET* 1.3 57.9 + - - +
78J TYR* 3.0 19.6 + - + -
79J HIS* 3.0 41.1 + - + -
86J ILE* 4.1 18.8 - - + -
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Residues in contact with MET 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J VAL* 2.9 24.3 + - + +
72J GLY* 3.8 2.7 - - - +
74J VAL* 1.3 74.3 - - - +
76J GLY* 1.3 64.5 + - - +
77J LYS 3.6 0.2 + - - -
79J HIS 3.3 22.7 + - - +
80J PRO* 4.0 0.3 - - - +
81J HIS 3.3 23.8 - - - +
83J ASP* 3.5 33.7 - - + -
86J ILE* 3.7 6.7 - - + -
121J MET* 5.8 0.7 - - + -
150J TYR* 3.7 4.0 + - - -
66L LYS* 3.1 44.3 + - + +
68L ALA* 3.6 20.0 - - + -
121L MET* 5.9 0.7 - - + -
122L ARG* 3.7 18.8 - - + -
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Residues in contact with GLY 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72J GLY 2.9 17.9 + - - -
73J ASP 3.8 1.3 - - - -
74J VAL 3.3 0.2 - - - -
75J MET* 1.3 76.5 - - - +
77J LYS* 1.3 60.3 - - - +
150J TYR* 2.6 24.4 + - - -
151J ASP* 4.5 3.5 - - - +
66L LYS* 4.1 21.8 - - - +
69L ARG* 4.9 7.0 - - - -
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Residues in contact with LYS 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J GLN* 3.4 20.2 + - - +
73J ASP* 2.8 40.8 + - - +
76J GLY* 1.3 79.3 - - - +
78J TYR* 1.3 91.1 + - + +
149J ASN* 2.9 31.8 + - - +
150J TYR* 3.9 1.8 - - - -
154J GLU* 3.8 31.7 - - + +
69L ARG* 4.8 20.4 - - + +
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Residues in contact with TYR 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J ARG* 3.3 55.3 + - + -
51J TYR* 3.6 22.4 - + - -
52J GLY* 4.0 20.2 - - - -
55J GLU* 3.6 27.0 - - - +
56J GLN* 5.1 0.7 + - - -
73J ASP* 4.5 5.8 - - - -
74J VAL* 3.0 16.4 + - + +
76J GLY 3.8 0.4 - - - -
77J LYS* 1.3 117.2 + - + +
79J HIS* 1.3 59.8 + - - +
80J PRO* 3.4 11.6 - - - +
149J ASN* 4.6 2.0 - - - -
150J TYR* 3.8 10.8 - - - +
154J GLU* 4.6 9.1 + - + -
155J ARG 4.0 10.1 - - - -
156J GLU* 4.0 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