Contacts of the helix formed by residues 63 - 77 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I A 5.3 4.8 + - - -
156I A 3.4 49.5 + - - -
157I A 4.3 20.4 + - - -
-153J A 3.1 50.5 + - - +
-152J G 3.6 20.6 + - - +
60S LEU 5.4 0.4 - - - -
61S LEU 4.5 6.3 - - - +
62S ILE* 1.3 75.8 - - - +
64S LYS* 1.3 67.0 + - - +
66S PRO* 3.9 18.7 - - + +
67S PHE* 3.4 16.1 + - - +
93S GLN* 2.9 8.0 + - - -
28T GLY 4.9 6.7 - - - +
29T ILE* 6.3 0.7 - - - -
30T THR* 5.0 9.9 - - - +
33T ALA* 5.2 2.9 - - + +
36T ARG* 4.6 5.6 - - - +
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Residues in contact with LYS 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-152J G 3.1 23.1 + - - +
-151J C 5.4 8.2 + - - +
-150J G 5.3 6.5 + - - -
60S LEU* 5.9 0.9 - - + -
62S ILE 3.9 0.2 + - - -
63S ARG* 1.3 71.8 - - - +
65S LEU* 1.3 65.9 + - + +
67S PHE* 3.3 4.5 + - - +
68S GLN* 2.9 46.0 + - + +
86S SER* 4.9 14.3 + - - -
89S VAL* 4.6 3.4 - - + +
90S MET* 3.8 32.4 - - + +
93S GLN* 3.6 16.4 - - - +
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Residues in contact with LEU 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-153J A 3.3 26.2 - - + +
-152J G 3.2 9.0 + - + +
64S LYS* 1.3 82.3 - - + +
66S PRO* 1.4 63.1 - - + +
68S GLN* 3.3 26.6 - - + +
69S ARG* 2.9 46.3 + - + +
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Residues in contact with PRO 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-153J A 3.3 33.7 - - - +
-152J G 4.4 0.2 - - - +
63S ARG* 3.9 17.5 - - + +
65S LEU* 1.4 86.9 - - + +
67S PHE* 1.3 56.8 + - - +
69S ARG* 3.4 25.2 + - - +
70S LEU* 2.9 28.3 + - - +
25T ASN 3.8 5.0 - - - +
28T GLY* 3.5 39.5 - - - +
29T ILE* 4.6 4.0 - - + -
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Residues in contact with PHE 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62S ILE* 3.7 27.1 - - + -
63S ARG 3.4 19.0 + - - +
64S LYS 3.3 3.7 + - - +
65S LEU 3.3 0.4 - - - -
66S PRO* 1.3 75.0 - - - +
68S GLN* 1.3 60.4 + - - +
70S LEU* 3.6 7.2 - - + +
71S VAL* 2.9 43.1 + - + +
89S VAL* 4.4 4.9 - - + -
92S LEU* 3.6 4.9 - - + -
93S GLN* 3.5 37.2 - - + -
96S CYS* 3.2 33.0 - - + -
29T ILE* 3.7 12.9 - - + +
58T LEU* 3.7 23.8 - - + -
62T LEU* 3.9 13.0 - - + -
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Residues in contact with GLN 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I C 4.3 4.0 + - - -
64S LYS* 2.9 33.0 + - - +
65S LEU* 3.3 28.6 - - + +
66S PRO 3.3 0.2 - - - -
67S PHE* 1.3 77.3 - - - +
69S ARG* 1.3 55.8 + - - +
71S VAL* 3.3 3.9 + - - +
72S ARG* 2.9 68.8 + - + +
84S PHE 4.4 2.8 + - - -
86S SER* 4.3 14.8 + - - +
89S VAL* 3.4 42.0 - - + +
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Residues in contact with ARG 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-154J A 5.1 1.8 - - - -
-153J A 2.5 35.8 + - - -
65S LEU* 2.9 28.2 + - + +
66S PRO* 3.4 27.2 - - - +
68S GLN* 1.3 76.1 - - + +
70S LEU* 1.3 56.8 + - - +
72S ARG* 3.8 7.7 - - - +
73S GLU* 2.9 23.7 + - - +
22T LEU* 4.1 19.8 - - + +
24T ASP 5.4 0.2 + - - -
25T ASN* 2.9 50.2 + - - +
28T GLY* 5.4 3.6 - - - -
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Residues in contact with LEU 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66S PRO 2.9 18.1 + - - +
67S PHE* 3.6 8.3 - - + +
68S GLN 3.3 0.2 - - - -
69S ARG* 1.3 74.9 - - - +
