Contacts of the helix formed by residues 50 - 74 (chain S) in PDB entry 6MZL
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 TYR 50 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181P PRO* 3.2 41.6 - - + +
182P LEU 3.4 25.9 + - - +
183P GLN* 3.9 25.9 + - + -
184P PRO* 5.0 4.0 - - + -
48S ASN 6.0 0.2 - - - -
49S PRO* 1.3 73.2 - - - +
51S THR* 1.3 65.1 + - - +
52S GLU* 3.2 18.6 - - + +
53S SER* 3.1 18.9 + - - +
54S VAL* 3.3 12.5 + - - +
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Residues in contact with THR 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S SER* 4.9 3.1 + - - -
37S ARG* 3.7 20.2 + - - +
49S PRO 3.4 3.2 + - - -
50S TYR* 1.3 68.3 - - - +
52S GLU* 1.3 76.5 + - - +
54S VAL* 3.2 12.8 + - - +
55S ASP* 2.9 41.0 + - - +
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Residues in contact with GLU 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184P PRO* 3.7 21.8 - - + +
50S TYR* 3.4 24.8 - - - +
51S THR* 1.3 90.9 + - + +
53S SER* 1.3 56.3 + - - +
55S ASP* 3.2 9.5 + - - +
56S ILE* 2.9 36.4 + - + +
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Residues in contact with SER 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182P LEU 3.1 24.0 + - - -
183P GLN 3.1 22.0 + - - -
184P PRO* 3.2 4.9 - - - +
187P MET* 4.2 11.5 - - - +
40S MET* 3.8 16.3 - - - +
50S TYR* 3.1 11.0 + - - +
52S GLU* 1.3 78.9 - - - +
54S VAL* 1.3 57.3 + - - +
56S ILE* 3.8 11.2 - - - +
57S LEU* 2.8 33.3 + - - +
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Residues in contact with VAL 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S SER* 3.5 45.8 - - - +
36S LEU* 4.1 5.4 - - + +
37S ARG* 3.6 30.7 - - + +
40S MET* 3.6 27.4 - - + -
49S PRO* 4.4 3.1 - - + -
50S TYR 3.3 15.2 + - - +
51S THR* 3.2 10.7 + - - +
53S SER* 1.3 76.4 - - - +
55S ASP* 1.3 57.3 + - - +
57S LEU* 3.4 1.6 + - - +
58S GLU* 2.9 28.1 + - - +
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Residues in contact with ASP 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S SER* 4.7 8.8 + - - -
51S THR* 2.9 30.1 + - - +
52S GLU* 3.7 9.1 - - - +
54S VAL* 1.3 73.8 - - - +
56S ILE* 1.3 62.4 + - + +
58S GLU* 3.3 20.1 + - - +
59S ASP* 3.0 34.5 + - - +
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Residues in contact with ILE 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184P PRO* 3.6 33.0 - - + -
187P MET* 5.1 7.0 - - + -
188P ARG* 3.6 39.9 - - + +
52S GLU* 2.9 21.1 + - + +
53S SER* 3.8 6.1 - - - +
55S ASP* 1.3 76.4 - - + +
57S LEU* 1.3 59.5 + - - +
59S ASP* 3.1 14.9 + - - +
60S LEU* 2.9 39.1 + - + +
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Residues in contact with LEU 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P PHE* 5.8 0.4 - - + -
162P VAL* 3.6 34.1 - - + -
165P VAL* 4.6 4.3 - - + -
166P VAL* 4.4 7.6 - - + -
187P MET* 3.8 28.5 - - + -
36S LEU* 3.6 21.8 - - + -
40S MET* 3.7 28.7 - - + -
53S SER 2.8 19.6 + - - +
54S VAL* 3.9 2.7 - - - +
56S ILE* 1.3 70.4 - - + +
58S GLU* 1.3 60.1 + - - +
60S LEU* 3.3 24.5 - - + +
61S VAL* 2.9 33.0 + - + +
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Residues in contact with GLU 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S LEU* 2.6 45.1 + - - +
32S PHE* 4.1 21.8 - - + +
