Contacts of the helix formed by residues 67 - 87 (chain R) in PDB entry 6VMS
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 THR 67 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 3.9 21.8 - - + +
64R ALA 5.5 3.6 - - - +
65R LEU 3.9 0.4 - - - -
66R GLN* 1.3 80.2 - - - +
68R THR* 1.3 72.0 + - - +
69R THR* 4.4 2.0 - - - +
70R ASN* 3.2 34.0 + - - +
71R TYR* 2.8 21.3 + - - -
142R TYR* 3.2 21.3 + - - +
143R ASN* 2.9 26.3 + - - -
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Residues in contact with THR 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R THR* 1.3 81.8 + - - +
69R THR* 1.3 63.0 + - - +
70R ASN 3.3 1.0 + - - -
71R TYR* 3.3 17.2 + - - +
72R LEU* 3.4 15.8 + - + +
131R ASP* 3.1 33.9 - - + +
142R TYR* 4.3 5.5 - - - -
143R ASN* 5.2 2.1 + - - -
148R SER* 3.6 16.0 + - - +
151R ARG* 3.0 25.2 + - - +
152R VAL* 3.9 26.1 - - + +
155R MET* 4.8 1.3 - - + -
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Residues in contact with THR 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP 3.6 7.3 + - - -
351A CYS* 3.4 44.8 + - + +
67R THR* 4.4 0.9 - - - +
68R THR* 1.3 76.2 - - - +
70R ASN* 1.3 64.2 + - - +
72R LEU* 3.4 10.7 + - + +
73R ILE* 2.9 36.5 + - - +
128R ILE* 4.8 16.3 - - + +
131R ASP* 2.8 36.1 - - + +
132R ARG* 5.1 0.7 - - + -
142R TYR* 3.8 4.3 + - - +
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Residues in contact with ASN 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP 4.6 6.1 + - - +
351A CYS 6.1 0.2 - - - -
59R VAL* 4.0 19.4 - - + +
65R LEU* 3.3 36.5 - - + +
67R THR* 3.2 32.0 + - - +
69R THR* 1.3 82.1 + - - +
71R TYR* 1.3 59.5 + - + +
73R ILE* 3.3 12.3 + - - +
74R VAL* 2.9 32.2 + - - +
430R ASN* 4.9 2.2 + - - +
433R PHE* 3.5 26.2 - - - -
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Residues in contact with TYR 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R VAL* 4.4 19.5 - - + -
65R LEU 4.6 0.7 + - - -
66R GLN* 3.5 37.0 + - - +
67R THR 2.8 32.1 - - - -
68R THR* 3.3 8.0 + - - +
69R THR 3.3 0.2 - - - -
70R ASN* 1.3 75.2 - - + +
72R LEU* 1.3 60.5 + - - +
74R VAL* 3.1 12.5 + - + +
75R SER* 2.9 28.8 + - - -
152R VAL* 4.3 17.9 - - + -
156R ILE* 4.5 7.4 - - + +
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Residues in contact with LEU 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R THR* 3.4 14.5 + - + +
69R THR* 3.4 6.9 + - - +
70R ASN 3.3 0.2 - - - -
71R TYR* 1.3 76.2 - - - +
73R ILE* 1.3 57.6 + - - +
75R SER* 3.2 6.8 + - - +
76R LEU* 2.9 27.4 + - - +
124R ASN* 4.4 10.9 + - + +
127R ALA* 3.9 37.7 - - + +
128R ILE* 3.6 28.4 - - + +
131R ASP* 4.4 8.1 - - + -
152R VAL* 4.0 7.9 - - + -
155R MET* 4.1 20.9 - - + -
156R ILE* 3.4 30.1 - - + +
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Residues in contact with ILE 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A CYS 5.7 2.0 - - - +
55R VAL* 3.6 25.8 - - + -
69R THR* 2.9 27.6 + - - +
70R ASN* 3.6 21.8 - - - +
71R TYR 3.2 0.2 - - - -
72R LEU* 1.3 75.2 - - - +
74R VAL* 1.3 56.9 + - - +
76R LEU* 3.2 12.9 + - + +
