Contacts of the helix formed by residues 41 - 62 (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 LEU 41 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ALA* 3.2 26.7 - - + +
39R THR 3.0 2.0 - - - -
40R LEU* 1.3 86.1 - - + +
42R THR* 1.3 61.8 + - - +
43R LEU* 2.9 7.2 + - - -
44R LEU* 2.9 37.8 + - + +
45R ILE* 3.5 6.5 + - - +
92R VAL* 4.3 11.2 - - + -
95R GLU* 5.4 6.1 - - + -
413R TRP* 3.4 50.5 - - + +
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Residues in contact with THR 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R THR* 3.3 19.2 + - - +
40R LEU* 2.8 2.9 + - - -
41R LEU* 1.3 76.7 - - - +
43R LEU* 1.3 66.6 + - + +
44R LEU 3.3 0.2 - - - -
45R ILE* 2.9 28.2 + - + +
46R ALA* 2.8 24.1 + - + +
92R VAL* 5.4 3.3 - - - +
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Residues in contact with LEU 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R LEU* 2.9 30.4 + - + +
41R LEU* 2.9 2.3 - - - +
42R THR* 1.3 79.3 - - + +
44R LEU* 1.3 69.9 + - + +
46R ALA* 2.9 11.1 + - + +
47R VAL* 2.8 32.3 + - + +
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Residues in contact with LEU 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R LEU* 2.9 29.9 + - + +
43R LEU* 1.3 79.4 - - + +
45R ILE* 1.3 63.9 + - + +
47R VAL* 3.0 20.5 + - + +
48R ILE* 3.1 22.1 + - + +
88R MET* 5.4 5.8 - - + -
413R TRP* 4.6 21.3 - - + -
416R TYR 5.8 1.1 - - - +
417R VAL* 4.7 23.8 - - + +
420R ALA* 5.0 15.3 - - + -
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Residues in contact with ILE 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R LEU 4.2 3.1 - - - +
42R THR* 2.9 37.6 + - + +
44R LEU* 1.3 76.8 - - - +
46R ALA* 1.3 61.4 + - - +
48R ILE* 3.3 11.3 - - - +
49R VAL* 3.2 24.9 - - + +
84R ALA* 3.8 26.0 - - + +
85R THR* 4.9 6.3 - - + -
88R MET* 3.7 33.0 - - + -
89R PRO* 4.5 14.8 - - + -
92R VAL* 4.8 6.7 - - + -
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Residues in contact with ALA 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R THR* 2.8 13.8 + - + +
43R LEU* 3.5 13.9 - - + +
45R ILE* 1.3 77.8 - - - +
47R VAL* 1.3 66.1 + - + +
49R VAL* 2.9 26.6 - - + +
50R PHE* 2.9 10.3 + - - +
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Residues in contact with VAL 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R LEU* 2.8 27.1 + - + +
44R LEU* 3.0 14.3 + - + +
46R ALA* 1.3 76.3 - - + +
48R ILE* 1.3 59.5 + - - +
50R PHE* 3.0 10.7 + - + +
51R GLY* 2.8 24.9 + - - -
420R ALA* 3.8 24.9 - - + +
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Residues in contact with ILE 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R LEU* 3.5 14.4 - - + +
45R ILE 3.3 11.0 - - - +
47R VAL* 1.3 76.3 - - - +
49R VAL* 1.3 83.2 + - + +
51R GLY* 3.0 1.1 + - - +
52R ASN* 2.4 53.3 + - - +
80R ASP 3.8 9.9 - - - +
81R LEU* 3.7 15.7 - - + -
84R ALA* 3.2 33.4 - - + -
88R MET* 6.4 1.8 - - + -
416R TYR 5.2 1.8 - - - +
419R SER* 4.1 8.5 - - - -
420R ALA* 3.6 35.2 - - + +
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Residues in contact with VAL 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R ILE* 3.2 20.0 - - + +
46R ALA* 2.9 28.9 - - + +
48R ILE* 1.3 94.5 - - + +
50R PHE* 1.3 60.2 + - + +
53R VAL* 2.8 36.1 + - + +
81R LEU* 3.6 18.6 - - + -
85R THR* 4.5 14.6 - - + -
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Residues in contact with PHE 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R ALA 2.9 11.7 + - - +
47R VAL* 3.4 11.7 - - + +
49R VAL* 1.3 81.9 - - + +
51R GLY* 1.3 67.9 + - - +
52R ASN 3.5 0.2 + - - -
53R VAL* 4.7 2.0 - - - -
54R LEU* 3.4 47.1 - - + +
424R ILE* 6.4 1.8 - - + -
437R PHE* 5.2 10.5 - + - -
441R LEU* 4.8 17.5 - - + -
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Residues in contact with GLY 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R VAL 2.8 13.6 + - - -
48R ILE* 3.5 1.6 - - - -
50R PHE* 1.3 84.6 - - - +
52R ASN* 1.3 57.0 + - - +
54R LEU* 4.9 0.9 - - - +
55R VAL* 3.1 26.9 + - - +
420R ALA 5.5 0.9 - - - -
423R PRO* 3.4 22.7 - - - +
424R ILE* 4.9 11.7 - - - -
437R PHE* 5.1 5.4 - - - -
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Residues in contact with ASN 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 2.4 51.4 + - - +
51R GLY* 1.3 67.5 - - - +
53R VAL* 1.3 60.0 + - - +
54R LEU 3.6 0.2 - - - -
