Contacts of the helix formed by residues 61 - 80 (chain A) in PDB entry 1JGN
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 SER 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A HIS* 2.9 32.0 + - - -
58A MET* 3.0 4.6 + - - -
60A GLU* 1.3 79.3 - - - +
62A PRO* 1.3 57.6 - - - +
63A GLU* 3.2 3.9 + - - +
64A SER* 3.0 34.0 + - - -
65A LEU* 2.7 38.4 + - - +
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Residues in contact with PRO 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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58A MET 4.7 1.1 - - - +
59A LEU 5.1 3.3 - - - +
60A GLU 3.5 8.1 - - - +
61A SER* 1.3 87.7 - - - +
63A GLU* 1.3 65.6 + - + +
65A LEU* 4.5 8.5 - - + -
66A ARG* 3.2 30.1 + - - +
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Residues in contact with GLU 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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61A SER* 3.2 2.2 - - - +
62A PRO* 1.3 84.8 - - + +
64A SER* 1.3 65.9 + - - +
66A ARG* 4.6 1.4 - - - +
67A SER* 3.3 22.9 + - - -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 5.0 7.6 + - - -
58A MET* 3.4 16.5 - - - +
61A SER* 3.0 26.4 + - - -
63A GLU* 1.3 79.5 - - - +
65A LEU* 1.3 62.8 + - - +
67A SER* 3.7 5.8 - - - -
68A LYS* 3.5 16.3 + - - +
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Residues in contact with LEU 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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31A LEU* 3.3 57.9 - - + -
35A MET* 5.2 1.6 - - + -
58A MET* 3.1 43.0 - - + +
59A LEU* 4.6 3.6 - - + -
61A SER 2.7 18.9 + - - +
62A PRO* 4.3 7.9 - - + +
64A SER* 1.3 73.5 - - - +
66A ARG* 1.3 60.6 + - + +
67A SER 2.9 4.3 - - - -
68A LYS* 2.7 27.7 + - + +
69A VAL* 3.0 19.4 + - + -
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Residues in contact with ARG 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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35A MET* 3.5 35.5 - - + +
62A PRO 3.2 19.8 + - - +
63A GLU* 4.6 1.1 - - - +
65A LEU* 1.3 83.9 - - + +
67A SER* 1.3 55.2 + - - +
69A VAL 3.7 0.2 - - - -
70A ASP* 2.7 68.1 + - - +
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Residues in contact with SER 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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63A GLU 3.3 20.2 + - - -
64A SER* 3.7 8.3 - - - -
65A LEU 2.9 0.4 - - - -
66A ARG* 1.3 82.7 - - - +
68A LYS* 1.3 62.9 + - - +
70A ASP* 3.1 22.0 + - - +
71A GLU* 3.6 5.5 + - - +
6B LEU* 5.3 0.2 - - - +
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Residues in contact with LYS 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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50A ILE* 3.3 36.8 - - - +
54A GLU* 3.0 29.4 + - - +
58A MET* 3.4 38.7 - - + +
64A SER 3.5 4.9 + - - +
65A LEU* 2.7 14.5 + - - +
67A SER* 1.3 70.1 - - - +
69A VAL* 1.3 64.1 - - + +
70A ASP 3.0 4.0 - - - -
71A GLU 3.1 11.8 + - - -
72A ALA 3.3 1.0 + - - -
6B LEU* 3.2 42.2 - - + +
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Residues in contact with VAL 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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28A LEU* 5.0 4.9 - - + -
31A LEU* 3.6 31.0 - - + -
32A ILE* 3.5 33.9 - - + -
35A MET* 3.3 37.0 - - + -
65A LEU* 3.0 15.5 + - + +
68A LYS* 1.3 78.8 - - + +
70A ASP* 1.3 66.2 + - - +
71A GLU 3.2 0.2 - - - -
72A ALA* 2.9 12.5 + - + +
73A VAL* 2.8 22.6 + - + +
6B LEU* 4.8 1.8 - - + -
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Residues in contact with ASP 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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35A MET* 5.0 2.9 - - - -
66A ARG* 2.7 48.1 + - - +
67A SER* 3.1 15.6 + - - +
69A VAL* 1.3 78.4 - - - +
71A GLU* 1.3 64.3 + - - +
73A VAL* 3.3 15.3 + - - +
74A ALA* 3.5 9.2 + - - +
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Residues in contact with GLU 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 SER 3.6 4.6 + - - +
68A LYS 3.1 10.8 + - - +
70A ASP* 1.3 80.1 - - - +
72A ALA* 1.3 59.6 + - - +
74A ALA* 2.8 27.5 + - + +
75A VAL* 2.9 17.2 + - - +
5B ASN* 3.2 38.4 - - + +
