Contacts of the helix formed by residues 56 - 71 (chain A) in PDB entry 1GM5
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 ASN 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU 3.1 9.4 + - - +
54A LEU 2.7 8.1 + - - +
55A GLU* 1.3 75.3 - - - +
57A LYS* 1.3 69.2 + - - +
58A ASP* 5.3 2.0 - - - +
59A LEU* 3.4 19.9 - - + +
60A GLU* 2.9 21.9 + - - +
99A PHE* 3.6 26.5 - - - -
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU 3.9 2.6 + - - -
56A ASN* 1.3 67.5 + - - +
58A ASP* 1.3 77.0 + - - +
60A GLU* 2.6 19.3 + - - +
61A GLU* 2.8 37.9 + - + +
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Residues in contact with ASP 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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56A ASN* 4.9 2.6 - - - +
57A LYS* 1.3 76.7 - - - +
59A LEU* 1.3 71.4 - - - +
60A GLU 2.2 3.3 + - - -
61A GLU* 2.2 39.0 + - - +
62A LYS* 2.4 45.9 + - + +
99A PHE* 5.0 3.4 - - + -
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Residues in contact with LEU 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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22A LEU* 4.0 20.9 - - + -
53A LEU* 4.3 13.9 - - + +
54A LEU* 3.0 41.5 - - + +
56A ASN* 3.4 21.5 - - + +
57A LYS 3.3 0.4 - - - -
58A ASP* 1.3 80.7 - - - +
60A GLU* 1.3 54.9 + - - +
62A LYS* 3.9 1.9 - - - +
63A LEU* 3.0 36.7 + - + +
99A PHE* 3.2 59.9 - - + -
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Residues in contact with GLU 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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54A LEU* 3.0 38.0 - - + +
55A GLU* 4.6 3.1 - - - +
56A ASN 2.9 20.6 - - - +
57A LYS* 2.6 15.1 + - - +
58A ASP 2.2 8.1 + - - -
59A LEU* 1.3 69.7 - - - +
61A GLU* 1.3 65.0 + - + +
63A LEU* 3.3 6.0 - - - +
64A GLN* 3.2 23.7 + - - +
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Residues in contact with GLU 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 LYS* 2.8 37.6 + - + +
58A ASP* 2.2 32.0 + - + +
60A GLU* 1.3 65.4 - - + +
62A LYS* 1.3 69.0 + - - +
63A LEU 2.7 3.0 + - - -
64A GLN* 3.1 23.0 + - - +
65A ALA* 3.4 10.7 + - - +
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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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58A ASP* 2.4 58.8 + - + +
59A LEU* 3.9 7.0 - - - +
61A GLU* 1.3 74.1 - - - +
63A LEU* 1.3 64.5 + - - +
65A ALA* 3.3 15.6 - - - +
66A PHE* 3.3 6.8 + - - +
91A MET* 4.2 29.7 - - + +
95A LEU* 4.9 3.8 - - + -
98A TRP* 4.0 27.4 - - + +
99A PHE* 4.5 10.1 - - + -
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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
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22A LEU* 5.1 10.1 - - + -
25A PHE* 4.7 12.3 - - + -
26A LEU* 5.1 5.4 - - + -
46A LEU* 5.9 4.0 - - + -
49A LEU* 5.9 3.6 - - + -
54A LEU* 5.1 14.1 - - + -
59A LEU* 3.0 26.7 + - + +
60A GLU* 3.3 7.6 - - - +
61A GLU 2.7 4.2 + - - -
62A LYS* 1.3 73.7 - - - +
64A GLN* 1.3 58.4 + - - +
66A PHE* 2.2 40.2 + - - +
67A LEU* 2.9 32.7 + - + -
95A LEU* 3.6 31.0 - - + -
99A PHE* 6.4 0.2 - - + -
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Residues in contact with GLN 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 GLU 3.2 12.4 + - - +
61A GLU* 3.1 12.1 + - - +
63A LEU* 1.3 78.4 - - - +
