Contacts of the helix formed by residues 31 - 49 (chain C) in PDB entry 4H7Y
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 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C PRO 3.3 5.7 + - - -
30C LEU* 1.3 76.0 - - - +
32C ASP* 1.3 57.7 + - - +
33C ALA* 3.2 11.1 + - - +
34C LEU* 2.8 39.3 + - - +
35C LEU* 2.9 28.3 + - - +
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Residues in contact with ASP 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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31C SER* 1.3 74.5 - - - +
33C ALA* 1.3 58.6 + - - +
35C LEU* 3.7 10.4 + - - +
36C ASN* 3.1 36.6 + - - +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER* 3.1 9.3 + - - +
32C ASP* 1.3 79.0 - - - +
34C LEU* 1.3 59.1 + - + +
36C ASN* 3.4 6.0 + - - +
37C LYS* 3.1 40.5 + - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ASN 4.8 3.8 - - - +
27C SER* 3.9 32.7 + - - +
28C VAL 5.2 1.3 - - - +
29C PRO 3.3 25.6 - - - +
30C LEU* 3.7 10.3 - - + +
31C SER* 2.8 29.7 + - - +
33C ALA* 1.3 70.9 - - + +
35C LEU* 1.3 65.6 + - - +
37C LYS* 3.4 15.9 + - + +
38C LEU* 3.0 24.6 + - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.5 23.9 - - + +
31C SER 2.9 17.9 + - - +
32C ASP* 3.9 11.7 - - - +
34C LEU* 1.3 76.0 - - - +
36C ASN* 1.3 60.9 + - - +
38C LEU* 3.3 2.8 + - + +
39C ILE* 2.9 48.8 + - + +
70C LEU* 3.8 33.4 - - + +
73C ILE* 3.9 24.9 - - + +
74C GLN* 4.0 24.2 - - + -
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Residues in contact with ASN 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 ASP* 3.1 25.3 + - - +
33C ALA* 3.8 6.5 - - - +
34C LEU 3.3 0.2 - - - -
35C LEU* 1.3 76.4 - - - +
37C LYS* 1.3 59.4 + - + +
39C ILE* 3.9 5.5 - - - +
40C GLY* 3.0 23.6 + - - -
74C GLN* 2.9 31.3 + - - +
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Residues in contact with LYS 37 (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 LEU* 4.4 7.3 - - + +
33C ALA* 3.1 27.2 + - - +
34C LEU* 3.9 15.9 - - + +
36C ASN* 1.3 74.3 - - + +
38C LEU* 1.3 61.2 + - - +
40C GLY* 3.4 2.0 + - - -
41C ARG* 3.0 27.9 + - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.1 5.6 - - - +
23C LEU* 3.7 31.8 - - + +
24C GLU* 3.7 39.9 - - + +
27C SER* 5.2 2.7 - - - +
30C LEU* 4.8 13.5 - - + -
34C LEU 3.0 18.1 + - - +
35C LEU* 3.6 5.4 - - + +
37C LYS* 1.3 75.3 - - - +
39C ILE* 1.3 65.2 + - - +
41C ARG* 3.1 4.8 + - + +
42C TYR* 3.0 42.3 + - + -
70C LEU* 3.7 33.2 - - + -
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Residues in contact with ILE 39 (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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35C LEU* 2.9 29.9 + - + +
36C ASN* 3.9 5.4 - - - +
38C LEU* 1.3 74.1 - - - +
40C GLY* 1.3 58.4 + - - +
42C TYR* 3.1 9.7 + - - +
43C SER* 2.8 30.2 + - - +
67C PHE* 3.9 10.9 - - + +
70C LEU* 3.6 46.2 - - + +
71C LYS* 3.7 28.7 - - + +
74C GLN* 3.6 31.6 - - - +
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Residues in contact with GLY 40 (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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36C ASN 3.0 15.6 + - - -
37C LYS* 3.7 4.7 - - - -
38C LEU 3.3 0.4 - - - -
39C ILE* 1.3 76.8 - - - +
41C ARG* 1.3 60.6 + - - +
43C SER* 3.3 9.5 + - - -
44C GLN* 3.2 28.2 + - - +
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Residues in contact with ARG 41 (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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16C TRP* 3.8 19.3 - - + -
19C LEU* 3.8 34.7 - - + +
20C LEU* 3.6 24.5 - - + +
23C LEU* 3.7 21.2 - - + +
37C LYS 3.0 13.4 + - - +
38C LEU 3.1 8.2 + - - +
40C GLY* 1.3 73.6 - - - +
42C TYR* 1.3 65.4 + - - +
44C GLN* 2.8 37.4 + - - +
