Contacts of the helix formed by residues 45 - 64 (chain A) in PDB entry 5UAK
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 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 5.3 1.7 - - - +
41A PRO 4.3 2.9 + - - -
42A SER* 4.1 8.4 + - - -
43A VAL 3.1 5.3 + - - -
44A ASP* 1.3 79.6 + - - +
46A ALA* 1.3 53.6 - - - +
47A ASP* 4.4 7.9 - - - -
48A ASN* 2.8 29.1 + - - +
49A LEU* 2.8 37.9 + - - +
154A ILE* 5.4 0.7 - - - -
1083A ASN* 4.2 14.1 + - - -
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Residues in contact with ALA 46 (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 SER* 1.3 71.1 - - - +
47A ASP* 1.3 54.7 + - - +
49A LEU* 4.3 7.2 - - - +
50A SER* 2.7 39.6 + - - -
154A ILE* 4.7 9.4 - - + +
158A SER* 3.9 5.6 - - - +
1079A HIS* 3.2 38.1 - - + +
1082A LEU* 3.7 24.2 - - + -
1083A ASN* 4.3 7.0 + - - +
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 3.2 5.8 - - - -
46A ALA* 1.3 77.5 + - - +
48A ASN* 1.3 66.9 + - - +
50A SER* 4.5 2.2 - - - -
51A GLU* 3.4 28.3 + - - +
1076A THR* 5.4 3.8 - - - +
1079A HIS* 3.2 33.4 + - - +
1083A ASN* 5.6 2.4 + - - -
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 3.8 17.6 + - - +
43A VAL* 3.8 14.2 - - - +
45A SER* 2.8 30.9 + - - +
47A ASP* 1.3 76.3 - - - +
49A LEU* 1.3 64.6 + - + +
50A SER 3.4 0.3 + - - -
51A GLU* 3.4 5.5 + - - +
52A LYS* 3.2 34.6 + - + +
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Residues in contact with LEU 49 (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 VAL* 3.4 23.3 - - + +
44A ASP* 5.0 0.9 - - - -
45A SER 2.8 23.9 + - - +
46A ALA* 4.2 4.9 - - - +
48A ASN* 1.3 76.8 - - + +
50A SER* 1.3 62.1 + - - +
52A LYS* 4.2 9.1 + - + +
53A LEU* 3.7 15.4 + - - +
77A PHE* 5.5 5.4 - - + -
150A MET 4.1 0.4 - - - +
151A GLN* 3.2 49.8 - - - +
154A ILE* 3.7 36.1 - - + -
155A ALA* 3.4 29.6 - - + +
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Residues in contact with SER 50 (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 ALA 2.7 24.2 + - - -
47A ASP* 4.5 3.1 - - - -
49A LEU* 1.3 72.7 - - - +
51A GLU* 1.3 53.9 + - - +
52A LYS 3.3 0.2 + - - -
53A LEU* 3.3 3.8 + - - +
54A GLU* 2.8 39.5 + - - +
155A ALA 5.1 5.4 - - - -
158A SER* 2.6 37.9 + - - -
159A LEU* 5.2 6.2 - - - +
162A LYS* 5.2 14.9 - - - -
1079A HIS* 4.4 3.4 - - - -
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Residues in contact with GLU 51 (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 ASP 3.4 19.7 + - - +
48A ASN* 3.4 5.3 + - - +
50A SER* 1.3 79.6 - - - +
52A LYS* 1.3 63.6 + - + +
54A GLU* 3.7 15.1 - - - +
55A ARG* 2.8 54.3 + - - +
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Residues in contact with LYS 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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48A ASN* 3.2 22.9 + - + +
49A LEU* 4.5 9.0 - - + +
50A SER 3.3 0.2 - - - -
51A GLU* 1.3 78.5 - - + +
53A LEU* 1.3 61.7 + - + +
55A ARG* 3.2 19.7 - - - +
56A GLU* 3.1 25.3 - - - +
76A CYS* 4.0 26.7 - - - -
77A PHE* 5.3 10.8 - - + -
151A GLN* 6.2 0.2 - - - +
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Residues in contact with LEU 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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49A LEU 3.7 12.7 + - - +
50A SER 3.3 2.7 + - - +
52A LYS* 1.3 78.2 - - + +
54A GLU* 1.3 57.9 + - - +
56A GLU* 3.8 4.0 - - + +
57A TRP* 2.8 38.1 + - + +
72A ALA 4.9 7.2 - - - +
73A LEU* 4.3 26.0 - - + -
76A CYS* 4.5 12.1 - - + -
77A PHE* 4.0 26.5 - - + -
151A GLN 5.3 0.2 - - - +
155A ALA* 3.3 31.2 - - + -
156A MET* 4.7 5.6 - - + +
159A LEU* 3.8 25.6 - - + -
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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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50A SER* 2.8 22.9 + - - +
51A GLU* 3.7 17.7 + - - +
52A LYS 3.3 0.2 - - - -
53A LEU* 1.3 73.5 - - - +
55A ARG* 1.3 53.8 + - - +
57A TRP* 3.7 4.3 - - - +