77R ALA* 2.9 28.4 + - + +
128R ILE* 4.0 15.9 - - + -
132R ARG* 5.5 3.6 - - - +
423R PRO* 5.8 4.3 - - + -
426R TYR* 3.8 40.8 - - + +
427R THR* 4.8 7.6 - - - +
433R PHE* 4.9 4.3 - - + -
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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
----------------------------------------------------------
55R VAL* 4.7 2.0 - - + -
56R CYS* 3.9 29.2 - - + +
59R VAL* 3.6 33.9 - - + -
70R ASN 2.9 20.4 + - - +
71R TYR* 3.1 13.9 + - + +
73R ILE* 1.3 76.4 - - - +
75R SER* 1.3 64.9 + - - +
77R ALA* 3.2 7.0 + - - +
78R VAL* 2.9 34.3 + - + +
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Residues in contact with SER 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R TYR 2.9 13.6 + - - -
72R LEU* 3.2 10.1 + - - -
74R VAL* 1.3 78.2 - - - +
76R LEU* 1.3 57.6 + - - +
78R VAL* 3.3 7.3 + - - +
79R ALA* 2.9 30.0 + - - +
124R ASN* 3.5 19.0 + - - -
156R ILE* 3.7 26.7 - - - +
160R TRP* 4.0 16.3 + - - +
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Residues in contact with LEU 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R ASN* 5.7 0.2 - - - +
72R LEU 2.9 13.4 + - - +
73R ILE* 3.4 14.4 - - + +
74R VAL 3.2 0.2 - - - -
75R SER* 1.3 77.2 - - - +
77R ALA* 1.3 57.9 + - - +
79R ALA* 3.3 4.9 + - - +
80R ASP* 2.9 41.0 + - - +
121R SER* 3.6 42.0 - - - +
124R ASN* 3.6 12.5 - - + +
125R LEU* 3.9 25.4 - - + -
128R ILE* 4.5 10.8 - - + -
422R ASN* 4.0 22.7 - - + +
423R PRO* 5.5 2.0 - - + -
426R TYR* 4.4 10.3 - - + -
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Residues in contact with ALA 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R ASN* 3.2 49.2 - - + +
55R VAL* 4.5 13.9 - - + -
56R CYS* 4.6 3.6 - - - -
73R ILE* 2.9 17.1 + - + +
74R VAL 3.8 4.3 - - - +
76R LEU* 1.3 76.2 - - - +
78R VAL* 1.3 57.9 + - - +
80R ASP* 3.2 1.9 + - - +
81R LEU* 2.9 32.4 + - - +
423R PRO* 5.3 0.9 - - + -
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Residues in contact with VAL 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R CYS* 4.0 19.5 - - - -
74R VAL* 2.9 27.1 + - + +
75R SER* 3.7 7.6 - - - +
77R ALA* 1.3 74.5 - - - +
79R ALA* 1.3 66.0 + - - +
81R LEU* 3.1 11.9 + - + +
82R LEU* 2.9 40.5 + - + +
160R TRP* 4.7 8.5 - - + -
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Residues in contact with ALA 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R SER 2.9 18.1 + - - +
76R LEU* 3.6 6.3 - - - +
78R VAL* 1.3 76.4 - - - +
80R ASP* 1.3 58.1 + - - +
82R LEU* 3.3 2.9 + - - +
83R VAL* 2.9 33.3 + - - +
117R MET* 3.9 16.4 - - - +
120R ALA* 4.1 8.3 - - + -
121R SER* 3.8 15.3 - - - +
124R ASN* 4.9 0.4 - - - +
160R TRP* 3.7 24.4 - - + -
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Residues in contact with ASP 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 3.8 3.9 - - + +
52R ASN* 3.5 22.7 - - - +
76R LEU* 2.9 29.3 + - - +
77R ALA 3.6 7.9 - - - +
78R VAL 3.2 0.2 - - - -
79R ALA* 1.3 76.5 - - - +
81R LEU* 1.3 58.5 + - - +
83R VAL* 3.3 7.6 + - - +
84R ALA* 2.9 29.1 + - - +