45C ALA* 3.1 17.5 + - - +
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Residues in contact with TYR 42 (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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17C LEU* 4.7 8.7 - - - +
20C LEU* 3.7 48.3 + - + +
21C LEU* 4.9 5.0 - - - +
24C GLU* 4.1 5.6 + - - -
38C LEU* 3.0 33.8 + - + +
39C ILE* 3.1 8.7 + - - +
41C ARG* 1.3 78.1 - - - +
43C SER* 1.3 56.5 + - - +
45C ALA* 3.2 4.6 + - - +
46C ILE* 2.9 33.6 + - - +
63C ILE* 3.5 37.7 - - + -
66C ARG* 3.2 31.8 - - + +
67C PHE* 3.7 23.3 - - + -
70C LEU* 3.8 21.1 - - + -
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Residues in contact with SER 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU 5.2 1.6 + - - -
48B ALA* 6.0 1.8 - - - -
39C ILE* 2.8 19.7 + - - +
40C GLY* 3.5 13.8 - - - -
41C ARG 3.2 0.2 - - - -
42C TYR* 1.3 76.9 - - - +
44C GLN* 1.3 58.8 + - - +
46C ILE* 3.3 7.6 + - - +
47C GLU* 3.0 29.5 + - - +
67C PHE* 3.4 21.5 - - - -
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Residues in contact with GLN 44 (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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16C TRP* 4.0 13.2 - - + -
40C GLY 3.2 11.8 + - - +
41C ARG* 2.8 48.0 + - - +
43C SER* 1.3 73.9 - - - +
45C ALA* 1.3 66.4 + - - +
47C GLU* 3.4 5.8 + - - +
48C ALA* 3.1 24.4 + - - +
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Residues in contact with ALA 45 (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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16C TRP* 3.4 43.4 - - + -
20C LEU* 4.0 15.9 - - + -
41C ARG 3.1 6.6 + - - +
42C TYR 3.2 8.3 + - - +
44C GLN* 1.3 80.2 - - - +
46C ILE* 1.3 63.6 + - - +
48C ALA* 3.1 10.0 + - - -
49C LEU* 3.1 23.7 + - + +
63C ILE* 4.2 8.7 - - + -
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Residues in contact with ILE 46 (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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44B GLN* 2.9 29.0 + - + +
47B GLU* 3.6 35.9 - - + +
42C TYR 2.9 19.1 + - - +
43C SER* 3.8 5.6 - - - +
45C ALA* 1.3 75.5 - - - +
47C GLU* 1.3 58.9 + - - +
48C ALA 3.5 0.3 + - - -
49C LEU* 3.6 10.3 - - - +
51C PRO* 5.6 0.4 - - + +
60C PHE* 5.6 1.8 - - + -
63C ILE* 4.0 19.7 - - + +
64C GLN* 4.0 21.7 + - - +
67C PHE* 3.4 50.3 - - + -
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Residues in contact with GLU 47 (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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16B TRP* 3.2 28.6 - - - -
41B ARG* 2.9 34.9 + - - -
44B GLN* 3.2 17.4 + - - +
48B ALA* 5.8 0.2 - - - +
43C SER 3.0 16.8 + - - +
44C GLN* 3.9 6.3 - - - +
45C ALA 3.2 0.2 - - - -
46C ILE* 1.3 78.2 - - - +
48C ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 48 (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 ASN* 2.9 45.0 + - - +
16C TRP* 4.0 13.5 - - + +
44C GLN 3.1 16.0 + - - +
45C ALA 3.1 5.6 + - - +
47C GLU* 1.3 78.6 - - - +
49C LEU* 1.3 58.1 + - - +
50C PRO* 3.3 9.9 - - - +
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Residues in contact with LEU 49 (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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44B GLN* 3.6 7.2 + - - -
11C ASN* 3.6 20.9 - - - +
12C ASN* 3.7 27.8 - - - -
13C PRO* 3.8 7.6 - - + -
16C TRP* 3.9 14.8 - - + -
45C ALA 3.1 20.0 + - - +
46C ILE* 3.6 3.2 + - - +
47C GLU 3.4 1.8 - - - -
48C ALA* 1.3 79.3 - - - +
50C PRO* 1.3 69.1 - - - +
51C PRO* 3.2 8.7 - - - +
54C TYR* 3.8 15.3 - - + -
60C PHE* 3.6 30.1 - - + -
63C ILE* 3.8 30.1 - - + -
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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