33S SER* 4.6 10.5 - - - +
36S LEU* 3.6 10.6 - - + +
54S VAL 2.9 13.1 + - - +
55S ASP* 3.3 25.7 - - - +
57S LEU* 1.3 75.7 - - - +
59S ASP* 1.3 60.3 + - - +
61S VAL* 3.3 5.9 + - - +
62S ILE* 3.0 43.3 + - + +
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Residues in contact with ASP 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Q ILE* 2.9 21.0 - - + +
55S ASP* 3.0 22.3 + - - +
56S ILE* 3.1 16.1 + - - +
58S GLU* 1.3 76.6 - - - +
60S LEU* 1.3 63.7 + - - +
62S ILE* 3.2 12.8 + - - +
63S GLU* 3.0 18.9 + - - +
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Residues in contact with LEU 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P PHE* 3.8 17.0 - - + -
165P VAL* 4.2 7.9 - - + -
187P MET* 5.3 2.7 - - + +
188P ARG* 6.2 2.0 - - + -
191P VAL* 3.7 34.1 - - + -
127Q TRP* 3.5 24.4 - - - +
128Q ILE* 3.6 21.6 + - + -
56S ILE* 2.9 25.9 + - + +
57S LEU* 3.3 36.3 - - + +
59S ASP* 1.3 72.7 - - - +
61S VAL* 1.3 58.5 + - - +
64S PHE* 2.9 33.6 + - - +
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Residues in contact with VAL 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P PHE* 3.6 41.5 - - + -
158P SER* 5.0 2.9 - - - +
161P PHE* 5.2 1.8 - - + -
162P VAL* 4.0 16.4 - - + -
32S PHE* 3.9 20.4 - - + -
36S LEU* 4.3 4.7 - - + -
57S LEU* 2.9 21.3 + - + +
58S GLU* 3.5 9.9 - - - +
59S ASP 3.2 0.4 - - - -
60S LEU* 1.3 77.5 - - + +
62S ILE* 1.3 57.0 + - - +
64S PHE* 3.3 6.2 + - - +
65S ILE* 2.9 47.6 + - + +
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Residues in contact with ILE 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU* 3.6 33.5 - - + +
31S LEU* 4.6 19.3 - - + -
32S PHE* 4.6 13.7 - - + -
58S GLU* 3.0 38.1 + - + +
59S ASP* 3.2 12.9 + - - +
61S VAL* 1.3 76.1 - - - +
63S GLU* 1.3 58.2 + - + +
65S ILE 3.4 0.3 + - - -
66S THR* 2.7 32.9 + - - +
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Residues in contact with GLU 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113Q VAL* 4.7 5.4 - - - +
117Q GLN* 2.7 43.1 + - - +
126Q MET* 5.5 1.2 - - - +
127Q TRP* 4.2 4.4 - - - -
128Q ILE* 3.0 59.5 + - - +
59S ASP 3.0 6.2 + - - +
62S ILE* 1.3 76.4 - - + +
64S PHE* 1.3 60.2 + - - +
66S THR* 3.4 11.4 - - + -
67S GLU* 2.9 32.5 + - + +
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Residues in contact with PHE 64 (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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154P MET* 5.0 2.0 - - - -
157P ILE* 3.8 22.7 - - + -
158P SER* 3.4 43.1 - - - -
161P PHE* 3.6 43.7 - + + -
200P ILE* 5.8 0.9 - - + -
127Q TRP* 3.3 47.0 - + + +
128Q ILE 4.9 0.8 - - - -
60S LEU 2.9 23.5 + - - +
61S VAL* 3.4 5.8 - - - +
63S GLU* 1.3 76.4 - - - +
65S ILE* 1.3 58.3 + - + +
68S MET* 2.9 47.6 + - + +
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Residues in contact with ILE 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P ILE* 3.7 31.6 - - + +
137P LEU* 3.7 29.2 - - + -
138P ILE* 3.8 28.0 - - + -
141P ILE* 4.9 0.7 - - + -
154P MET* 3.9 20.6 - - + -
158P SER* 3.6 20.4 - - - +
32S PHE* 4.9 1.6 - - + -
61S VAL* 2.9 33.8 + - + +
64S PHE* 1.3 73.9 - - - +
66S THR* 1.3 53.6 + - - +
68S MET* 3.8 0.7 - - - +
69S THR* 2.5 41.0 + - - +