55R VAL* 4.2 2.8 + - - -
56R CYS* 3.9 7.3 - - - -
76R LEU* 5.7 0.2 - - - +
77R ALA* 3.2 47.8 - - + +
80R ASP* 3.5 19.0 - - - +
81R LEU* 3.6 18.2 - - + +
419R SER 3.2 21.2 + - - -
423R PRO* 3.1 24.9 - - - +
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Residues in contact with VAL 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R VAL* 2.8 29.2 + - + +
50R PHE* 4.7 1.1 - - - -
52R ASN* 1.3 75.7 - - - +
54R LEU* 1.3 82.2 + - + +
55R VAL 3.2 2.5 + - - -
56R CYS* 3.8 8.3 - - + +
57R MET* 3.2 30.4 + - + +
81R LEU* 4.4 19.5 - - + -
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Residues in contact with LEU 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R PHE* 3.4 53.0 + - + +
51R GLY 4.9 0.2 - - - +
53R VAL* 1.3 92.5 - - + +
55R VAL* 1.3 58.7 + - - +
57R MET* 3.4 11.5 + - + +
58R ALA* 2.9 28.6 + - - +
437R PHE* 4.2 27.1 - - + -
440R ILE* 4.0 28.6 - - + +
441R LEU* 4.3 16.4 - - + -
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Residues in contact with VAL 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R GLY 3.1 23.3 - - - +
52R ASN* 4.6 0.2 - - - -
53R VAL 3.2 1.2 - - - +
54R LEU* 1.3 75.0 - - - +
56R CYS* 1.3 67.3 + - - +
58R ALA* 3.1 6.4 + - - +
59R VAL* 2.9 36.5 + - + +
73R ILE* 3.6 34.5 - - + +
74R VAL* 4.7 3.1 - - + -
77R ALA* 4.5 10.1 - - + -
423R PRO* 4.1 8.7 - - + +
427R THR* 3.7 27.8 - - + +
433R PHE* 4.8 7.9 - - + -
437R PHE* 4.6 4.9 - - + -
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Residues in contact with CYS 56 (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 ASN 3.9 17.9 - - - -
53R VAL* 3.8 10.5 - - + +
55R VAL* 1.3 78.8 - - - +
57R MET* 1.3 74.1 + - + +
59R VAL* 3.2 2.4 + - - +
60R SER* 2.9 24.5 + - - -
74R VAL* 3.9 35.2 - - + +
77R ALA* 4.6 2.2 - - - -
78R VAL* 4.0 19.7 - - - -
81R LEU* 5.2 3.6 - - - -
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Residues in contact with MET 57 (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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53R VAL* 3.2 21.9 + - + +
54R LEU* 3.4 17.9 + - + +
55R VAL 3.1 0.8 - - - -
56R CYS* 1.3 87.7 - - + +
58R ALA* 1.3 58.1 + - - +
60R SER* 3.2 8.6 + - - -
61R ARG* 2.9 49.2 + - - +
440R ILE* 4.7 9.2 - - + -
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Residues in contact with ALA 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R LEU 2.9 15.1 + - - +
55R VAL* 3.7 4.9 - - - +
57R MET* 1.3 75.2 - - - +
59R VAL* 1.3 63.3 + - - +
61R ARG* 4.6 2.0 - - - -
62R GLU* 3.2 29.1 + - - +
65R LEU* 3.7 3.5 - - - +
433R PHE* 4.1 17.7 - - + -
436R ALA* 3.9 17.5 - - + -
437R PHE* 4.8 4.7 - - + -
440R ILE* 3.5 24.7 - - + +
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Residues in contact with VAL 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R VAL* 2.9 22.6 + - + +
56R CYS 3.6 4.3 - - - +
58R ALA* 1.3 78.3 - - - +
60R SER* 1.3 62.1 + - - +
62R GLU 3.8 6.8 - - - +
65R LEU* 3.5 29.3 - - + +
70R ASN* 4.0 24.7 - - + +
71R TYR* 4.4 23.6 - - + -
74R VAL* 3.6 28.3 - - + -
433R PHE* 4.3 14.4 - - + -
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Residues in contact with SER 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R CYS 2.9 16.3 + - - -
57R MET* 3.9 10.8 - - - -
59R VAL* 1.3 79.4 - - - +
61R ARG* 1.3 62.5 + - - +
62R GLU 4.5 2.4 - - - +
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Residues in contact with ARG 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R MET* 2.9 32.5 + - - +
58R ALA* 4.2 2.9 - - - +
60R SER* 1.3 80.4 - - - +
62R GLU* 1.3 71.6 + - + +
439R LYS* 4.1 22.8 + - - +
440R ILE* 3.4 35.0 + - + +
442R HIS* 5.0 12.3 + - - -
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Residues in contact with GLU 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R ALA 3.2 17.9 + - - +
59R VAL 3.8 10.6 - - - +
60R SER 4.5 2.3 - - - +
61R ARG* 1.3 87.0 + - + +
63R LYS* 1.3 62.8 + - - +
64R ALA* 4.4 3.2 + - - +
65R LEU* 4.1 24.6 - - + +
66R GLN* 5.6 0.3 - - - +
432R GLU* 4.6 11.8 - - - +
436R ALA* 3.9 28.0 - - + +
439R LYS* 3.9 32.3 + - - +
440R ILE* 6.0 1.7 - - + +
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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
------------------------------------------------------------
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