Contacts of the helix formed by residues 58 - 77 (chain A) in PDB entry 1JEY
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET 3.4 13.4 + - - -
49A PHE* 3.5 26.7 - - - +
51A SER* 3.7 18.4 - - - +
57A LEU* 1.3 77.6 - - - +
59A PRO* 1.3 72.2 - - - +
60A PHE* 3.1 5.4 + - - +
61A ASP* 3.1 24.7 + - + +
62A MET* 3.0 20.7 + - - +
128A GLN* 4.2 13.7 + - - +
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Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA 3.5 6.5 - - - +
48A MET* 3.1 36.3 - - - +
50A GLU 3.3 18.6 - - - +
51A SER* 4.7 1.1 - - - -
52A GLN* 4.7 8.5 - - - +
57A LEU 4.4 2.0 - - - +
58A THR* 1.3 81.5 - - - +
60A PHE* 1.3 49.4 - - - -
62A MET* 3.3 14.2 - - + +
63A SER* 2.8 36.9 + - - -
171A ASN* 3.7 11.7 - - + +
205A LEU* 3.6 31.9 - - + +
206A LYS 5.3 0.7 - - - +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.9 15.7 - - + -
43A ASP 4.0 6.7 - - - -
44A ALA* 5.2 0.2 - - + -
48A MET* 2.9 32.0 + - + +
49A PHE* 3.5 35.4 - + + -
58A THR* 3.1 4.7 - - - +
59A PRO* 1.3 74.1 - - - +
61A ASP* 1.3 63.7 + - - +
63A SER* 3.1 4.6 + - - -
64A ILE* 2.9 54.1 + - + +
87A PHE* 3.8 23.6 - + - -
122A PHE* 3.8 17.0 - - + -
128A GLN* 5.0 7.2 - - + -
131A PHE* 3.6 36.1 - + + -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 4.0 20.3 - - + +
58A THR* 3.1 19.8 + - + +
60A PHE* 1.3 84.3 - - + +
62A MET* 1.3 63.2 + - - +
64A ILE* 3.8 2.8 - - - +
65A GLN* 2.8 54.4 + - - +
122A PHE 5.2 1.1 - - - +
123A LYS* 4.0 2.6 - - - -
124A GLY* 3.1 41.1 + - - +
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Residues in contact with MET 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 3.7 15.7 - - + +
57A LEU* 3.5 35.3 - - + +
58A THR 3.0 13.6 + - - +
59A PRO* 3.3 13.5 - - + +
61A ASP* 1.3 77.9 - - - +
63A SER* 1.3 57.0 + - - +
66A CYS* 3.0 30.7 + - - +
205A LEU* 4.4 17.9 - - - -
236A SER 4.8 1.1 - - - +
237A SER* 3.5 26.7 - - - +
238A LYS 3.9 17.5 - - - +
239A LEU* 3.6 31.4 - - + +
242A LEU* 3.8 12.3 - - + +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.3 14.6 - - - -
48A MET* 4.0 1.2 - - - +
59A PRO 2.8 18.5 + - - -
60A PHE* 3.3 10.3 - - - -
62A MET* 1.3 73.6 - - - +
64A ILE* 1.3 66.4 + - - +
66A CYS* 3.2 2.6 + - - +
67A ILE* 3.0 30.3 + - - +
169A PHE* 3.4 36.3 - - - +
205A LEU* 3.4 9.5 - - - +
242A LEU* 4.1 8.2 - - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 5.1 1.6 - - + -
60A PHE* 2.9 47.7 + - + +
61A ASP* 3.8 5.2 - - - +
63A SER* 1.3 70.5 - - - +
65A GLN* 1.3 65.9 + - - +
67A ILE* 3.0 14.2 + - + +
68A GLN* 3.0 25.9 + - - +
87A PHE* 3.7 37.2 - - + -
119A LEU* 3.3 34.8 - - + +
122A PHE* 4.1 21.8 - - + +
123A LYS* 4.2 5.6 - - - +
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.1 26.0 - - - +
61A ASP* 2.8 41.8 + - - +
62A MET 3.9 2.9 - - - +
64A ILE* 1.3 76.4 - - - +
66A CYS* 1.3 59.6 + - - +
68A GLN* 3.5 4.3 + - - +
69A SER* 3.0 26.6 + - - -
123A LYS* 3.2 42.4 + - + +
124A GLY* 4.7 1.2 - - - +
239A LEU* 3.7 25.5 - - + +
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Residues in contact with CYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET 3.0 18.6 + - - +
63A SER* 3.6 4.9 - - - +
65A GLN* 1.3 75.5 - - - +
67A ILE* 1.3 65.3 + - - +
69A SER* 3.3 9.2 - - - -
70A VAL* 3.3 21.2 + - - +
169A PHE* 4.2 6.7 - - - -
239A LEU* 4.2 10.7 - - + +
242A LEU* 4.0 19.7 - - + -
243A LEU* 4.2 11.2 - - - -
246A VAL* 3.4 44.2 - - - -
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.6 39.3 - - + -
42A VAL* 3.6 31.4 - - + -
63A SER 3.0 19.2 + - - +
64A ILE* 3.5 12.8 - - + +
66A CYS* 1.3 74.8 - - - +
68A GLN* 1.3 66.7 + - - +
70A VAL* 3.2 7.2 + - - +
71A TYR* 3.0 51.1 + - + -
85A VAL* 4.2 11.4 - - + -
119A LEU* 4.1 10.8 - - + -
169A PHE* 4.1 9.9 - - + -
