Contacts of the helix formed by residues 23 - 36 (chain C) in PDB entry 4U1D
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 GLU 23 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C LEU* 2.9 39.5 + - + +
21C VAL* 4.3 21.1 - - + +
22C GLY* 1.3 78.3 - - - +
24C LYS* 1.3 63.0 + - - +
25C GLN 3.3 2.9 - - - -
26C ALA* 3.2 16.9 + - + +
27C ALA* 2.9 18.7 + - - +
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Residues in contact with LYS 24 (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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19C ILE* 4.7 25.6 - - + +
22C GLY* 3.0 17.3 + - - +
23C GLU* 1.3 75.6 - - - +
25C GLN* 1.3 62.1 + - - +
27C ALA* 3.1 10.4 + - - +
28C LEU 3.0 18.5 + - - -
58C ILE* 4.3 3.3 - - + +
62C LEU* 3.6 38.2 - - + +
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Residues in contact with GLN 25 (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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23C GLU 3.3 0.6 - - - -
24C LYS* 1.3 79.5 - - - +
26C ALA* 1.3 57.6 + - - +
28C LEU* 3.5 4.6 + - + +
29C GLN* 3.0 29.5 + - + +
62C LEU* 3.9 10.7 - - + +
64C LYS* 2.9 41.0 + - + +
67C LEU* 5.7 2.4 - - + +
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Residues in contact with ALA 26 (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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18C LEU* 3.8 14.4 - - + +
23C GLU* 3.2 35.1 + - + +
25C GLN* 1.3 77.6 - - - +
27C ALA* 1.3 57.4 + - - +
29C GLN* 3.8 6.3 - - - +
30C SER* 2.9 27.5 + - - -
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 3.7 28.9 - - + +
18C LEU* 3.7 10.5 - - + +
19C ILE* 3.8 14.1 - - + -
23C GLU 2.9 12.8 + - - +
24C LYS 3.1 8.9 + - - +
26C ALA* 1.3 75.4 - - - +
28C LEU* 1.3 64.8 + - - +
30C SER* 2.6 25.3 + - - -
31C LEU* 3.1 12.9 + - - +
58C ILE* 4.7 5.4 - - + -
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Residues in contact with LEU 28 (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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24C LYS 3.0 8.7 + - - +
25C GLN* 3.8 8.3 - - + +
27C ALA* 1.3 75.7 - - - +
29C GLN* 1.3 62.0 + - - +
31C LEU* 3.2 5.5 + - - +
32C HIS* 3.0 22.0 + - - +
55C PHE* 3.4 46.2 - - + +
58C ILE* 3.7 17.6 - - + +
59C GLY* 3.5 22.0 - - - +
62C LEU* 4.2 8.5 - - + -
64C LYS* 3.6 36.6 - - + +
67C LEU* 3.6 21.1 - - + -
68C LEU* 5.9 0.2 - - + -
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Residues in contact with GLN 29 (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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25C GLN* 3.0 20.2 + - + +
26C ALA* 3.9 7.4 - - - +
28C LEU* 1.3 77.7 - - - +
30C SER* 1.3 59.5 + - - +
32C HIS* 3.6 12.7 + - - +
33C ASP* 2.8 62.1 + - - +
67C LEU* 3.9 25.7 - - + +
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Residues in contact with SER 30 (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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11C ALA 5.1 1.4 + - - -
14C ARG* 4.9 13.0 - - - -
15C ALA* 4.4 8.5 + - - +
18C LEU* 4.2 14.5 - - - +
26C ALA 2.9 17.4 + - - -
27C ALA* 2.6 20.6 + - - -
29C GLN* 1.3 76.8 - - - +
31C LEU* 1.3 66.7 + - - +
33C ASP* 3.4 12.2 + - - +
34C PHE* 3.3 18.7 + - - +
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Residues in contact with LEU 31 (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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11C ALA* 3.9 28.0 - - + +
12C ILE* 4.7 1.6 - - - +
15C ALA* 4.0 8.3 - - + -
27C ALA 3.1 8.6 + - - +
28C LEU* 3.7 7.0 - - - +
30C SER* 1.3 78.6 + - - +
32C HIS* 1.3 67.1 + - - +
34C PHE* 3.1 13.6 + - - +
35C ILE* 3.1 18.2 + - - +
51C VAL* 3.7 25.1 - - + +
54C LYS* 3.6 20.9 - - + -
55C PHE* 3.5 42.6 - - + +
58C ILE* 3.6 19.1 - - + -
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Residues in contact with HIS 32 (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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28C LEU 3.0 12.3 + - - +
29C GLN* 3.7 15.6 + - - +
30C SER 3.3 0.2 - - - -
31C LEU* 1.3 77.1 - - - +
33C ASP* 1.3 68.3 + - - +
35C ILE* 3.6 2.9 - - - +
36C THR* 2.9 49.7 + - + +
55C PHE* 3.5 32.9 - + + -
67C LEU* 3.4 31.4 - - + +
70C ASP* 3.0 27.5 + - - -
71C GLY* 3.7 16.2 + - - -
74C GLN* 4.1 3.6 - - - -
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Residues in contact with ASP 33 (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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29C GLN* 2.8 43.8 + - - +
30C SER* 3.4 10.4 - - - +
31C LEU 3.2 0.2 - - - -
32C HIS* 1.3 79.2 + - - +
34C PHE* 1.3 61.8 + - - +
36C THR* 3.7 6.3 + - - -
37C ALA* 3.3 22.0 + - - +
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Residues in contact with PHE 34 (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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6C PHE* 4.4 14.4 - - + -
7C ARG 3.8 33.0 - - - -
8C PRO* 4.1 4.7 - - + -
11C ALA* 4.0 14.4 - - + -
30C SER 3.3 7.9 + - - +
31C LEU* 3.1 12.4 + - - +
33C ASP* 1.3 79.4 - - - +
35C ILE* 1.3 60.8 + - + +
37C ALA* 3.3 14.2 - - + +
39C ARG* 3.5 28.4 + - - -
40C ILE* 3.2 22.8 - - + +
48C VAL* 4.5 13.7 - - + -
51C VAL* 3.7 37.5 - - + -
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Residues in contact with ILE 35 (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 LEU 3.4 12.1 - - - +
32C HIS* 3.6 7.0 - - - +
34C PHE* 1.3 77.5 - - + +
36C THR* 1.3 62.9 + - + +
37C ALA 3.3 1.6 - - - -
40C ILE* 3.7 14.6 - - - +
48C VAL* 4.4 4.3 - - + -
51C VAL* 3.6 33.2 - - + +
52C VAL* 3.6 38.1 - - + +
55C PHE* 3.6 38.1 - - + -
71C GLY* 4.4 14.6 - - - +
72C LEU* 6.1 0.2 - - + -
75C TYR* 3.6 25.2 - - + +
78C LEU* 4.0 2.4 - - - +
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Residues in contact with THR 36 (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 HIS* 2.9 44.6 + - + +
33C ASP* 3.8 5.8 + - - -
35C ILE* 1.3 83.1 - - + +
37C ALA* 1.3 65.9 + - - +
38C ARG* 3.8 2.1 + - - +
71C GLY 4.1 12.1 - - - +
74C GLN* 3.5 50.1 + - + -
75C TYR 4.6 0.2 - - - +
78C LEU* 3.7 12.0 - - - +
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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