Contacts of the helix formed by residues 67 - 86 (chain A) in PDB entry 5U5S
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 ASP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLN* 4.6 9.9 - - + -
7A LEU* 3.4 17.9 - - - +
65A TYR 3.6 0.2 - - - -
66A ARG* 1.3 87.9 - - + +
68A ALA* 1.3 63.2 + - - +
69A GLN* 2.9 16.3 + - + +
70A GLU* 2.7 53.4 + - - +
71A PHE 3.3 7.4 + - - -
112A ASP* 5.6 2.9 - - - +
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Residues in contact with ALA 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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6A GLN* 3.4 13.8 - - + +
7A LEU* 4.1 0.2 - - - +
10A CYS* 3.2 28.9 - - - -
13A ILE* 6.6 0.2 - - + -
67A ASP* 1.3 73.4 - - - +
69A GLN* 1.3 60.7 + - - +
71A PHE* 3.4 2.8 - - - +
72A ALA* 2.7 29.1 + - - +
107A TYR* 3.4 10.7 - - + -
110A MET* 3.3 35.4 - - + -
112A ASP* 5.2 0.8 + - - +
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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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67A ASP* 2.9 16.4 + - + +
68A ALA* 1.3 77.6 - - - +
70A GLU* 1.3 53.6 + - + +
72A ALA* 3.3 3.3 + - - +
73A ALA* 2.7 35.8 + - + +
76A ARG* 3.7 27.7 - - - +
107A TYR* 3.0 25.7 + - - +
112A ASP* 5.6 3.6 + - - +
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Residues in contact with GLU 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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64A ASP 4.3 5.6 - - - +
65A TYR* 3.8 15.2 - - + -
66A ARG* 2.8 42.7 + - - +
67A ASP* 2.7 29.1 + - - +
69A GLN* 1.3 69.6 - - + +
71A PHE* 1.3 64.9 + - - +
73A ALA* 3.3 8.1 - - - +
74A ASP* 3.0 30.8 + - - +
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Residues in contact with PHE 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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10A CYS* 3.3 55.2 - - + -
13A ILE* 4.2 24.2 - - + -
14A LEU* 3.8 31.6 - - + -
17A LEU* 5.3 0.7 - - + -
56A VAL* 3.7 17.3 - - + -
60A MET* 4.5 1.8 - - + -
65A TYR* 3.4 21.6 - + + -
67A ASP 3.3 3.8 + - - +
68A ALA* 3.4 6.5 - - - +
69A GLN 3.2 0.4 - - - -
70A GLU* 1.3 77.1 - - - +
72A ALA* 1.3 72.8 + - + +
74A ASP* 2.9 4.0 + - - +
75A VAL* 2.8 54.7 + - + +
103A PHE* 3.8 14.1 - + - -
107A TYR* 4.8 4.3 - + - -
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Residues in contact with ALA 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 ALA 2.7 20.6 + - - +
69A GLN* 3.3 7.4 + - - +
71A PHE* 1.3 74.3 - - - +
73A ALA* 1.3 57.4 + - - +
75A VAL* 3.2 10.8 - - - +
76A ARG* 2.9 58.5 + - - +
103A PHE* 4.1 4.4 - - + -
107A TYR* 3.6 25.6 - - + -
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Residues in contact with ALA 73 (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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69A GLN* 2.7 23.1 + - + +
70A GLU* 3.3 11.9 - - - +
72A ALA* 1.3 73.3 - - - +
74A ASP* 1.3 59.9 + - - +
76A ARG* 3.2 16.7 - - - +
77A LEU* 3.0 33.7 + - + +
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Residues in contact with ASP 74 (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 MET* 3.6 23.4 - - - +
56A VAL* 4.2 7.2 - - + -
59A LYS* 3.1 28.9 + - - -
65A TYR* 3.3 29.9 + - + +
70A GLU* 3.0 21.0 + - - +
71A PHE 2.9 4.9 + - - +
73A ALA* 1.3 77.3 - - - +
75A VAL* 1.3 64.9 + - - +
77A LEU* 3.2 15.5 + - - +
78A MET 3.1 15.9 + - - -
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Residues in contact with VAL 75 (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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17A LEU* 4.5 3.8 - - + -
53A LEU* 4.0 23.3 - - + -
56A VAL* 4.3 10.0 - - + +
71A PHE* 2.8 40.8 + - + +
72A ALA* 3.2 14.8 - - - +
74A ASP* 1.3 73.1 - - - +
76A ARG* 1.3 61.2 + - - +
78A MET* 3.1 20.8 + - + +
79A PHE* 3.3 28.8 + - + -
103A PHE* 3.3 32.5 - - + -
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Residues in contact with ARG 76 (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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69A GLN* 3.7 22.4 - - - +
72A ALA* 2.9 43.5 + - - +
73A ALA* 3.2 13.8 - - - +
75A VAL* 1.3 76.1 - - - +
77A LEU* 1.3 56.9 + - + +
79A PHE* 3.2 13.8 + - + +
80A SER* 2.6 42.0 + - - +
103A PHE* 4.3 16.2 - - + -
107A TYR* 5.3 8.7 - - - -
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Residues in contact with LEU 77 (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 HIS* 3.7 51.1 - - + +