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Residues in contact with THR 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU* 4.5 1.4 - - - +
141P ILE* 3.5 26.7 - - + +
117Q GLN* 6.4 0.2 - - - +
62S ILE* 2.7 26.6 + - - +
63S GLU* 3.4 16.4 - - + -
64S PHE 3.2 0.4 - - - -
65S ILE* 1.3 76.3 - - - +
67S GLU* 1.3 59.2 + - + +
69S THR* 3.2 2.8 + - - -
70S HIS* 2.9 56.2 + - + +
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Residues in contact with GLU 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201P PRO 5.8 0.9 - - - -
117Q GLN* 4.5 9.6 + - - +
121Q GLU* 3.4 24.2 - - - +
125Q ASN* 4.7 16.4 + - - +
126Q MET 5.7 0.7 - - - +
127Q TRP* 3.5 26.0 - - + -
63S GLU* 2.9 18.6 + - + +
66S THR* 1.3 72.3 - - + +
68S MET* 1.3 60.9 + - - +
70S HIS* 3.3 19.2 + - - +
71S LYS* 2.9 57.9 + - + +
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Residues in contact with MET 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P MET* 4.0 19.7 - - + +
157P ILE* 4.3 28.0 - - + -
201P PRO* 6.0 1.8 - - - -
127Q TRP* 3.6 25.0 - - + -
64S PHE* 2.9 42.5 + - + +
65S ILE 3.8 4.0 - - - +
67S GLU* 1.3 75.5 - - - +
69S THR* 1.3 56.1 + - - +
71S LYS* 3.4 9.3 + - + +
72S ALA* 2.9 30.6 + - + +
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Residues in contact with THR 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138P ILE* 4.2 12.1 - - + +
141P ILE* 3.8 22.4 - - + +
142P THR* 3.7 30.5 - - + -
154P MET* 3.9 10.7 - - + +
65S ILE* 2.5 34.9 + - - +
66S THR* 3.5 5.1 - - - -
68S MET* 1.3 72.8 - - - +
70S HIS* 1.3 60.1 + - - +
72S ALA* 3.6 6.5 - - + +
73S MET* 2.9 34.4 + - + +
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Residues in contact with HIS 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P ILE* 3.6 26.9 - - + +
66S THR* 2.9 34.4 + - + +
67S GLU* 3.3 28.0 + - - +
69S THR* 1.3 75.3 - - - +
71S LYS* 1.3 65.5 + - - +
73S MET* 3.7 15.2 + - + +
74S SER* 3.4 21.3 + - - -
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Residues in contact with LYS 71 (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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125Q ASN* 5.9 3.8 - - - +
127Q TRP* 5.9 2.2 - - + -
67S GLU* 2.9 44.0 + - + +
68S MET* 3.8 11.0 - - + +
70S HIS* 1.3 79.0 - - - +
72S ALA* 1.3 64.1 + - - +
74S SER* 3.5 20.8 + - - -
75S ILE* 3.8 15.2 + - - +
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Residues in contact with ALA 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P MET* 5.9 3.8 - - + -
68S MET* 2.9 18.9 + - + +
69S THR* 3.2 9.8 + - + +
71S LYS* 1.3 75.7 - - - +
73S MET* 1.3 65.3 + - + +
75S ILE* 3.3 26.3 + - - +
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Residues in contact with MET 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P ILE* 4.1 10.1 - - + +
142P THR* 3.7 36.3 - - + +
69S THR* 2.9 31.4 + - + +
70S HIS* 3.7 29.8 - - + +
72S ALA* 1.3 77.9 - - + +
74S SER* 1.3 60.9 + - - +
75S ILE 3.1 6.7 + - - -
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Residues in contact with SER 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S HIS 3.4 16.7 + - - -
71S LYS* 3.7 17.6 + - - -
72S ALA 3.3 0.6 - - - -
73S MET* 1.3 77.9 - - - +
75S ILE* 1.3 61.6 + - - +
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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