Contacts of the helix formed by residues 45 - 64 (chain C) in PDB entry 2UYK
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 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO 3.5 0.4 - - - -
44C ALA* 1.3 79.1 - - - +
46C VAL* 1.3 66.6 + - - +
47C GLN* 2.9 35.7 + - - +
48C ASP* 3.1 25.1 + - - +
49C GLN* 3.0 27.0 + - - +
86C THR* 5.2 0.5 - - - +
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ALA 3.9 2.0 + - - -
45C ASP* 1.3 78.9 + - - +
47C GLN* 1.3 60.4 + - - +
49C GLN* 4.1 8.1 - - + -
50C ALA* 2.8 29.8 + - - +
83C ASP* 3.8 41.1 - - + +
86C THR* 3.7 24.2 - - + -
87C ILE* 4.0 16.2 - - + -
118C LYS* 3.7 30.7 - - + +
119C LEU* 5.1 2.0 - - + -
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Residues in contact with GLN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASP* 2.9 17.2 + - - +
46C VAL* 1.3 80.8 - - - +
48C ASP* 1.3 61.5 + - - +
50C ALA 3.5 0.2 + - - -
51C ARG* 3.1 26.9 + - - +
86C THR* 3.9 21.5 - - + -
90C VAL* 3.7 20.0 - - + +
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Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO* 3.7 23.4 - - + +
44C ALA 5.6 0.2 + - - -
45C ASP* 3.1 24.8 + - - +
47C GLN* 1.3 79.2 - - - +
49C GLN* 1.3 65.1 + - - +
51C ARG* 3.4 6.2 + - - +
52C LEU* 3.0 25.5 + - - +
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Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C PRO* 3.3 31.2 - - + +
42C ILE* 3.7 11.0 - - - +
43C PRO* 2.9 34.0 + - + +
44C ALA* 4.0 2.6 + - - +
45C ASP 3.0 12.0 + - - +
46C VAL* 3.3 9.2 + - - +
48C ASP* 1.3 77.4 - - - +
50C ALA* 1.3 56.6 + - - +
52C LEU 3.3 0.5 + - - -
53C SER* 2.9 34.3 + - - -
116C ASP 5.6 0.6 + - - -
117C VAL* 3.9 2.0 - - - +
118C LYS* 2.8 58.8 + - - +
119C LEU* 3.8 8.0 - - + +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL 2.8 20.8 + - - +
47C GLN 3.7 4.3 - - - +
49C GLN* 1.3 73.0 - - - +
51C ARG* 1.3 64.4 + - - +
53C SER* 3.4 1.7 + - - -
54C LEU* 3.1 29.6 + - + +
87C ILE* 4.3 20.4 - - + +
90C VAL* 3.9 20.9 - - + -
119C LEU* 3.8 24.2 - - + +
121C ILE* 4.7 0.5 - - - +
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Residues in contact with ARG 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLN 3.1 18.2 + - - +
48C ASP* 3.8 7.0 - - - +
49C GLN 3.3 0.2 - - - -
50C ALA* 1.3 76.7 - - - +
52C LEU* 1.3 56.1 + - - +
54C LEU* 3.2 5.6 + - - +
55C GLU* 2.8 59.3 + - + +
90C VAL* 3.5 17.7 + - + +
93C GLN* 5.0 1.4 - - - +
94C PHE* 4.1 27.7 - - - +
97C GLU* 2.9 37.4 + - - -
98C HIS* 4.9 5.1 - - - -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PRO* 3.5 31.2 - - + -
35C VAL 4.1 4.9 - - - +
36C OCS 3.7 32.8 - - + +
37C PRO* 4.2 3.8 - - + -
43C PRO* 3.5 25.4 - - + -
48C ASP 3.0 17.7 + - - +
49C GLN 3.3 3.1 + - - +
51C ARG* 1.3 73.9 - - - +
53C SER* 1.3 66.0 + - - +
55C GLU* 3.2 10.4 + - + +
56C ASN* 2.9 42.4 + - - +
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Residues in contact with SER 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN* 3.8 16.4 + - - +
33C ILE 3.7 6.0 - - - -
34C PRO* 3.3 25.7 - - - +
49C GLN 2.9 20.6 + - - -
50C ALA 3.9 3.6 - - - -
52C LEU* 1.3 76.7 - - - +
54C LEU* 1.3 62.8 + - - +
56C ASN* 3.3 7.0 + - - +
57C VAL* 3.0 27.5 + - - +
119C LEU* 3.5 9.2 - - - +
121C ILE* 4.0 17.9 - - - -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA* 3.1 21.2 + - + +
51C ARG* 3.5 7.0 - - - +
53C SER* 1.3 76.4 - - - +
55C GLU* 1.3 57.0 + - - +
57C VAL* 3.2 6.5 + - + +
58C LYS* 2.9 28.9 + - - +
74C MET* 4.3 18.4 - - + -
87C ILE* 6.5 0.2 - - + -
90C VAL* 4.2 7.6 - - + -
91C TYR* 3.7 46.4 - - + +