51A MET* 5.0 6.1 - - + -
73A ALA* 3.0 21.3 + - + +
74A ASP* 3.3 15.7 - - - +
76A ARG* 1.3 78.8 - - + +
78A MET* 1.3 56.9 + - - +
80A SER* 3.8 12.3 - - - -
81A ASN* 2.9 32.9 + - + +
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Residues in contact with MET 78 (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 PHE* 3.4 46.4 - - + -
51A MET* 3.1 30.7 - - + +
52A ASP* 4.0 8.3 - - - +
53A LEU* 3.7 26.2 - - + -
56A VAL* 5.4 0.2 - - + -
74A ASP 3.1 10.2 + - - +
75A VAL* 3.1 17.2 + - + +
77A LEU* 1.3 74.4 - - - +
79A PHE* 1.3 99.2 + - + +
81A ASN* 2.8 24.4 + - - +
82A CYS* 3.0 17.2 - - - -
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Residues in contact with PHE 79 (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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17A LEU* 4.9 3.4 - - + -
29A PHE* 4.2 9.0 - + - -
75A VAL* 3.3 27.8 + - + -
76A ARG* 3.2 14.4 + - + +
78A MET* 1.3 103.1 - - + +
80A SER* 1.3 62.1 + - - +
82A CYS* 3.3 9.0 - - - +
83A TYR* 3.2 34.8 + - + -
96A ALA* 3.9 25.4 - - + -
99A LEU* 3.7 41.7 - - + -
100A GLN* 4.4 13.9 - - + +
103A PHE* 3.6 31.4 - + + -
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Residues in contact with SER 80 (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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76A ARG* 2.6 29.6 + - - +
77A LEU* 3.4 17.7 - - - -
78A MET 3.1 0.2 - - - -
79A PHE* 1.3 77.4 - - - +
81A ASN* 1.3 63.3 + - - +
83A TYR* 3.1 13.7 + - - +
84A LYS* 3.1 25.0 + - - +
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Residues in contact with ASN 81 (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 TYR* 4.5 4.5 + - - -
47A ILE* 3.1 44.1 - - + +
49A HIS* 3.3 25.5 + - + +
51A MET 3.6 12.9 + - - +
77A LEU* 2.9 21.7 + - + +
78A MET* 2.8 29.6 + - - +
80A SER* 1.3 75.5 - - - +
82A CYS* 1.3 62.9 + - - +
84A LYS* 3.2 19.2 + - + +
85A TYR* 3.2 4.2 + - - +
287B ALY 3.7 17.3 - - - +
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Residues in contact with CYS 82 (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 PHE* 3.8 29.8 - - - -
78A MET* 3.0 25.8 - - - -
79A PHE* 3.3 10.5 - - - +
81A ASN* 1.3 78.8 + - - +
83A TYR* 1.3 58.4 + - + +
85A TYR 3.3 0.5 + - - -
86A ASN* 3.0 38.5 + - - +
92A VAL* 4.6 6.5 - - + +
93A VAL* 4.4 1.1 - - - +
96A ALA* 4.4 12.6 - - + -
287B ALY 3.4 32.5 - - + -
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Residues in contact with TYR 83 (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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79A PHE* 3.2 20.4 + - + -
80A SER* 3.1 11.0 + - - +
82A CYS* 1.3 74.3 - - - +
84A LYS* 1.3 66.2 + - - +
86A ASN 3.5 14.4 - - - +
93A VAL* 3.6 36.1 - - + -
96A ALA* 3.5 12.6 - - + -
97A ARG* 3.1 32.5 + - + +
100A GLN* 3.0 31.4 + - - -
281B HIS 4.7 3.3 + - - -
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Residues in contact with LYS 84 (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* 3.1 37.7 + - + +
47A ILE* 4.6 2.0 - - + +
48A LYS* 4.7 17.0 - - - +
80A SER* 3.1 19.7 + - - +
81A ASN* 3.2 15.9 + - - +
83A TYR* 1.3 78.2 - - - +
85A TYR* 1.3 61.4 + - - +
281B HIS* 3.4 43.8 + - + +
284B LEU* 5.8 0.3 - - - +
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Residues in contact with TYR 85 (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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40A LEU* 3.2 38.6 - - + +
42A ASP* 4.6 6.6 - - + -
43A TYR* 4.4 25.5 + + - -
46A ILE* 3.9 26.7 - - + -
47A ILE* 3.9 7.4 - - + -
81A ASN 3.2 7.2 + - - +
84A LYS* 1.3 81.9 - - - +
86A ASN* 1.3 81.3 + - - +
87A PRO* 3.6 7.3 - - - +
281B HIS* 4.1 6.6 + - - +
283B LEU 4.8 3.8 - - - +
284B LEU* 5.8 4.4 - - + +
285B ARG* 3.1 35.8 + - + +
287B ALY 3.3 50.9 - - + +
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Residues in contact with ASN 86 (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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82A CYS 3.0 10.9 + - - +
83A TYR* 3.5 15.3 - - - +
85A TYR* 1.3 82.8 - - - +
87A PRO* 1.3 70.9 - - + +
88A PRO* 3.9 0.7 - - - +
90A HIS* 3.6 13.7 + - + -
92A VAL* 3.3 21.1 - - + +
93A VAL* 3.2 27.1 - - + +
281B HIS 5.1 1.1 - - - -
287B ALY 2.9 65.5 + - - +
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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