Contacts of the helix formed by residues 49 - 61 (chain C) in PDB entry 4I6U
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 THR 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASN* 3.3 42.4 + - - +
48B LEU 3.5 5.6 - - - -
49B THR* 4.0 13.2 - - + +
50B ILE* 5.4 0.7 - - - -
48C LEU* 1.3 78.9 - - - +
50C ILE* 1.3 60.2 + - - +
51C LYS* 4.1 0.3 - - - +
52C SER* 3.0 29.1 + - - +
53C LEU* 3.0 26.7 + - - +
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Residues in contact with ILE 50 (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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3B SER* 5.0 0.2 - - - +
5B LEU* 3.6 22.8 - - + +
6B LEU* 3.9 35.4 - - + +
9B VAL* 4.5 17.0 - - + -
47B ASN* 3.7 0.9 + - - +
48B LEU* 3.0 40.4 + - + +
50B ILE* 3.7 30.1 - - + +
53B LEU* 4.6 11.2 - - + -
49C THR* 1.3 73.2 - - - +
51C LYS* 1.3 57.2 + - - +
53C LEU* 3.2 12.7 + - + +
54C GLU* 2.9 26.2 + - - +
68C PHE* 6.1 1.6 - - + -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 3.9 34.1 - - - +
6B LEU* 3.6 21.6 - - + +
46B ARG 5.6 0.2 - - - -
47B ASN* 3.2 38.7 + - - +
49C THR* 3.2 1.2 - - - +
50C ILE* 1.3 76.8 - - - +
52C SER* 1.3 55.7 + - - +
54C GLU* 3.1 11.5 + - - +
55C LEU* 3.0 32.6 + - + +
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Residues in contact with SER 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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33C LEU* 4.1 8.2 - - - +
37C PHE* 4.0 31.4 - - - -
48C LEU* 4.2 4.5 - - - -
49C THR* 3.0 31.6 + - - +
51C LYS* 1.3 71.2 - - - +
53C LEU* 1.4 66.7 + - - +
55C LEU* 3.2 13.7 + - - +
56C ILE* 2.9 26.9 + - - +
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Residues in contact with LEU 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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5B LEU* 4.3 7.9 - - + -
50B ILE* 4.4 19.7 - - + -
9C VAL* 4.4 6.5 - - + -
13C ILE* 4.1 19.7 - - + -
48C LEU* 3.9 15.8 - - + +
49C THR 3.0 13.3 + - - +
50C ILE* 3.2 13.0 + - + +
52C SER* 1.4 77.9 - - - +
54C GLU* 1.3 57.0 + - - +
56C ILE* 3.2 7.3 + - + +
57C MET* 2.9 34.5 + - + +
67C PHE* 3.9 32.1 - - + -
68C PHE* 4.2 26.2 - - + -
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Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 4.3 20.2 + - - +
3B SER* 2.7 33.2 + - - -
4B PHE* 3.6 10.2 + - - +
5B LEU* 3.1 33.7 + - + +
50C ILE 2.9 12.4 + - - +
51C LYS* 3.1 11.5 + - - +
53C LEU* 1.3 78.1 - - - +
55C LEU* 1.3 58.0 + - + +
57C MET* 3.3 13.2 + - + +
58C LYS* 2.9 29.4 + - + +
64C ASP* 5.0 1.8 - - - +
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Residues in contact with LEU 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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31C SER* 3.4 34.5 - - - +
32C ASN* 5.2 3.4 - - + +
33C LEU* 4.1 22.0 - - + -
51C LYS* 3.0 18.7 + - + +
52C SER* 3.2 11.8 + - - +
54C GLU* 1.3 75.4 - - - +
56C ILE* 1.3 57.2 + - - +
58C LYS* 3.3 23.5 + - + +
59C GLY 2.9 22.9 + - - -
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Residues in contact with ILE 56 (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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13C ILE* 4.0 30.1 - - + -
27C LEU* 3.9 7.1 - - + +
31C SER* 4.2 5.4 - - - -
33C LEU* 3.7 20.9 - - + -
37C PHE* 4.8 0.4 - - + -
38C ILE* 4.1 12.6 - - + -
41C ILE* 3.8 29.6 - - + -
48C LEU* 4.0 14.4 - - + -
52C SER 2.9 18.2 + - - +
53C LEU* 3.5 9.6 - - + +
55C LEU* 1.3 73.0 - - - +
57C MET* 1.3 60.0 + - + +
59C GLY* 3.1 2.6 + - - -
60C LEU* 2.9 47.9 + - + +
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Residues in contact with MET 57 (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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43A ARG* 3.7 13.2 - - - +
5B LEU* 3.5 33.0 - - + -
53C LEU* 2.9 30.6 + - + +
54C GLU* 3.5 11.4 - - - +
56C ILE* 1.3 74.9 - - + +
58C LYS* 1.3 57.3 + - - +
60C LEU* 3.4 3.2 + - + -
61C GLU* 3.0 22.5 + - - -
62C VAL* 3.2 25.7 + - + +
63C SER 4.5 0.2 - - - +
64C ASP* 3.5 28.5 - - - +
67C PHE* 3.7 46.0 - - + -
68C PHE* 4.6 2.9 - - + -
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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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24A GLN* 5.8 1.8 - - - -
39A SER* 3.7 26.2 - - - +
43A ARG* 3.7 19.9 - - - +
30C LYS* 4.0 18.9 + - - +
31C SER* 4.7 4.6 + - - +
32C ASN* 5.7 2.6 - - - +
54C GLU* 2.9 17.0 + - + +
55C LEU* 3.5 30.4 - - + +
57C MET* 1.3 75.7 - - - +
59C GLY* 1.3 66.3 + - - +
61C GLU* 3.1 20.1 + - - +
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Residues in contact with GLY 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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22C MET* 3.6 2.1 - - - +
27C LEU* 4.1 11.2 - - - -
30C LYS* 2.7 65.7 + - - +
31C SER 4.1 1.3 - - - -
55C LEU 2.9 14.9 + - - -
56C ILE 3.1 3.8 + - - -
58C LYS* 1.3 78.8 - - - +
60C LEU* 1.3 53.6 + - - +
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Residues in contact with LEU 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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13C ILE* 4.4 11.4 - - + +
16C ILE* 3.8 28.7 - - + +
17C ARG* 3.6 39.5 - - + +
20C LYS* 3.4 23.8 + - + +
22C MET* 4.4 9.4 - - - -
27C LEU* 3.9 17.3 - - + -
30C LYS* 4.5 2.0 + - - -
56C ILE* 2.9 36.6 + - + +
57C MET* 3.8 5.2 - - - +
59C GLY* 1.3 75.0 - - - +
61C GLU* 1.3 67.8 + - - +
62C VAL* 3.9 15.7 - - + -
67C PHE* 5.1 2.7 - - + -
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Residues in contact with GLU 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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14A LYS* 4.8 13.8 + - - -
24A GLN* 5.8 1.7 + - - -
43A ARG* 4.2 18.2 - - + +
20C LYS* 3.4 17.1 + - - +
30C LYS* 3.4 31.8 + - - +
57C MET 3.0 6.8 + - - -
58C LYS 3.1 14.6 + - - +
60C LEU* 1.3 77.8 - - - +
62C VAL* 1.3 59.0 + - - +
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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
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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