Contacts of the helix formed by residues 32 - 47 (chain C) in PDB entry 4IP8
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 32 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C MET* 4.8 3.8 - - - +
27C ALA* 5.3 0.2 - - - +
29C TYR* 2.7 33.5 + - - +
31C GLY* 1.3 77.0 - - - +
33C ASP* 1.3 68.8 + - - +
34C LYS 3.3 2.9 - - - -
35C TYR* 3.2 12.5 + - - +
36C PHE* 3.2 39.3 + - - -
97C PRO* 3.9 24.2 - - - -
100C LEU* 4.4 3.8 - - - -
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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
----------------------------------------------------------
68B PHE* 5.8 2.4 - - - -
24C MET* 3.5 28.9 - - - +
29C TYR 5.2 1.4 - - - +
31C GLY* 3.4 4.3 + - - -
32C SER* 1.3 80.6 + - - +
34C LYS* 1.3 79.3 + - + +
36C PHE* 3.5 2.8 + - - +
37C HIS* 2.9 37.3 + - + -
66C GLN* 4.4 14.9 + - - -
71C HIS* 5.3 5.7 - - - -
79C ASP* 5.4 0.3 - - - +
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLY 4.8 4.9 + - - +
32C SER 3.3 0.4 - - - -
33C ASP* 1.3 88.4 + - + +
35C TYR* 1.3 66.0 + - - +
37C HIS* 3.2 7.4 + - - +
38C ALA* 2.9 24.8 + - - +
71C HIS* 5.9 1.8 - - - -
75C ASP* 4.5 14.4 + - - +
78C ALA* 3.9 33.2 - - + +
79C ASP* 3.0 29.8 + - - +
82C ALA* 3.7 6.1 - - + +
95C PHE* 3.6 32.5 - - + +
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLY 5.3 0.2 + - - -
32C SER 3.2 9.0 + - - +
34C LYS* 1.3 80.0 - - - +
36C PHE* 1.3 69.7 + + - +
38C ALA* 3.3 2.6 + - - +
39C ARG* 2.7 50.7 + - + +
92C PRO* 3.2 32.9 - - + +
93C ASN* 3.3 22.5 + - - -
95C PHE* 3.6 24.5 + - - +
96C ARG* 3.1 29.3 + - + -
97C PRO* 4.2 5.6 - - + -
100C LEU* 3.6 23.8 - - + -
104C TYR* 2.6 31.1 + - - -
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 3.5 31.6 - - - +
23C ASP* 3.6 32.3 - - + -
24C MET* 3.7 25.4 - - + -
27C ALA* 4.2 8.1 - - + -
32C SER* 3.2 44.6 + - - -
33C ASP 4.1 4.3 - - - +
34C LYS 3.3 0.4 - - - -
35C TYR* 1.3 85.5 - + - +
37C HIS* 1.3 61.8 + - - +
39C ARG* 4.0 15.3 - - - +
40C GLY* 2.9 25.3 + - - -
100C LEU* 4.3 5.8 - - + -
104C TYR* 4.0 28.7 - + + -
204C P4C 3.9 9.3 - - - +
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Residues in contact with HIS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C MET* 5.0 3.4 - - - +
33C ASP* 2.9 32.0 + - + -
34C LYS* 3.5 8.2 - - - +
36C PHE* 1.3 76.3 - - - +
38C ALA* 1.3 63.4 + - - +
40C GLY* 4.1 0.2 - - - -
41C ASN* 2.8 32.4 + - - +
62C ARG* 3.2 41.3 + - - -
66C GLN* 4.2 8.7 + - - -
79C ASP* 3.5 39.2 + - + +
82C ALA* 4.1 9.2 - - + -
83C ASN* 3.3 14.1 - - - +
204C P4C 3.2 25.6 - - - +
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Residues in contact with ALA 38 (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 LYS 2.9 16.6 + - - +
35C TYR 3.5 4.5 - - - +
37C HIS* 1.3 77.0 - - - +
39C ARG* 1.3 56.9 + - - +
41C ASN 3.4 1.2 + - - -
42C TYR* 2.9 30.3 + - - +
82C ALA 3.5 21.5 + - - +
85C TRP* 4.9 0.2 - - + -
86C GLY* 3.5 10.3 - - - +
92C PRO* 3.8 18.4 - - + -
95C PHE* 3.9 20.2 - - + -
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP 4.9 0.4 + - - -
19C ARG* 3.5 27.9 + - - +
20C ALA* 3.5 28.7 - - - +
23C ASP* 2.8 31.7 + - - -
35C TYR* 2.7 34.5 + - + +
36C PHE* 4.0 14.1 - - - +
38C ALA* 1.3 73.7 - - - +
40C GLY* 1.3 58.7 + - - +
42C TYR* 3.3 1.3 + - + +
43C ASP* 2.8 56.8 + - - +
92C PRO* 3.6 20.8 - - + +
