Contacts of the helix formed by residues 55 - 71 (chain A) in PDB entry 4B23
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 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 1.3 73.3 - - - +
56A ASP* 1.3 65.6 + - - +
57A ALA* 3.9 6.7 + - - +
58A ALA* 3.3 15.4 + - - +
59A THR* 2.9 24.1 + - - -
17Y G 3.1 24.7 + - - +
18Y G 3.9 14.6 + - - -
19Y T 6.0 0.3 - - - -
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Residues in contact with ASP 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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51A SER* 5.7 4.6 - - - -
54A LEU 4.9 1.9 - - - +
55A SER* 1.3 73.3 - - - +
57A ALA* 1.3 57.9 + - - +
59A THR* 3.3 6.8 + - - -
60A ASN* 2.8 43.6 + - - +
150A PHE* 6.1 1.2 - - - -
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Residues in contact with ALA 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 SER* 3.2 7.0 + - - +
56A ASP* 1.3 79.1 - - - +
58A ALA* 1.3 63.0 + - - +
60A ASN* 3.1 12.4 + - - +
61A SER* 3.0 22.9 + - - -
18Y G 3.4 26.7 - - - +
19Y T 4.0 19.1 - - - +
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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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54A LEU* 4.3 6.1 - - + -
55A SER* 3.3 17.2 + - - +
57A ALA* 1.3 78.3 - - - +
59A THR* 1.3 61.6 + - - +
61A SER* 2.7 22.2 + - - -
62A ILE* 3.2 15.1 + - - +
17Y G 3.3 41.9 - - + +
18Y G 3.5 16.5 + - - +
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Residues in contact with THR 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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47A ARG* 4.5 4.3 - - - +
50A THR* 3.8 25.5 + - + -
51A SER* 3.4 33.3 - - - +
54A LEU* 3.5 11.3 + - - +
55A SER 2.9 19.8 + - - -
56A ASP* 3.5 7.4 - - - -
58A ALA* 1.3 76.3 - - - +
60A ASN* 1.3 63.3 + - - +
62A ILE* 3.3 6.5 + - - +
63A ILE* 3.0 30.2 + - + +
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Residues in contact with ASN 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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47A ARG* 5.8 1.6 + - - -
56A ASP* 2.8 39.4 + - - +
57A ALA* 3.1 9.5 + - - +
59A THR* 1.3 75.3 - - - +
61A SER* 1.3 60.7 + - - +
63A ILE* 3.9 4.5 - - - +
64A ASN* 2.9 44.7 + - - +
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Residues in contact with SER 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 ALA 3.0 7.2 + - - -
58A ALA* 2.7 20.1 + - - -
60A ASN* 1.3 76.1 - - - +
62A ILE* 1.3 65.3 + - - +
64A ASN* 3.5 10.7 + - - +
65A LYS* 3.2 41.6 + - - +
17Y G 4.2 5.0 + - - -
18Y G 3.4 32.0 + - - -
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Residues in contact with ILE 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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50A THR* 4.2 7.9 - - + -
54A LEU* 3.6 30.5 - - + -
58A ALA 3.2 11.6 + - - +
59A THR 3.7 6.5 - - - +
60A ASN 3.2 0.6 - - - -
61A SER* 1.3 77.4 + - - +
63A ILE* 1.3 61.3 + - - +
65A LYS* 3.2 6.3 + - - +
66A PHE* 2.9 25.5 + - - +
93A CYS* 3.8 22.4 - - - +
94A GLY* 3.4 21.3 - - - +
95A PHE* 3.9 40.4 - - + +
16Y T 4.8 0.9 - - - +
17Y G 4.2 16.8 - - - -
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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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46A ILE* 5.1 2.0 - - + -
47A ARG* 4.0 36.3 - - + +
