Contacts of the helix formed by residues 63 - 79 (chain W) in PDB entry 6L49
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 ARG 63 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I A 3.7 35.1 + - - +
188I C 3.7 4.0 - - - +
-184J A 3.6 25.6 - - - +
-183J A 2.4 42.5 + - - +
61W LEU 5.0 0.4 - - - +
62W ILE* 1.3 81.8 - - - +
64W LYS* 1.3 64.3 + - - +
65W LEU 3.6 0.4 - - - -
66W PRO* 3.3 30.2 - - + +
67W PHE* 3.4 23.2 + - - +
93W GLN* 4.3 0.2 + - - -
28X GLY* 2.4 33.0 + - - -
30X THR* 3.3 20.0 + - - +
33X ALA* 4.3 6.5 - - - +
36X ARG* 4.9 3.6 - - - +
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Residues in contact with LYS 64 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I C 2.8 27.0 + - - +
189I C 3.8 29.2 + - - +
62W ILE 4.9 2.7 - - - +
63W ARG* 1.3 74.7 - - - +
65W LEU* 1.3 58.0 + - - +
67W PHE* 3.8 1.6 - - - +
68W GLN* 2.9 33.8 + - - +
89W VAL* 5.1 2.3 - - - +
90W MET* 4.7 25.3 - - + +
93W GLN* 4.5 16.2 - - - +
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Residues in contact with LEU 65 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I A 5.7 1.1 - - + -
187I A 3.4 22.0 - - + +
188I C 2.5 39.3 + - + +
189I C 6.0 1.6 - - - +
64W LYS* 1.3 71.4 - - - +
66W PRO* 1.4 64.9 - - + +
68W GLN* 3.4 22.2 + - - +
69W ARG* 2.9 46.9 + - + +
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Residues in contact with PRO 66 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I A 3.3 38.4 - - - +
62W ILE* 6.2 0.4 - - + -
63W ARG* 3.3 42.6 - - + +
65W LEU* 1.4 87.8 - - + +
67W PHE* 1.3 57.7 + - - +
69W ARG* 3.4 15.8 + - - +
70W LEU* 2.9 25.6 + - - +
25X ASN 3.4 10.2 + - - +
28X GLY* 3.7 19.3 - - - +
29X ILE* 5.3 1.6 - - + -
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Residues in contact with PHE 67 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62W ILE* 3.8 34.5 - - + +
63W ARG 3.4 19.5 + - - +
64W LYS 4.0 2.2 - - - +
65W LEU 3.4 0.4 - - - -
66W PRO* 1.3 78.1 - - - +
68W GLN* 1.3 57.3 + - - +
70W LEU* 3.6 5.9 - - + +
71W VAL* 2.9 51.5 + - + +
89W VAL* 4.5 8.5 - - + -
92W LEU* 4.2 4.3 - - + -
93W GLN* 3.7 45.5 - - + +
96W CYS* 4.2 8.7 - - + -
29X ILE* 3.8 12.6 - - + +
58X LEU* 3.8 21.5 - - + -
62X LEU* 3.7 24.9 - - + -
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Residues in contact with GLN 68 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-193J T 4.7 4.0 + - - -
64W LYS* 2.9 21.4 + - - +
65W LEU* 3.5 25.5 - - - +
67W PHE* 1.3 77.3 - - - +
69W ARG* 1.3 57.3 + - + +
71W VAL* 3.4 3.0 + - - +
72W ARG* 2.9 71.1 + - + +
84W PHE* 5.6 1.5 - - + +
86W SER* 5.8 2.4 + - - -
89W VAL* 4.1 32.7 - - + +
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Residues in contact with ARG 69 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I A 5.0 2.0 - - - -
187I A 2.9 42.6 + - - -
65W LEU* 2.9 29.9 + - + +
66W PRO* 3.5 19.5 - - - +
67W PHE 3.3 0.2 - - - -
68W GLN* 1.3 73.9 - - + +
70W LEU* 1.3 60.8 + - - +
72W ARG* 3.8 11.1 - - - +
73W GLU* 2.9 30.0 + - - +
25X ASN* 3.2 47.0 + - - +
28X GLY* 5.4 1.2 - - - -
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Residues in contact with LEU 70 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66W PRO 2.9 17.0 + - - +
67W PHE* 3.6 6.7 - - + +
68W GLN 3.3 0.2 - - - -
69W ARG* 1.3 75.2 - - - +
71W VAL* 1.3 59.3 + - - +
73W GLU* 3.3 9.3 + - - +
74W ILE* 2.9 56.3 + - + +
25X ASN* 3.6 19.2 - - - +
26X ILE* 3.5 39.3 - - + +
29X ILE* 3.9 22.9 - - + -
58X LEU* 4.5 6.7 - - + -
59X LYS* 4.9 3.8 - - - +
62X LEU* 3.9 19.5 - - + -
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Residues in contact with VAL 71 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67W PHE* 2.9 44.1 + - + +
