Contacts of the helix formed by residues 55 - 70 (chain A) in PDB entry 2JM5
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 GLY 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A SER* 3.4 6.2 + - - -
54A LYS* 1.3 86.6 - - - +
56A PRO* 1.3 63.9 - - - +
57A GLN* 3.2 7.9 - - - -
58A GLN* 2.9 26.9 + - - +
59A ILE* 3.0 13.8 + - - +
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Residues in contact with PRO 56 (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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54A LYS* 3.3 11.8 - - + +
55A GLY* 1.3 81.5 - - - +
57A GLN* 1.3 63.8 + - + +
59A ILE* 3.1 22.8 - - + +
60A HIS* 3.0 23.9 - - + +
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Residues in contact with GLN 57 (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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55A GLY* 4.9 5.5 + - - +
56A PRO* 1.3 79.7 - - + +
58A GLN* 1.3 88.7 + - - +
60A HIS* 3.1 19.8 + - - +
61A LEU* 3.0 39.5 + - + +
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Residues in contact with GLN 58 (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 PHE* 5.2 0.2 - - - -
53A SER* 3.3 24.9 - - - +
55A GLY* 2.9 13.8 + - - +
57A GLN* 1.3 92.4 - - - +
59A ILE* 1.3 55.7 + - - +
61A LEU* 3.2 27.7 + - - +
62A LYS* 2.8 63.2 + - + +
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Residues in contact with ILE 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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50A PHE* 3.3 29.5 - - + +
53A SER* 4.2 14.6 - - - +
54A LYS 4.9 0.7 - - - -
55A GLY 3.0 22.4 + - - +
56A PRO* 3.1 20.0 - - + +
58A GLN* 1.3 76.6 - - - +
60A HIS* 1.3 53.9 + - - +
63A ALA* 2.8 37.9 + - - +
96A PRO* 3.6 20.4 - - + +
97A THR 3.4 23.6 - - - +
98A LEU* 3.6 31.9 - - + +
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Residues in contact with HIS 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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56A PRO* 3.0 29.0 + - + +
57A GLN* 3.1 12.8 + - - +
59A ILE* 1.3 78.5 - - + +
61A LEU* 1.3 68.8 + - + +
64A LYS* 3.0 42.9 + - + +
94A THR 3.6 21.7 + - - -
95A GLN* 5.0 1.3 - - - -
96A PRO* 3.5 27.7 + - + +
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Residues in contact with LEU 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 GLN* 3.0 37.5 - - + +
58A GLN* 3.3 30.1 - - - +
60A HIS* 1.3 82.7 - - + +
62A LYS* 1.3 58.5 + - - +
64A LYS* 3.7 2.3 - - - +
65A ALA* 2.8 31.1 + - - +
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Residues in contact with LYS 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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49A ASP* 2.7 36.1 + - - +
50A PHE* 3.6 34.5 - - + -
53A SER* 5.0 5.1 - - - -
58A GLN* 2.8 47.2 + - + +
61A LEU* 1.3 73.6 - - - +
63A ALA* 1.3 61.5 + - - +
65A ALA* 3.3 7.0 + - + +
66A ILE* 3.0 31.6 + - + +
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Residues in contact with ALA 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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50A PHE* 3.6 13.5 - - + -
59A ILE 2.8 23.9 + - - +
60A HIS 4.1 1.1 - - - +
62A LYS* 1.3 70.5 - - - +
64A LYS* 1.3 52.1 + - - +
66A ILE 3.1 1.2 + - - -
67A TYR* 2.7 32.4 + - - +
93A ILE* 3.6 12.8 - - + -
96A PRO* 3.5 24.9 - - + -
100A SER* 4.9 1.8 - - - +
101A PHE* 3.0 23.6 - - + -
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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
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60A HIS* 3.0 31.6 + - + +
61A LEU* 4.0 2.7 - - - +
63A ALA* 1.3 77.3 - - + +
65A ALA* 1.3 57.0 + - - +
67A TYR* 3.6 12.6 - - + -
68A GLU* 2.9 44.2 + - - +
93A ILE* 3.6 47.9 + - + +
94A THR* 4.3 10.1 - - - +
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Residues in contact with ALA 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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61A LEU 2.8 18.6 + - - +
62A LYS* 3.5 10.3 - - + +
63A ALA 3.2 0.2 - - - -
64A LYS* 1.3 78.2 - - - +
66A ILE* 1.3 63.5 + - + +
68A GLU* 4.0 3.0 - - - +
69A LYS* 3.1 27.4 + - - +
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Residues in contact with ILE 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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43A PHE* 4.5 5.4 - - + +
46A ALA* 3.4 44.0 - - + +
47A CYS* 3.7 21.5 - - - +
50A PHE* 4.1 8.3 - - + -
62A LYS* 3.0 18.8 + - + +
65A ALA* 1.3 75.1 - - + +
67A TYR* 1.3 61.1 + - - +
69A LYS* 4.5 1.1 - - - -
70A PHE* 2.8 60.6 + - + +
71A ILE 3.5 0.3 + - - -
101A PHE* 3.6 27.1 - - + -
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Residues in contact with TYR 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 ALA 2.7 18.3 + - - +
64A LYS* 3.4 13.7 - - + +
66A ILE* 1.3 75.5 - - - +
68A GLU* 1.3 72.3 + - + +
71A ILE* 2.8 61.4 + - + -
72A GLN* 2.9 38.2 + - - -
89A ILE* 3.6 11.7 - - + -
90A THR* 3.1 44.4 + - + +
93A ILE* 3.6 32.2 - - + +
101A PHE* 3.9 0.9 - - + -
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Residues in contact with GLU 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 LYS* 2.9 32.5 + - - +
65A ALA* 4.3 2.8 - - - +
67A TYR* 1.3 91.1 - - + +
69A LYS* 1.3 56.7 + - - +
72A GLN* 3.4 17.0 + - + +
74A ASP 4.1 1.6 - - - +
75A ALA* 3.2 19.4 - - - +
76A PRO* 3.4 7.9 - - - +
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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
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39A GLU* 5.9 0.4 - - - +
65A ALA 3.1 17.9 + - - +
66A ILE* 4.0 3.1 - - - +
68A GLU* 1.3 79.9 - - - +
70A PHE* 1.3 91.0 + - + +
75A ALA* 3.3 5.5 - - - +
76A PRO* 3.7 20.9 - - + -
77A LYS* 3.2 39.2 + - + +
78A GLU 3.2 6.4 + - - -
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Residues in contact with PHE 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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39A GLU* 3.5 45.3 - - + -
40A ASN* 6.1 0.2 - - - -
42A GLU* 4.8 3.1 - - + -
43A PHE* 3.5 25.4 - + + -
46A ALA* 4.6 10.1 - - + -
66A ILE* 2.8 37.5 + - + +
67A TYR 3.2 0.6 + - - -
69A LYS* 1.3 119.3 - - + +
71A ILE* 1.3 63.1 + - - +
72A GLN 3.0 9.7 - - - +
77A LYS* 3.9 13.7 - - + -
78A GLU* 3.4 2.0 - - - +
79A VAL* 2.9 49.7 + - + +
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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
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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