Contacts of the helix formed by residues 62 - 83 (chain A) in PDB entry 5JJA
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 ASP 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 4.4 20.8 - - + -
60A LEU 3.8 1.6 + - - -
61A SER* 1.3 84.2 + - - +
63A LEU* 1.3 63.3 + - - +
64A LYS* 3.3 3.1 - - - -
65A TRP* 3.2 25.6 + - + -
66A LYS* 2.9 22.8 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO 4.0 20.4 - - - +
60A LEU* 3.6 26.7 - - + +
61A SER 4.1 6.1 - - - +
62A ASP* 1.3 76.7 - - - +
64A LYS* 1.3 62.7 + - - +
66A LYS* 3.7 13.9 - - + +
67A GLU* 3.0 24.6 + - - +
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP 3.3 0.4 - - - -
63A LEU* 1.3 78.6 - - - +
65A TRP* 1.3 99.5 + - + +
67A GLU* 3.4 6.1 + - - +
68A VAL* 3.0 35.4 + - + +
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Residues in contact with TRP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.6 27.3 - + + -
62A ASP* 3.2 29.2 + - + +
64A LYS* 1.3 111.0 - - + +
66A LYS* 1.3 66.6 + - - +
68A VAL* 3.3 23.4 + - + +
69A LYS* 3.1 23.6 + - - +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.9 29.4 - - + -
54A ASP 3.2 27.1 + - - -
55A PHE* 3.9 37.4 - - + +
58A ASP 4.1 1.0 + - - -
59A PRO 3.9 16.0 + - - -
61A SER* 2.8 33.7 + - - +
62A ASP* 2.9 12.6 + - - +
63A LEU* 3.7 14.6 - - + +
65A TRP* 1.3 77.6 - - - +
67A GLU* 1.3 57.1 + - - +
69A LYS 3.3 0.9 + - - -
70A ARG* 3.0 16.4 + - - +
133A HIS* 2.9 29.9 + - + +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU 3.0 18.1 + - - +
64A LYS* 3.6 7.0 - - - +
66A LYS* 1.3 74.5 - - - +
68A VAL* 1.3 66.5 + - + +
70A ARG* 2.9 44.7 + - - -
71A ALA* 2.9 27.5 + - + +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 5.0 12.1 - - - +
64A LYS* 3.0 24.5 + - + +
65A TRP* 3.3 31.8 + - + +
67A GLU* 1.3 75.7 - - + +
69A LYS* 1.3 59.3 + - - +
71A ALA* 3.5 5.2 + - - +
72A ALA* 3.1 27.5 + - + +
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN 4.8 2.7 - - - +
49A CYS* 2.9 30.1 + - - +
51A VAL 2.6 30.8 + - - +
52A LEU* 4.1 4.9 - - - +
53A PHE* 3.8 10.3 - - + +
65A TRP 3.1 13.1 + - - +
66A LYS 3.6 7.4 - - - +
68A VAL* 1.3 76.6 - - - +
70A ARG* 1.3 65.6 + - - +
72A ALA* 3.2 6.7 + - - +
73A LEU* 3.0 39.0 + - + +
102A ASN* 2.8 27.8 + - - -
133A HIS* 3.6 34.0 + - + +
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Residues in contact with ARG 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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66A LYS 3.0 16.9 + - - +
67A GLU* 2.9 43.3 + - - +
69A LYS* 1.3 78.0 - - - +
71A ALA* 1.3 71.2 + - - +
73A LEU* 3.3 3.7 + - - +
74A SER* 2.9 52.5 + - - -
132A PRO* 4.1 13.2 - - + +
133A HIS* 3.8 10.9 + - + -
136A LEU* 3.4 27.4 - - + +
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Residues in contact with ALA 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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67A GLU* 2.9 22.3 + - + +
68A VAL* 3.9 5.4 - - - +
70A ARG* 1.3 95.3 - - - +
72A ALA* 1.3 57.8 + - - +
74A SER* 3.3 4.6 + - - -
75A GLU* 2.9 33.9 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.5 24.0 - - + +
48A GLN* 4.8 10.1 - - + +
49A CYS* 3.9 15.3 - - - -
68A VAL* 3.1 18.5 + - + +
69A LYS* 3.2 6.7 + - - +
71A ALA* 1.3 76.4 - - - +
73A LEU* 1.3 62.5 + - - +
75A GLU* 3.2 9.9 + - - +
76A MET* 3.0 29.3 + - - +
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Residues in contact with LEU 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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49A CYS* 3.8 20.2 - - + -
69A LYS* 3.0 37.6 + - + +
70A ARG* 3.6 7.6 - - - +
72A ALA* 1.3 76.6 - - - +
74A SER* 1.3 61.5 + - - +
76A MET* 3.4 9.5 + - + +
77A VAL* 3.1 27.9 + - - +
98A MET* 4.0 23.6 - - + -
133A HIS* 3.8 27.8 - - - +
136A LEU* 3.8 20.2 - - + +
137A VAL* 4.1 21.1 - - + -
140A PHE* 4.8 4.0 - - + -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 2.9 35.4 + - - -
71A ALA* 3.6 5.8 - - - -
73A LEU* 1.3 76.4 - - - +
75A GLU* 1.3 62.6 + - - +
77A VAL* 3.4 10.7 + - - +
78A GLU* 3.2 29.4 + - - +
136A LEU* 4.6 12.3 - - - +