6B LEU* 3.5 30.4 + - + +
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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
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28A LEU* 5.5 0.2 - - + -
32A ILE* 4.9 0.7 - - + -
43A ILE* 3.2 23.8 - - + -
47A LEU* 3.7 18.2 - - + -
68A LYS 3.3 3.9 + - - +
69A VAL* 2.9 30.5 + - + +
71A GLU* 1.3 78.7 - - - +
73A VAL* 1.3 59.7 + - - +
75A VAL* 3.0 33.9 - - - +
76A LEU* 3.2 6.9 - - - +
6B LEU* 4.2 2.1 - - + +
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Residues in contact with VAL 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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32A ILE* 4.4 1.1 - - + -
35A MET* 4.0 29.2 - - + -
38A THR* 3.2 34.4 - - + +
43A ILE* 3.9 17.3 - - + -
69A VAL 2.8 15.5 + - - +
70A ASP* 3.5 11.0 - - - +
72A ALA* 1.3 75.0 - - - +
74A ALA* 1.3 62.8 + - - +
76A LEU* 3.4 16.8 + - - +
77A GLN* 3.5 9.9 + - + +
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Residues in contact with ALA 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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70A ASP 3.5 4.1 + - - +
71A GLU* 2.8 23.6 + - + +
73A VAL* 1.3 77.9 - - - +
75A VAL* 1.3 63.0 + - - +
76A LEU 3.0 2.4 + - - -
77A GLN* 3.2 10.5 + - - +
78A ALA* 3.1 23.3 + - - +
5B ASN* 5.0 6.1 - - - +
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Residues in contact with VAL 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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46A MET* 3.5 17.0 - - + +
47A LEU* 4.0 17.3 - - + -
71A GLU 2.9 18.6 + - - +
72A ALA* 3.0 22.9 + - - +
74A ALA* 1.3 74.2 - - - +
76A LEU* 1.3 70.1 + - + +
78A ALA* 3.6 4.2 + - - +
79A HIS* 2.8 28.1 + - - +
2B VAL* 5.6 0.9 - - - +
4B SER* 3.6 24.5 - - - +
5B ASN* 4.2 20.2 - - - +
6B LEU* 4.6 6.3 - - + +
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Residues in contact with LEU 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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38A THR* 4.0 9.2 - - + -
39A LEU* 3.5 39.3 - - + +
42A LYS* 3.6 20.6 - - + -
43A ILE* 3.3 35.9 - - + -
46A MET* 4.0 5.8 - - + -
72A ALA 3.2 9.0 - - - +
73A VAL 3.4 9.4 + - - +
74A ALA 3.0 0.4 - - - -
75A VAL* 1.3 94.4 - - + +
77A GLN* 1.3 61.0 + - - +
78A ALA 3.0 1.3 - - - -
79A HIS* 2.7 26.8 + - + +
80A GLN* 3.0 17.3 + - + +
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Residues in contact with GLN 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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38A THR* 4.4 13.9 - - + +
73A VAL* 3.5 13.0 + - + +
74A ALA* 3.2 11.3 + - - +
76A LEU* 1.3 80.6 - - - +
78A ALA* 1.3 58.0 + - - +
80A GLN* 3.9 2.9 + - - +
81A ALA* 3.2 22.9 + - - +
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Residues in contact with ALA 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 ALA 3.1 14.3 + - - +
75A VAL* 3.9 6.5 - - - +
76A LEU 3.0 0.4 - - - -
77A GLN* 1.3 78.0 - - - +
79A HIS* 1.3 64.9 + - - +
80A GLN 3.4 0.2 - - - -
81A ALA* 3.9 7.0 - - - -
82A LYS* 3.0 50.4 + - + +
2B VAL* 4.8 3.2 - - + +
3B LYS 5.8 2.7 - - - +
5B ASN* 5.3 6.1 - - - +
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Residues in contact with HIS 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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39A LEU* 6.4 0.7 - - + -
42A LYS* 3.8 26.1 + - + -
46A MET* 3.3 34.8 - - + +
75A VAL 2.8 16.4 + - - +
76A LEU* 2.7 23.3 + - + +
78A ALA* 1.3 74.6 - - - +
80A GLN* 1.3 62.2 + - + +
82A LYS 4.4 0.2 - - - -
83A GLU* 3.1 43.3 + - + +
2B VAL* 3.7 34.7 - - + +
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Residues in contact with GLN 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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39A LEU* 5.2 17.1 - - + +
76A LEU* 3.0 12.3 + - + +
77A GLN* 4.6 2.9 - - - +
79A HIS* 1.3 81.9 - - + +
81A ALA* 1.3 62.0 + - - +
83A GLU* 3.9 13.7 - - - +
84A ALA* 3.4 27.2 + - - +
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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
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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