65A ALA* 1.3 70.8 + - - +
67A LEU* 4.4 6.9 - - - +
68A ASP* 2.5 38.0 + - - +
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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 GLU 3.4 6.1 + - - +
62A LYS* 3.3 14.8 - - - +
63A LEU 2.9 0.8 + - - -
64A GLN* 1.3 86.6 - - - +
66A PHE* 1.3 63.9 + - - +
68A ASP* 3.1 7.1 + - - +
69A TYR* 2.8 17.5 + - - +
91A MET* 6.3 0.7 - - + -
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Residues in contact with PHE 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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26A LEU* 5.0 4.5 - - + -
29A VAL* 4.5 14.1 - - + -
62A LYS 3.3 6.4 + - - +
63A LEU* 2.2 29.0 + - + +
65A ALA* 1.3 66.4 - - - +
67A LEU* 1.3 80.0 + - + +
68A ASP 2.4 18.4 + - - -
69A TYR* 2.5 24.5 + + + +
70A VAL* 3.1 22.0 + - + -
88A SER* 3.9 25.8 - - - -
91A MET* 3.3 45.5 - - + -
92A ILE* 3.6 29.8 - - + -
95A LEU* 4.7 13.7 - - + -
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Residues in contact with LEU 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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25A PHE* 3.6 20.6 - - + -
26A LEU* 6.1 2.0 - - + -
29A VAL* 5.8 4.5 - - + -
42A ILE* 4.5 11.3 - - + +
46A LEU* 3.0 41.1 - - + -
63A LEU* 2.9 39.1 + - + +
64A GLN* 4.1 6.5 - - - +
66A PHE* 1.3 86.4 - - + +
68A ASP* 1.3 53.2 + - - +
70A VAL* 4.0 6.4 - - - +
71A LYS* 2.4 47.3 + - + +
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Residues in contact with ASP 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 GLN* 2.5 30.5 + - - +
65A ALA* 3.1 8.5 - - - +
66A PHE 2.4 9.1 + - - -
67A LEU* 1.3 72.8 - - - +
69A TYR* 1.3 62.7 + - - +
71A LYS* 3.8 24.2 + - - +
72A GLU* 4.1 5.9 + - - +
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Residues in contact with TYR 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 ALA 2.8 10.2 + - - +
66A PHE* 2.5 21.8 + + + +
68A ASP* 1.3 68.5 - - - +
70A VAL* 1.3 64.3 + - + +
72A GLU* 2.7 58.6 - - - +
83A TYR* 4.0 3.1 + - - -
84A ARG* 3.4 41.1 + - + +
87A LYS* 2.8 49.2 + - + +
88A SER* 5.5 5.2 - - - -
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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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29A VAL* 5.0 11.4 - - + -
32A MET* 5.7 1.6 - - + -
33A LEU* 6.3 4.3 - - + -
37A VAL* 4.3 5.6 - - + -
42A ILE* 4.5 12.8 - - + -
66A PHE* 3.1 31.3 + - + +
67A LEU* 4.1 8.5 - - - +
69A TYR* 1.3 76.9 - - + +
71A LYS* 1.3 55.2 - - - +
72A GLU 2.1 24.0 + - - -
73A ILE* 2.7 46.2 + - + +
84A ARG* 4.7 2.9 - - - +
88A SER* 4.0 23.6 - - - +
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Residues in contact with LYS 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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37A VAL* 4.8 2.0 - - - -
39A THR* 3.7 24.4 - - + +
42A ILE* 4.9 18.6 - - + -
43A HIS* 2.2 49.5 + - + +
67A LEU* 2.4 39.0 - - + +
68A ASP* 3.8 19.6 + - - +
69A TYR 3.6 0.4 + - - -
70A VAL* 1.3 77.8 - - + +
72A GLU* 1.3 60.7 + - - +
73A ILE* 3.3 3.4 - - - -
74A PRO* 3.4 12.3 - - - +
75A ASN* 4.2 2.6 + - - -
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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
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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