Contacts of the helix formed by residues 57 - 72 (chain A) in PDB entry 1U5T
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLU* 2.1 39.3 + - - -
54A LEU* 3.7 1.8 + - - -
56A ALA* 1.3 77.7 - - - +
58A PRO* 1.3 70.2 - - - -
59A GLU* 3.4 5.6 - - - -
60A PHE* 2.7 16.7 + - - -
61A ARG* 3.1 18.8 + - - +
128A ASN* 4.9 0.2 - - - +
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Residues in contact with PRO 58 (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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57A SER* 1.3 77.8 - - - +
59A GLU* 1.3 71.8 - - - +
61A ARG* 2.7 57.6 + - + +
62A SER* 2.8 16.1 + - - -
128A ASN* 3.5 26.9 - - - +
129A VAL 4.2 3.8 - - - -
130A GLY* 4.1 17.7 - - - +
133A ASP* 3.8 12.5 - - - +
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Residues in contact with GLU 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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57A SER* 2.9 3.9 + - - -
58A PRO* 1.3 91.4 - - - +
60A PHE* 1.3 65.4 + - - +
62A SER* 3.3 5.5 + - - -
63A LYS* 3.0 23.8 + - - +
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Residues in contact with PHE 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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46A PHE* 3.2 29.6 - + - -
47A ALA* 6.2 0.2 - - - -
50A HIS* 3.0 51.6 - + + -
53A GLU* 2.6 37.2 - - + +
54A LEU* 3.5 17.9 - - + -
57A SER* 2.7 14.3 + - - +
59A GLU* 1.3 75.0 - - - +
61A ARG* 1.3 69.1 + - - +
63A LYS* 3.2 28.9 - - + +
64A PHE* 2.9 23.6 + + + +
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Residues in contact with ARG 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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54A LEU* 3.1 31.8 + - + +
55A GLN* 3.4 18.6 + - - +
56A ALA* 3.9 1.4 - - - +
57A SER 3.1 23.8 + - - +
58A PRO* 2.7 45.8 + - + +
60A PHE* 1.3 79.5 - - - +
62A SER* 1.3 63.5 + - - +
64A PHE* 2.7 14.4 + - - +
65A MET* 3.4 17.5 + - + +
88A VAL* 5.3 3.1 - - + -
91A PHE* 2.7 37.3 - - - -
92A TYR* 3.2 27.6 - - + +
128A ASN* 3.7 7.5 + - - +
133A ASP* 2.6 31.5 + - - +
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Residues in contact with SER 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 PRO 2.8 12.0 + - - -
59A GLU* 3.7 9.4 - - - -
61A ARG* 1.3 70.8 - - - +
63A LYS* 1.3 67.8 + - - +
65A MET* 2.8 20.5 + - - +
66A HIS* 2.8 41.3 + - - -
92A TYR* 5.3 0.2 + - - -
132A ASP* 4.2 27.5 + - - -
133A ASP* 5.1 1.0 + - - -
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Residues in contact with LYS 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 PHE* 4.4 15.9 - - - -
59A GLU 3.0 11.8 + - - +
60A PHE* 3.2 43.5 - - + +
61A ARG 3.0 1.4 + - - -
62A SER* 1.3 77.0 + - - +
64A PHE* 1.3 67.5 + - - +
65A MET 2.6 14.0 + - - -
66A HIS* 3.1 15.2 + - - +
67A MET* 3.7 21.1 + - - +
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Residues in contact with PHE 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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43A LEU* 3.4 37.7 - - + -
46A PHE* 4.8 14.4 - + + -
47A ALA* 4.0 17.9 - - + -
54A LEU* 3.8 19.3 - - + -
60A PHE* 3.3 18.2 - + + +
61A ARG 2.7 10.3 + - - +
63A LYS* 1.3 77.9 - - + +
65A MET* 1.3 61.1 + - + -
67A MET* 4.2 10.4 - - - +
68A CYS* 2.8 21.5 + - - -
75A PRO* 4.3 5.2 - - + -
78A LEU* 3.5 26.7 - - + -
79A PHE* 3.2 40.4 - + - -
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Residues in contact with MET 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 ARG* 4.1 20.9 - - + +
62A SER* 2.8 11.1 + - - +
63A LYS 2.6 6.5 + - - -
64A PHE* 1.3 79.2 - - + +
66A HIS* 1.3 54.6 + - + +
67A MET 2.4 18.7 + - - -
68A CYS* 2.8 16.3 + - - +
69A SER* 2.9 15.0 + - - -
75A PRO* 3.5 30.7 - - + +
76A LEU* 5.3 0.9 - - + +
79A PHE* 3.8 25.4 - - + -
92A TYR* 3.4 42.2 - - + +
136A LYS* 5.0 12.6 - - + +
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Residues in contact with HIS 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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62A SER* 2.8 46.5 + - - +
63A LYS* 3.1 7.8 + - - +
65A MET* 1.3 75.7 - - + +
67A MET* 1.3 51.5 + - - +
69A SER* 3.4 13.7 + - - -
70A SER* 2.6 24.6 + - - -
132A ASP* 3.9 16.6 + - - +
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Residues in contact with MET 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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39A PHE* 5.0 10.5 - - + -
43A LEU* 3.9 27.8 - - + -
46A PHE* 4.0 29.8 - - + -
63A LYS* 3.8 23.6 - - - +
64A PHE* 4.2 11.0 - - - +
65A MET 2.4 14.6 + - - -
66A HIS* 1.3 68.2 - - - +
68A CYS* 1.3 57.1 + - - +
69A SER 2.9 3.4 - - - -
70A SER* 2.6 32.0 + - - -
71A ILE* 3.1 18.8 + - + +
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Residues in contact with CYS 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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43A LEU* 4.3 6.1 - - - -
64A PHE* 2.8 56.8 - - - -
65A MET* 2.8 9.6 + - - +
67A MET* 1.3 76.4 - - - +
69A SER* 1.3 49.4 + - - +
71A ILE* 3.7 9.7 - - - +
72A GLY 2.6 13.6 + - - -
73A ILE* 2.6 57.4 + - + +
75A PRO* 4.2 9.2 - - + -
78A LEU* 3.6 12.6 - - + -
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Residues in contact with SER 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 MET 2.9 9.4 + - - -
66A HIS* 3.4 24.2 + - - -
67A MET 2.7 1.4 + - - -
68A CYS* 1.3 76.8 - - - +
70A SER* 1.3 69.1 + - - +
72A GLY* 3.1 13.7 + - - +
73A ILE 4.6 2.7 - - - +
75A PRO* 5.5 0.8 - - - +
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Residues in contact with SER 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 HIS 2.6 28.1 + - - -
67A MET* 2.6 15.1 + - - -
69A SER* 1.3 73.1 + - - +
71A ILE* 1.3 67.9 + - - +
72A GLY* 4.3 0.2 - - - -
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Residues in contact with ILE 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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36A LEU* 4.1 35.1 - - + +
39A PHE* 3.7 34.5 - - + -
40A GLN* 5.3 0.2 - - - +
43A LEU* 3.5 33.4 - - + -
67A MET* 3.9 15.3 - - + +
68A CYS* 3.8 4.3 - - - +
70A SER* 1.3 79.7 - - - +
72A GLY* 1.3 60.7 + - - +
73A ILE* 3.3 30.3 - - + -
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Residues in contact with GLY 72 (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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68A CYS 2.6 13.3 + - - -
69A SER* 3.4 12.1 - - - -
70A SER 3.1 1.8 - - - -
71A ILE* 1.3 76.6 - - - +
73A ILE* 1.3 66.4 + - - +
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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