71S VAL* 1.3 59.4 + - - +
73S GLU* 3.3 7.0 + - - +
74S ILE* 2.9 51.8 + - + +
25T ASN* 3.6 12.1 - - + +
26T ILE* 3.8 48.2 - - + +
29T ILE* 4.0 22.0 - - + -
58T LEU* 4.2 5.2 - - + -
59T LYS* 5.7 2.2 - - + -
62T LEU* 3.8 26.2 - - + -
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Residues in contact with VAL 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67S PHE* 2.9 47.0 + - + +
68S GLN* 3.7 6.5 - - - +
70S LEU* 1.3 75.3 - - - +
72S ARG* 1.3 59.5 + - - +
74S ILE* 3.8 0.9 - - - +
75S ALA* 2.9 30.0 + - - +
84S PHE* 3.7 32.1 - - + -
89S VAL* 5.0 9.2 - - + -
92S LEU* 3.8 28.3 - - + -
62T LEU* 4.6 2.5 - - + -
66T ILE* 3.9 18.5 - - + +
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Residues in contact with ARG 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I C 2.5 52.4 + - - -
148I A 5.1 8.2 + - - -
68S GLN* 2.9 55.9 + - - +
69S ARG* 3.8 8.2 - - - +
71S VAL* 1.3 75.0 - - - +
73S GLU* 1.3 57.5 + - - +
75S ALA* 3.8 0.9 - - - +
76S GLN* 2.9 30.3 + - - +
82S LEU 4.6 9.3 + - - +
84S PHE* 3.7 31.1 + - + +
22T LEU* 3.8 23.9 - - + +
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Residues in contact with GLU 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S ARG 2.9 17.0 + - - +
70S LEU* 3.8 10.0 - - - +
71S VAL 3.3 0.2 - - - -
72S ARG* 1.3 75.6 - - - +
74S ILE* 1.3 63.7 + - + +
76S GLN* 3.4 9.0 + - - +
77S ASP* 3.0 31.6 + - - +
22T LEU* 3.4 31.5 - - + +
23T ARG* 3.5 5.4 - - - +
24T ASP* 4.3 6.1 + - - -
25T ASN* 2.8 45.6 + - - +
26T ILE* 5.1 4.9 + - - +
59T LYS* 6.1 1.2 - - - -
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Residues in contact with ILE 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70S LEU* 2.9 39.2 + - + +
71S VAL 4.0 2.7 - - - +
73S GLU* 1.3 80.7 - - + +
75S ALA* 1.3 62.2 + - - +
77S ASP* 3.3 18.6 + - - +
78S PHE* 3.3 31.0 - - + -
59T LYS* 4.2 30.5 - - + +
62T LEU* 3.7 39.3 - - + +
63T GLU* 4.4 6.1 - - + -
66T ILE* 4.0 17.5 - - + -
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Residues in contact with ALA 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S VAL 2.9 18.8 + - - +
72S ARG 4.1 1.3 - - - +
74S ILE* 1.3 77.5 - - - +
76S GLN* 1.3 57.6 + - - +
77S ASP 3.2 0.2 - - - -
78S PHE* 3.3 7.6 + - - +
79S LYS 2.9 30.7 + - - +
82S LEU* 4.0 14.6 - - + +
84S PHE* 3.6 30.1 - - + -
66T ILE* 3.7 14.4 - - + -
70T VAL* 4.6 2.0 - - + -
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Residues in contact with GLN 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S ARG 2.9 16.6 + - - +
73S GLU* 3.7 6.8 - - - +
74S ILE 3.2 0.2 - - - -
75S ALA* 1.3 77.1 - - - +
77S ASP* 1.3 64.2 + - - +
78S PHE 3.4 0.5 + - - -
79S LYS 3.5 16.8 + - - -
80S THR* 4.1 30.7 + - + +
81S ASP 5.3 1.8 - - - +
82S LEU* 6.3 0.4 - - - -
20T LYS 5.4 3.7 + - - +
21T VAL* 5.9 4.6 - - - +
22T LEU* 3.4 35.1 + - + +
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Residues in contact with ASP 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73S GLU* 3.0 23.1 - - - +
74S ILE* 3.6 12.9 - - - +
75S ALA 3.2 0.4 - - - -
76S GLN* 1.3 80.2 - - - +
78S PHE* 1.3 69.7 + - + +
59T LYS* 5.5 5.2 + - - -
63T GLU* 5.6 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) + - + + + + + -
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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