121R SER* 3.1 18.7 + - - -
419R SER* 2.7 50.8 + - - +
422R ASN* 4.7 2.8 + - - +
423R PRO* 4.3 3.6 - - - +
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Residues in contact with LEU 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 3.7 8.5 - - + -
49R VAL* 3.6 38.8 - - + -
52R ASN* 3.6 24.7 - - + +
53R VAL* 4.4 18.4 - - + -
56R CYS* 5.2 3.1 - - - -
77R ALA 2.9 16.5 + - - +
78R VAL* 3.5 18.4 - - + +
80R ASP* 1.3 78.1 - - - +
82R LEU* 1.3 60.2 + - + +
84R ALA 3.3 0.9 + - - -
85R THR* 2.8 40.6 + - + +
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Residues in contact with LEU 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R VAL* 2.9 30.4 + - + +
79R ALA 3.3 0.8 + - - +
81R LEU* 1.3 76.1 - - + +
83R VAL* 1.3 61.6 + - - +
85R THR* 4.0 4.7 - - - +
86R LEU* 2.9 57.5 + - + +
87R VAL* 3.5 2.3 + - - +
117R MET* 3.2 47.1 - - + -
160R TRP* 4.3 10.8 - - + -
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Residues in contact with VAL 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R ALA 2.9 16.0 + - - +
80R ASP* 3.5 11.0 - - - +
81R LEU 3.3 0.2 - - - -
82R LEU* 1.3 75.8 - - - +
84R ALA* 1.3 60.8 + - + +
87R VAL* 3.2 16.3 + - + +
88R MET* 2.8 32.0 + - + +
113R LEU 5.4 0.2 - - - +
114R ASP* 5.1 0.7 - - - +
117R MET* 3.2 36.8 - - + +
118R CYS* 4.2 9.2 - - - +
121R SER* 5.0 1.8 - - - +
416R TYR* 3.5 39.0 - - + -
419R SER* 4.6 12.1 - - - +
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Residues in contact with ALA 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R ILE* 3.8 21.3 - - + +
48R ILE* 3.2 44.9 - - + -
80R ASP 2.9 8.4 + - - +
81R LEU 3.3 1.1 + - - +
83R VAL* 1.3 79.8 - - - +
85R THR* 1.3 62.2 + - + +
88R MET* 3.1 30.4 - - + +
89R PRO* 3.2 7.6 - - - +
419R SER* 6.5 0.2 - - - -
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Residues in contact with THR 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R ILE* 4.9 7.2 - - + -
49R VAL* 4.5 16.8 - - + -
81R LEU* 2.8 28.4 + - + +
82R LEU* 4.0 3.6 - - - +
84R ALA* 1.3 86.5 - - + +
86R LEU* 1.3 76.9 + - - +
87R VAL 3.7 0.2 - - - -
89R PRO* 3.7 16.2 - - - +
90R TRP* 4.9 2.9 - - - -
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Residues in contact with LEU 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R LEU* 2.9 44.2 + - + +
85R THR* 1.3 93.2 - - - +
87R VAL* 1.3 61.2 + - + +
89R PRO* 4.3 0.2 - - - -
90R TRP* 2.8 33.8 - - + -
110R PHE* 4.9 0.9 - - - -
113R LEU* 3.9 36.0 - - + +
117R MET* 5.3 1.1 - - + -
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Residues in contact with VAL 87 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R LEU 4.2 6.7 - - - +
83R VAL* 3.2 17.5 + - - +
86R LEU* 1.3 77.1 - - - +
88R MET* 1.3 69.4 + - - +
89R PRO* 3.3 2.7 - - - -
90R TRP* 3.0 13.9 + - - +
91R VAL* 3.5 0.6 + - + -
110R PHE* 3.1 36.1 - - + +
113R LEU* 3.3 24.2 - - + +
114R ASP* 3.3 43.3 - - + +
117R MET* 5.1 0.4 - - + -
416R TYR* 3.7 18.4 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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