103C LYS 4.9 1.2 + - - -
104C TYR* 3.1 34.4 + - - +
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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
----------------------------------------------------------
16C ASP* 4.2 7.8 - - - +
17C MET* 3.4 20.6 - - - +
20C ALA* 3.6 24.6 - - - +
36C PHE 2.9 12.9 + - - -
37C HIS 4.1 0.4 - - - -
39C ARG* 1.3 77.7 - - - +
41C ASN* 1.3 55.9 + - - +
43C ASP* 3.3 4.4 + - - +
44C ALA* 3.0 24.3 + - - +
204C P4C 5.8 0.4 - - - -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C MET* 3.9 10.6 - - - +
37C HIS 2.8 19.2 + - - +
38C ALA 3.9 1.3 - - - +
40C GLY* 1.3 75.1 - - - +
42C TYR* 1.3 57.5 + - - +
44C ALA* 4.0 0.7 - - - +
45C ALA* 2.9 32.1 + - - +
55C ALA* 3.2 13.9 - - - +
59C SER* 3.1 13.2 + - - -
62C ARG* 4.3 0.2 - - - +
83C ASN* 2.8 53.6 + - - +
86C GLY 4.0 2.2 - - - -
87C ARG* 3.0 37.0 + - - +
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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
----------------------------------------------------------
38C ALA 2.9 18.9 + - - +
39C ARG* 3.5 4.9 - - + +
41C ASN* 1.3 75.5 - - - +
43C ASP* 1.3 78.6 + - - +
45C ALA* 3.8 2.4 - - - +
46C LYS* 3.1 38.8 + - + +
86C GLY* 3.3 21.9 + - - +
89C GLY* 3.4 23.6 - - - -
90C LYS 3.5 19.7 - - - -
91C ASP* 5.0 1.1 - - - -
92C PRO* 3.7 22.7 - - + -
205C P4C 3.7 24.9 + - - +
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP* 3.2 33.7 - - + +
19C ARG* 4.0 17.2 + - - +
39C ARG* 2.8 55.4 + - - +
40C GLY* 3.7 3.2 + - - +
42C TYR* 1.3 87.3 - - - +
44C ALA* 1.3 62.5 + - - +
46C LYS* 3.3 20.5 + - - +
47C ARG* 3.7 5.2 + - - +
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Residues in contact with ALA 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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13C GLY* 3.6 27.4 - - - +
16C ASP* 3.7 8.2 + - + +
17C MET* 4.2 2.5 - - + -
40C GLY 3.0 16.4 + - - +
41C ASN 4.0 0.2 - - - +
43C ASP* 1.3 73.7 - - - +
45C ALA* 1.3 66.1 + - - +
47C ARG* 2.9 21.3 + - - +
51C GLY* 3.3 27.4 - - - +
55C ALA* 3.9 14.1 - - + -
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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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41C ASN 2.9 19.9 + - - +
42C TYR* 3.8 5.2 - - - +
44C ALA* 1.3 75.9 - - - +
46C LYS* 1.3 61.6 + - - +
48C GLY* 3.0 18.7 + - - +
51C GLY 4.3 0.4 - - - -
52C VAL* 3.9 25.4 - - + +
55C ALA* 5.0 0.4 - - - +
87C ARG* 3.4 28.7 - - + +
205C P4C 4.0 16.7 - - - +
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 3.1 29.7 + - + +
43C ASP* 3.4 15.9 - - - +
44C ALA 3.1 0.8 - - - -
45C ALA* 1.3 75.7 - - - +
47C ARG* 1.3 62.4 + - - +
48C GLY* 3.2 0.9 + - - -
205C P4C 3.8 34.5 - - - +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 3.2 41.0 - - + +
12C ASP* 3.5 25.9 + - + +
13C GLY 4.0 13.0 - - - +
15C ARG* 3.7 8.3 - - - +
16C ASP* 2.8 39.0 + - - +
19C ARG* 5.1 1.2 - - - +
43C ASP 3.7 2.7 + - - +
44C ALA 2.9 15.7 + - - +
46C LYS* 1.3 78.4 - - - +
48C GLY* 1.3 56.1 + - - +
51C GLY* 4.5 0.9 - - - -
201C SO4 3.2 46.2 + - - -
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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
------------------------------------------------------------
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