Contacts of the helix formed by residues 51 - 65 (chain A) in PDB entry 4GAB
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 3.0 30.0 + - - +
22A LYS 5.1 0.6 - - - +
23A SER* 2.9 32.3 + - - +
25A LEU* 3.9 20.0 - - + -
28A VAL* 4.1 14.3 - - + +
45A CYS* 5.9 0.3 - - - -
49A TYR* 3.4 24.1 + - - +
50A GLN* 1.3 78.1 - - - +
52A GLU* 1.3 73.3 + - - +
53A HIS* 3.2 4.9 - - - -
54A GLU* 3.2 15.2 + - - +
55A VAL* 3.3 12.7 + - - +
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Residues in contact with GLU 52 (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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45A CYS* 3.4 16.4 - - + +
46A ALA 3.3 29.2 + - - +
47A TYR* 3.6 8.6 - - - +
50A GLN* 3.8 1.6 - - - +
51A ASN* 1.3 80.7 - - - +
53A HIS* 1.3 58.1 + - - +
55A VAL* 3.3 5.9 + - - -
56A GLY 2.9 24.6 + - - -
77A SER* 2.4 32.4 + - - -
96A THR* 2.8 33.8 + - - +
99A ASP* 3.5 21.4 + - + +
100A LEU* 3.5 14.5 - - + +
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Residues in contact with HIS 53 (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 LEU* 3.5 38.9 - - + +
50A GLN 4.0 12.0 + - - -
51A ASN* 4.1 3.8 - - - -
52A GLU* 1.3 79.3 + - - +
54A GLU* 1.3 72.0 + - + +
56A GLY 3.4 0.3 + - - -
57A GLU* 3.0 39.2 + - - +
95A LYS* 5.9 0.8 + - - -
99A ASP* 3.3 35.0 + - + +
101A LYS* 3.3 11.6 + - - +
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Residues in contact with GLU 54 (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 LEU* 3.6 25.4 - - + +
26A GLY* 2.9 33.0 + - - -
28A VAL* 3.6 24.1 - - + +
29A LYS* 3.8 24.2 + - + +
51A ASN 3.2 4.2 + - - +
53A HIS* 1.3 86.9 + - + +
55A VAL* 1.3 65.8 + - - +
57A GLU* 3.3 17.9 + - - +
58A ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 55 (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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20A THR* 4.4 10.8 - - + -
28A VAL* 4.0 22.8 - - + +
32A VAL* 4.2 16.2 - - + -
43A ILE* 4.2 10.8 - - + -
45A CYS* 3.9 17.9 - - + -
51A ASN* 3.3 17.5 + - - +
52A GLU* 3.3 10.9 + - - +
54A GLU* 1.3 75.2 - - - +
56A GLY* 1.3 63.2 + - - +
58A ALA* 3.2 4.2 + - - +
59A ILE* 3.0 36.3 + - + +
100A LEU* 3.8 17.5 - - + -
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Residues in contact with GLY 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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52A GLU 2.9 11.1 + - - -
53A HIS 3.6 4.5 - - - -
54A GLU 3.2 0.2 - - - -
55A VAL* 1.3 77.3 - - - +
57A GLU* 1.3 60.4 + - - +
59A ILE* 3.5 3.9 + - - +
60A GLN* 3.0 26.3 + - - +
99A ASP 3.7 9.0 - - - -
100A LEU* 3.3 27.4 - - - +
101A LYS* 3.8 8.1 - - - +
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Residues in contact with GLU 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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29A LYS* 2.9 39.0 + - - +
53A HIS* 3.0 33.4 + - - +
54A GLU* 3.3 16.3 + - - +
56A GLY* 1.3 75.4 - - - +
58A ALA* 1.3 63.7 + - - +
60A GLN* 3.8 5.3 - - - +
61A GLU* 3.1 31.1 + - - +
101A LYS* 3.9 20.4 + - - +
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Residues in contact with ALA 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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29A LYS* 3.4 32.2 - - + +
32A VAL* 3.6 21.1 - - + -
33A LYS* 3.9 13.1 - - + +
54A GLU 3.1 11.2 + - - +
55A VAL 3.2 8.0 + - - +
57A GLU* 1.3 78.2 - - - +
59A ILE* 1.3 62.5 + - - +
61A GLU* 3.4 2.4 + - - +
62A LYS* 3.0 29.2 + - - +
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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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32A VAL* 4.3 12.3 - - + -
36A ILE* 4.5 12.8 - - + -
43A ILE* 5.0 1.6 - - + -
55A VAL* 3.0 36.9 + - + +
56A GLY* 3.9 6.5 - - - +
58A ALA* 1.3 75.9 - - - +
60A GLN* 1.3 65.2 + - - +
62A LYS* 3.2 2.4 + - - +
63A ILE* 3.0 35.6 + - + +
68A VAL* 5.1 0.2 - - - +
73A LEU* 3.7 24.2 - - + -
75A ILE* 3.7 35.7 - - + -
100A LEU* 4.9 4.5 - - + +
102A LEU* 4.3 18.8 - - + -
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Residues in contact with GLN 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 GLY 3.0 17.3 + - - +
57A GLU* 3.8 7.2 + - - +
59A ILE* 1.3 78.6 - - - +
61A GLU* 1.3 65.3 + - + +
63A ILE* 3.4 8.0 + - - +
64A GLN* 3.2 38.8 + - - +
101A LYS* 3.8 37.4 - - + +
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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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29A LYS* 2.8 27.5 + - - -
33A LYS* 2.3 40.2 + - - +
57A GLU* 3.1 22.0 + - - +
58A ALA 3.8 3.4 - - - +
60A GLN* 1.3 79.3 - - + +
62A LYS* 1.3 65.6 + - + +
64A GLN* 3.5 13.4 + - - +
65A GLU* 3.0 34.4 + - - +
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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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33A LYS* 3.7 37.8 - - + +
36A ILE* 4.0 22.7 - - + -
37A ASP* 2.9 34.2 + - - +
58A ALA 3.0 20.5 + - - +
59A ILE 3.8 3.1 - - - +
61A GLU* 1.3 76.1 - - - +
63A ILE* 1.3 59.3 + - - +
65A GLU* 2.9 31.8 + - - +
66A LYS 3.3 2.6 + - - -
67A ALA* 2.9 41.2 + - + +
68A VAL* 3.5 17.6 + - + -
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Residues in contact with ILE 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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59A ILE* 3.0 38.5 + - + +
60A GLN* 3.8 7.0 - - - +
61A GLU 3.3 0.2 - - - -
62A LYS* 1.3 76.8 - - - +
64A GLN* 1.3 60.3 + - + +
66A LYS* 3.0 26.2 + - - +
68A VAL* 3.5 29.4 - - + +
69A LYS* 5.3 1.1 - - - -
70A ARG* 4.1 36.6 - - + +
73A LEU* 4.3 1.6 - - + -
102A LEU* 5.5 1.8 - - + -
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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 GLN* 3.2 34.3 + - - +
61A GLU* 3.6 13.0 - - - +
63A ILE* 1.3 76.1 - - + +
65A GLU* 1.3 60.5 + - + +
66A LYS* 3.1 16.8 + - - +
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Residues in contact with GLU 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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33A LYS* 5.7 2.6 + - - -
61A GLU* 3.0 22.3 + - - +
62A LYS* 2.9 42.5 + - - +
64A GLN* 1.3 77.6 - - + +
66A LYS* 1.3 69.3 + - - +
67A ALA* 4.0 9.1 - - + +
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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
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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