94C PHE* 3.7 45.8 - - + -
95C PHE* 4.6 0.4 - - + -
121C ILE* 3.7 22.0 - - + -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG 4.6 1.9 - - - +
51C ARG* 2.8 65.8 + - + +
52C LEU* 3.2 14.6 + - + +
54C LEU* 1.3 71.9 - - - +
56C ASN* 1.3 59.2 + - - +
58C LYS* 3.3 23.2 + - - +
59C ALA* 2.8 29.6 + - - +
94C PHE* 4.1 8.9 - - - -
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Residues in contact with ASN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG 3.8 9.9 - - - +
10C ALA* 3.7 4.7 - - - +
11C PRO* 3.4 24.0 - - + +
32C GLN* 3.6 20.4 + - + +
33C ILE 2.9 26.5 + - - -
35C VAL 3.1 19.0 + - - +
37C PRO* 3.9 10.7 - - - +
52C LEU* 2.9 23.5 + - - +
53C SER 3.5 5.6 - - - +
55C GLU* 1.3 75.1 - - - +
57C VAL* 1.3 65.8 + - - +
59C ALA* 3.4 10.5 + - - +
60C ILE* 3.4 19.4 + - - +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 4.5 6.7 - - + +
32C GLN* 3.7 11.9 - - + -
53C SER 3.0 18.0 + - - +
54C LEU* 3.5 10.1 - - + +
56C ASN* 1.3 75.0 - - - +
58C LYS* 1.3 65.3 + - - +
60C ILE* 3.1 16.0 + - - +
61C VAL* 3.1 22.1 + - + +
71C ILE* 4.2 7.0 - - + -
74C MET* 4.0 11.0 - - + -
94C PHE* 6.2 0.7 - - + -
121C ILE* 3.6 38.6 - - + +
123C ALA* 3.7 25.6 - - + -
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Residues in contact with LYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU 2.9 16.7 + - - +
55C GLU* 3.5 24.7 + - - +
57C VAL* 1.3 79.3 - - - +
59C ALA* 1.3 57.5 + - - +
61C VAL* 3.2 6.4 + - - +
62C VAL* 2.8 47.7 + - + +
68C VAL* 3.8 16.2 - - + -
71C ILE* 5.5 1.6 - - - -
94C PHE* 3.9 11.4 - - + -
98C HIS* 2.8 41.9 + - + +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 3.9 5.5 + - + +
9C ARG* 3.2 51.4 - - + +
10C ALA* 3.9 2.7 - - + +
55C GLU 2.8 17.4 + - - +
56C ASN 3.6 6.3 - - - +
57C VAL 3.2 0.2 - - - -
58C LYS* 1.3 74.7 - - - +
60C ILE* 1.3 56.8 + - - +
62C VAL* 4.0 4.8 - - - +
63C ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.5 18.8 - - + +
7C THR* 4.2 6.1 - - + -
10C ALA* 4.0 13.2 - - + -
19C GLN* 3.5 38.8 - - + +
20C GLY* 3.9 15.3 - - - -
29C THR* 3.9 17.5 - - + -
32C GLN* 3.3 41.5 - - + +
56C ASN 3.5 10.3 - - - +
57C VAL 3.1 6.7 + - - +
59C ALA* 1.3 73.6 - - - +
61C VAL* 1.3 66.6 + - - +
63C ALA* 3.3 4.9 + - - -
64C ALA* 3.1 19.4 + - - +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 5.1 5.4 - - + -
29C THR* 4.1 18.4 - - + -
57C VAL* 3.1 22.9 + - + +
58C LYS* 3.7 8.7 - - - +
60C ILE* 1.3 77.8 - - - +
62C VAL* 1.3 61.1 + - + +
64C ALA* 3.1 16.9 + - - +
65C GLY 3.5 0.2 + - - -
66C LEU* 3.1 32.3 + - + +
67C SER 3.5 28.0 - - - +
68C VAL* 4.7 1.6 - - + +
71C ILE* 4.2 15.9 - - + -
123C ALA* 5.0 1.6 - - + -
125C ALA* 4.3 17.5 - - + -
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LYS* 2.8 49.5 + - + +
59C ALA* 4.1 4.7 - - - +
61C VAL* 1.3 69.5 - - + +
63C ALA* 1.3 60.7 + - - +
65C GLY* 2.9 20.3 + - - -
66C LEU 3.3 17.3 - - - +
67C SER* 4.9 6.3 - - - -
68C VAL 5.2 1.8 - - - +
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.5 19.4 - - + +
6C GLU 4.7 3.8 - - - +
7C THR* 3.8 20.0 - - - +
59C ALA 2.9 20.7 + - - +
60C ILE 3.3 6.3 + - - +
62C VAL* 1.3 76.0 - - - +
64C ALA* 1.4 59.4 + - - +
65C GLY 3.2 0.7 + - - -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.5 32.0 - - + +
22C ASP* 3.9 9.0 - - - +
27C VAL* 3.9 22.0 - - + -
60C ILE 3.1 4.9 + - - +
61C VAL 3.1 12.1 + - - +
63C ALA* 1.4 74.3 - - - +
65C GLY* 1.3 56.6 + - - +
66C LEU* 4.7 1.6 - - + +
127C ARG* 2.7 28.0 + - - +
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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