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Residues in contact with GLU 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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29A GLY* 3.4 24.3 + - - -
30A ILE* 3.2 26.1 + - + +
41A LEU* 5.6 0.3 - - - +
45A LYS* 3.3 31.9 + - + -
71A ALA* 2.9 21.3 + - - +
72A ALA* 3.4 8.2 - - - +
74A SER* 1.3 75.9 - - - +
76A MET* 1.3 57.5 + - - +
78A GLU* 3.2 8.9 + - + +
79A TYR* 2.9 29.4 + - + +
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Residues in contact with MET 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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30A ILE* 4.1 10.1 - - + -
42A PHE* 3.7 16.8 - - + -
45A LYS* 3.7 22.0 - - + +
46A LEU* 3.4 40.2 - - + -
49A CYS* 3.7 30.3 - - - -
72A ALA 3.0 18.9 + - - +
73A LEU* 3.8 17.3 - - + +
74A SER 3.4 0.2 - - - -
75A GLU* 1.3 74.3 - - - +
77A VAL* 1.3 62.3 + - - +
79A TYR* 3.8 6.4 - - - +
80A ILE* 3.2 20.6 + - - +
98A MET* 4.3 3.1 - - + -
140A PHE* 3.5 25.3 - - + -
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Residues in contact with VAL 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 LEU 3.1 16.7 + - - +
74A SER* 3.5 10.5 - - - +
75A GLU 3.3 0.2 - - - -
76A MET* 1.3 76.5 - - - +
78A GLU* 1.3 65.7 + - - +
80A ILE* 3.6 4.5 - - - +
81A THR* 2.6 33.7 + - - +
136A LEU* 4.3 9.2 - - + +
139A GLU* 3.6 22.9 - - + +
140A PHE* 3.7 37.5 - - + +
143A ARG* 3.5 28.0 - - + +
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Residues in contact with GLU 78 (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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74A SER* 3.2 19.6 + - - +
75A GLU* 3.2 8.7 + - + +
77A VAL* 1.3 84.4 - - - +
79A TYR* 1.3 61.3 + - - +
81A THR* 3.3 0.6 + - - -
82A HIS* 2.9 62.7 + - + +
143A ARG* 5.0 3.5 + - - -
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Residues in contact with TYR 79 (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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30A ILE* 3.6 44.9 - - + +
31A ARG* 3.9 14.6 - - + -
38A GLN* 2.8 40.9 + - - +
39A GLU* 4.9 0.9 + - - -
42A PHE* 3.7 32.1 - + + -
75A GLU 2.9 16.8 + - - +
76A MET* 3.8 6.7 - - - +
78A GLU* 1.3 76.3 - - - +
80A ILE* 1.3 61.9 + - - +
83A ASN* 2.7 54.0 + - - +
86A VAL* 3.2 35.5 + - + +
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Residues in contact with ILE 80 (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 PHE* 3.6 34.8 - - + -
76A MET 3.2 13.2 + - - +
77A VAL 3.6 6.3 - - - +
79A TYR* 1.3 78.5 - - + +
81A THR* 1.3 63.8 + - - +
83A ASN 3.6 11.1 - - - +
84A ARG* 3.8 6.1 + - - -
86A VAL* 4.3 7.7 - - + +
87A ILE* 4.3 21.7 - - + +
140A PHE* 3.6 20.9 - - + +
143A ARG* 3.7 17.3 - - + +
144A PHE* 3.4 37.0 - - + +
147A SER* 4.3 11.1 + - - +
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Residues in contact with THR 81 (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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77A VAL 2.6 24.3 + - - -
78A GLU* 4.2 0.9 - - - -
80A ILE* 1.3 79.1 - - - +
82A HIS* 1.3 84.2 + - + +
83A ASN 3.6 0.7 - - - -
84A ARG* 3.9 16.3 + - - -
143A ARG* 2.6 42.4 + - - +
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Residues in contact with HIS 82 (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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31A ARG* 4.6 10.1 + - - +
78A GLU* 2.9 45.0 + - + +
81A THR* 1.3 98.3 - - + +
83A ASN* 1.3 70.6 + - - +
84A ARG* 4.8 2.2 - - - -
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Residues in contact with ASN 83 (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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31A ARG* 2.8 44.2 + - - +
78A GLU 4.3 0.6 + - - -
79A TYR* 2.7 49.9 + - - +
80A ILE 3.6 8.0 - - - +
81A THR 3.6 0.6 - - - -
82A HIS* 1.3 83.9 - - - +
84A ARG* 1.3 85.6 + - - +
86A VAL* 3.8 25.2 - - + +
149A ASP* 4.3 2.1 - - - +
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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