50A THR* 3.8 26.5 - - + +
59A THR* 3.0 27.7 + - + +
60A ASN* 4.0 5.6 - - - +
62A ILE* 1.3 75.0 - - - +
64A ASN* 1.3 56.5 + - - +
66A PHE* 3.1 10.8 + - + +
67A CYS* 2.7 51.1 + - - +
76A PHE* 4.4 13.5 - - + -
95A PHE* 4.3 12.1 - - + -
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Residues in contact with ASN 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 ASN* 2.9 34.4 + - - +
61A SER* 3.6 9.8 - - - +
63A ILE* 1.3 78.6 - - - +
65A LYS* 1.3 58.5 + - + +
67A CYS* 3.3 5.2 + - - +
68A THR* 2.8 37.4 + - - +
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Residues in contact with LYS 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 SER* 3.2 30.1 + - - +
62A ILE* 3.5 6.6 - - - +
64A ASN* 1.3 79.0 - - + +
66A PHE* 1.3 65.0 + - - +
68A THR* 3.1 7.1 + - - -
69A GLN* 2.9 28.2 + - - +
92A GLU 4.8 3.6 - - - +
93A CYS* 3.4 34.4 + - + +
17Y G 6.2 2.0 - - - -
18Y G 4.6 8.9 + - - -
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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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46A ILE* 4.6 3.6 - - + -
62A ILE 2.9 14.2 + - - +
63A ILE* 3.2 15.5 - - + +
65A LYS* 1.3 76.6 - - - +
67A CYS* 1.3 56.2 + - - +
70A CYS* 3.0 53.6 + - + +
76A PHE* 3.7 31.9 - + - -
77A PRO* 3.7 25.4 - - + +
82A ILE* 3.8 26.5 - - + -
90A LEU* 3.4 26.5 - - + -
93A CYS* 4.0 9.8 - - - -
95A PHE* 3.6 31.9 - + + -
103A ILE* 4.9 4.7 - - + -
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Residues in contact with CYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 5.1 3.4 - - - -
63A ILE* 2.7 32.7 + - - +
64A ASN* 3.8 4.3 - - - +
66A PHE* 1.3 72.0 - - - +
68A THR* 1.3 65.7 + - - +
71A SER* 3.0 26.7 + - - +
74A ASP* 3.7 18.7 - - - +
75A GLU 3.7 20.6 - - - +
76A PHE* 3.8 32.3 - - - -
77A PRO* 3.9 5.8 - - - -
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Residues in contact with THR 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 ASN* 2.8 28.7 + - - +
65A LYS* 3.6 7.9 - - - -
67A CYS* 1.3 75.2 - - - +
69A GLN* 1.3 62.0 + - + +
71A SER 3.7 8.3 - - - +
74A ASP* 4.2 24.7 + - - +
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Residues in contact with GLN 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 LYS* 2.9 16.0 + - + +
66A PHE 4.6 0.2 - - - +
68A THR* 1.3 79.2 + - + +
70A CYS* 1.3 75.0 - - - +
71A SER 3.2 8.0 + - - +
89A THR* 5.4 11.8 - - + +
93A CYS* 5.1 8.1 - - - -
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Residues in contact with CYS 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 PHE* 3.0 41.0 + - + +
69A GLN* 1.3 83.7 - - - +
71A SER* 1.3 56.7 + - - +
77A PRO* 3.6 17.2 - - + +
81A GLN* 3.6 28.6 + - + +
82A ILE* 5.9 0.9 - - + -
85A THR* 4.5 21.1 - - - +
89A THR* 5.5 2.0 - - - -
90A LEU* 4.3 11.2 - - - -
93A CYS* 4.5 11.9 - - - -
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Residues in contact with SER 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 CYS 3.0 16.4 + - - +
68A THR 3.7 16.3 - - - +
69A GLN 3.2 5.4 - - - +
70A CYS* 1.3 80.7 - - - +
72A ASP* 1.3 59.1 + - - +
73A ASN* 2.6 32.4 + - - -
74A ASP 4.1 1.8 + - - -
75A GLU* 2.8 30.2 + - - +
76A PHE 4.5 1.6 + - - -
77A PRO* 4.2 9.9 - - - -
81A GLN* 4.1 7.5 + - - +
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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