58A ASP* 2.8 37.5 + - + +
159A LEU* 4.6 6.9 - - + +
162A LYS* 4.0 22.9 + - - +
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Residues in contact with ARG 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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51A GLU* 2.8 45.3 + - - +
52A LYS* 3.2 20.6 - - - +
54A GLU* 1.3 76.5 - - - +
56A GLU* 1.3 65.2 + - + +
58A ASP* 3.5 7.8 - - - +
59A ARG* 3.0 56.3 + - - +
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Residues in contact with GLU 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 LYS 3.1 20.8 + - - +
53A LEU* 3.8 7.4 - - + +
55A ARG* 1.3 79.6 - - + +
57A TRP* 1.3 58.6 + - - +
59A ARG* 3.3 22.4 + - - +
60A GLU* 2.9 30.2 + - - +
72A ALA* 4.5 17.4 - - + +
75A ARG* 2.9 33.7 + - - +
76A CYS* 3.9 33.6 + - + +
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Residues in contact with TRP 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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53A LEU 2.8 22.4 + - - +
54A GLU* 3.9 4.3 - - - +
56A GLU* 1.3 71.0 - - - +
58A ASP* 1.3 55.4 + - - +
60A GLU* 4.0 15.7 - - + -
61A LEU* 2.8 57.3 + - + +
67A PRO* 3.8 26.2 - - + -
68A LYS 3.8 6.7 - - - -
69A LEU* 3.6 42.4 - - + -
72A ALA* 4.2 11.8 - - + +
159A LEU* 5.3 13.0 - - + -
372A GLN* 5.0 6.3 - - + -
375A LEU* 3.4 38.0 - - + +
376A GLN* 6.1 5.6 - - + -
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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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54A GLU* 2.8 25.3 + - + +
55A ARG* 3.5 9.6 - - - +
56A GLU 3.3 0.2 - - - -
57A TRP* 1.3 74.3 - - - +
59A ARG* 1.3 61.5 + - - +
61A LEU* 3.3 8.2 + - - +
62A ALA* 3.2 24.1 + - - +
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Residues in contact with ARG 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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55A ARG* 3.0 54.5 + - - +
56A GLU* 3.3 35.0 + - - +
58A ASP* 1.3 74.3 - - - +
60A GLU* 1.3 62.1 + - + +
62A ALA* 3.7 4.9 + - - +
63A SER* 3.0 27.0 + - - -
75A ARG* 5.0 12.1 - - - +
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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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56A GLU 2.9 19.7 + - - +
57A TRP* 3.7 15.7 - - + +
59A ARG* 1.3 77.0 - - + +
61A LEU* 1.3 63.9 + - - +
63A SER* 3.1 14.1 + - - -
64A LYS* 3.8 26.0 + - - +
67A PRO* 3.4 33.1 - - + +
68A LYS 3.8 18.1 + - - +
71A ASN* 3.5 24.8 + - - -
72A ALA* 4.1 10.5 - - + +
75A ARG* 5.2 8.2 + - - +
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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 TRP* 2.8 50.2 + - + +
58A ASP* 3.3 8.5 + - - +
60A GLU* 1.3 75.1 - - - +
62A ALA* 1.3 64.3 + - + +
63A SER 3.6 0.2 + - - -
64A LYS 3.8 11.6 - - - +
67A PRO* 4.2 17.7 - - + +
375A LEU* 6.0 0.7 - - + -
376A GLN* 5.7 6.3 - - - +
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Residues in contact with ALA 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* 3.2 16.0 + - - +
59A ARG* 4.3 5.4 - - - +
60A GLU 3.4 0.2 - - - -
61A LEU* 1.3 84.8 - - + +
63A SER* 1.3 63.7 + - - +
64A LYS 4.6 0.6 - - - +
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Residues in contact with SER 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 ARG 3.0 18.2 + - - -
60A GLU* 3.1 10.9 + - - -
62A ALA* 1.3 80.3 - - - +
64A LYS* 1.3 85.1 + - - +
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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 GLU* 3.8 29.8 + - - +
61A LEU 3.8 13.2 - - - +
62A ALA 4.6 0.3 - - - +
63A SER* 1.3 100.6 + - - +
65A LYS* 1.3 64.1 + - - +
66A ASN 4.2 16.6 - - - +
67A PRO* 4.5 3.9 - - + +
71A ASN* 4.9 7.9 - - - +
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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
------------------------------------------------------------
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