68W GLN* 3.7 6.1 - - - +
70W LEU* 1.3 74.6 - - - +
72W ARG* 1.3 58.2 + - - +
74W ILE 3.4 0.7 + - - -
75W ALA* 2.9 27.9 + - - +
84W PHE* 3.6 25.1 - - + -
89W VAL* 4.7 9.4 - - + -
92W LEU* 4.0 21.8 - - + -
62X LEU* 4.0 8.5 - - + -
66X ILE* 3.7 30.0 - - + +
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Residues in contact with ARG 72 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-193J T 3.1 43.6 + - - +
-192J G 4.0 19.1 + - - -
68W GLN* 2.9 55.5 + - - +
69W ARG* 3.8 11.7 - - - +
70W LEU 3.3 0.2 - - - -
71W VAL* 1.3 76.2 - - - +
73W GLU* 1.3 56.6 + - - +
75W ALA* 3.4 1.6 + - - +
76W GLN* 2.9 35.8 + - + +
82W LEU 4.5 9.9 + - - -
84W PHE* 3.7 28.6 - - + +
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Residues in contact with GLU 73 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69W ARG 2.9 17.4 + - - +
70W LEU* 3.8 11.8 - - - +
72W ARG* 1.3 72.7 - - - +
74W ILE* 1.3 61.9 + - + +
76W GLN* 3.3 6.7 + - - +
77W ASP* 2.9 45.0 + - - +
25X ASN* 3.4 36.5 - - - +
26X ILE* 4.3 4.2 + - - +
59X LYS* 5.1 10.7 + - - -
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Residues in contact with ILE 74 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70W LEU* 2.9 42.0 + - + +
71W VAL 3.9 3.4 - - - +
73W GLU* 1.3 76.7 - - + +
75W ALA* 1.3 62.9 + - - +
77W ASP* 3.3 19.5 + - - +
78W PHE* 3.2 15.8 - - + -
59X LYS* 4.1 30.7 - - + +
62X LEU* 3.7 26.2 - - + -
63X GLU* 3.8 32.5 - - + -
66X ILE* 3.7 22.2 - - + -
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Residues in contact with ALA 75 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71W VAL 2.9 19.1 + - - +
72W ARG 3.8 3.6 - - - +
74W ILE* 1.3 75.9 - - - +
76W GLN* 1.3 53.3 - - - +
78W PHE* 2.9 6.2 + - - +
79W LYS* 2.6 39.4 + - - +
82W LEU* 4.6 14.6 - - + +
84W PHE* 3.6 25.6 - - + -
66X ILE* 3.8 17.0 - - + +
70X VAL* 5.0 1.6 - - + -
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Residues in contact with GLN 76 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72W ARG* 2.9 24.1 + - + +
73W GLU* 3.3 8.0 + - + +
75W ALA* 1.3 73.5 - - - +
77W ASP* 1.3 65.8 + - - +
78W PHE 3.4 0.9 + - - -
79W LYS 3.4 12.2 + - - +
80W THR* 3.3 35.9 - - - +
81W ASP* 3.2 23.1 + - - +
82W LEU* 4.3 5.0 + - - +
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Residues in contact with ASP 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73W GLU* 2.9 27.5 + - - +
74W ILE* 3.3 16.3 - - - +
75W ALA 3.2 0.6 - - - -
76W GLN* 1.3 79.0 - - - +
78W PHE* 1.3 69.6 + - + +
59X LYS* 4.7 11.4 + - - -
63X GLU* 5.0 8.0 - - + +
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Residues in contact with PHE 78 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74W ILE* 3.2 30.3 + - + -
75W ALA* 2.9 6.1 + - - +
76W GLN 4.4 1.1 - - - -
77W ASP* 1.3 89.6 - - + +
79W LYS* 1.3 60.7 + - + +
63X GLU* 3.2 35.9 - - + -
66X ILE* 3.7 14.6 - - + -
67X ARG* 3.5 56.1 - - + -
70X VAL* 4.6 14.6 - - + -
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Residues in contact with LYS 79 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75W ALA 2.6 23.4 + - - +
76W GLN* 3.4 11.0 + - - +
77W ASP 4.0 0.4 - - - -
78W PHE* 1.3 74.8 - - - +
80W THR* 1.3 89.0 + - - +
81W ASP* 3.9 6.1 + - - +
82W LEU* 3.6 37.2 - - + +
70X VAL* 4.0 12.6 - - + -
74X GLU* 3.3 44.2 - - + +
79X LYS* 5.2 10.2 - - - +
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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) + - + + + + + -
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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