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.0 12.6 + - - +
65A GLN* 3.7 8.9 - - - +
67A ILE* 1.3 76.0 - - - +
69A SER* 1.3 53.5 + - - +
71A TYR* 2.9 6.5 + - - +
72A ILE* 2.8 47.7 + - + +
116A ILE* 4.0 18.7 - - + +
119A LEU* 3.6 33.2 + - + +
120A ASP* 3.1 33.2 + - - +
123A LYS* 2.9 49.6 + - - +
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLN 3.0 13.1 + - - -
66A CYS* 3.3 13.7 - - - -
68A GLN* 1.3 79.6 - - - +
70A VAL* 1.3 57.0 + - - +
72A ILE* 3.2 7.6 + - - +
73A SER* 2.8 36.5 + - - -
239A LEU* 5.9 0.3 - - - +
243A LEU* 4.3 27.3 - - - +
247A ARG* 6.0 1.6 - - - -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.8 1.3 - - + -
40A PHE* 3.9 25.8 - - + -
66A CYS* 3.3 14.8 + - - +
67A ILE 3.2 6.3 + - - +
69A SER* 1.3 77.0 - - - +
71A TYR* 1.3 61.5 + - - +
73A SER* 4.1 0.6 - - - +
74A LYS* 2.8 48.6 + - + +
83A LEU* 5.1 1.8 - - + -
243A LEU* 5.8 3.4 - - + -
246A VAL* 3.6 27.6 - - + -
250A GLU* 3.6 40.4 - - + +
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Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.8 15.7 - + - -
67A ILE* 3.0 44.0 + - + +
68A GLN* 2.9 11.5 + - - +
70A VAL* 1.3 80.3 - - - +
72A ILE* 1.3 62.6 + - - +
74A LYS* 3.4 3.8 + - - +
75A ILE* 3.2 23.4 + - - +
83A LEU* 3.7 33.4 - - + +
84A ALA 3.9 6.1 + - - -
85A VAL* 3.1 15.8 - - + +
106A GLN* 2.7 29.3 + - - -
111A PRO* 3.7 23.8 - - + +
115A ARG* 4.0 13.2 + - + -
116A ILE* 3.8 21.5 - - + -
119A LEU* 3.8 15.0 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLN* 2.8 33.6 + - + +
69A SER* 3.8 5.6 - - - +
71A TYR* 1.3 70.4 - - - +
73A SER* 1.3 60.4 + - - +
75A ILE* 2.9 6.4 + - + +
76A ILE* 2.8 44.7 + - + +
116A ILE* 3.4 36.1 - - + -
123A LYS* 6.2 0.4 - - - +
484A GLN* 6.0 0.7 - - - +
487A PHE* 6.1 0.2 - - + -
488A ARG* 4.1 25.1 - - - +
491A GLU* 4.8 6.3 - - - +
316B TYR* 4.8 2.9 - - - +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A SER* 2.8 24.5 + - - -
70A VAL* 4.1 1.3 - - - -
72A ILE* 1.3 73.1 - - - +
74A LYS* 1.3 63.9 + - - +
76A ILE* 3.1 12.0 + - - +
77A SER* 3.0 26.8 + - - -
247A ARG* 5.5 5.4 + - - -
250A GLU* 3.8 21.1 + - - -
427B MET* 4.6 17.2 - - - +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 5.5 1.1 - - - -
70A VAL* 2.8 41.5 + - + +
71A TYR 3.5 6.1 - - - +
73A SER* 1.3 76.8 - - - +
75A ILE* 1.3 60.2 + - - +
77A SER* 3.9 2.0 + - - +
78A SER 3.4 0.9 + - - -
79A ASP* 2.8 71.0 + - + +
81A ASP* 2.9 17.7 + - + +
83A LEU* 4.3 15.7 - - + -
111A PRO* 4.4 14.0 - - + +
250A GLU* 2.5 38.1 + - - +
251A THR* 3.1 17.8 + - - +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR 3.2 7.9 + - - +
72A ILE* 2.9 10.1 + - + +
74A LYS* 1.3 75.1 - - - +
76A ILE* 1.3 69.1 + - + +
77A SER 3.1 2.0 - - - -
78A SER* 3.0 16.0 + - - +
111A PRO* 4.0 14.1 - - + -
112A GLY* 4.2 16.2 - - - +
116A ILE* 3.3 32.1 - - + -
283A PRO* 5.6 0.2 - - - +
487A PHE* 3.9 15.3 - - + -
316B TYR* 3.4 48.5 - - + -
317B GLY* 4.0 22.1 + - - +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 2.8 38.7 + - + +
73A SER* 3.1 10.5 + - - +
75A ILE* 1.3 77.7 - - + +
77A SER* 1.3 57.4 + - - +
78A SER 3.8 0.5 + - - -
280A ALA* 5.2 4.9 - - + +
281A LEU 4.9 4.9 - - - +
283A PRO* 4.4 8.8 - - - +
483A LEU* 3.9 27.5 - - + +
484A GLN* 5.0 14.4 - - - +
487A PHE* 3.4 51.5 - - + -
488A ARG* 5.0 2.9 - - - +
316B TYR* 6.0 0.2 - - + -
428B GLU* 4.5 17.0 - - + +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A SER 3.0 17.5 + - - -
74A LYS* 3.9 7.1 + - - +
75A ILE 3.1 0.2 - - - -
76A ILE* 1.3 78.4 - - - +
78A SER* 1.3 70.5 + - - +
79A ASP* 3.2 10.0 + - - +
280A ALA* 6.4 2.2 - - - -
428B GLU 6.2 0.4 - - - -
431B ARG* 5.8 5.6 - - - -
4C T 5.3 1.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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