Contacts of the helix formed by residues 32 - 46 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B MET* 5.0 4.7 + - - +
29B TYR* 2.8 41.0 + - - +
31B GLY* 1.3 77.9 - - - +
33B ASP* 1.3 67.7 + - - +
34B LYS 3.3 2.7 - - - -
35B TYR* 3.0 14.1 + - - +
36B PHE* 3.1 41.1 + - - -
97B PRO* 3.9 14.1 - - - -
100B LEU* 4.4 4.7 - - - -
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Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 4.3 22.6 - - - +
29B TYR 4.8 0.2 + - - -
31B GLY* 3.4 7.1 + - - -
32B SER* 1.3 80.1 + - - +
34B LYS* 1.3 81.4 + - + +
36B PHE* 3.1 3.5 + - - +
37B HIS* 3.1 47.4 + - + -
66B GLN* 4.3 9.9 + - - -
71B HIS* 5.4 4.2 - - - -
79B ASP* 4.4 2.8 - - - +
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY 5.1 1.7 + - - +
32B SER 3.3 0.8 - - - -
33B ASP* 1.3 94.0 + - + +
35B TYR* 1.3 63.5 + - - +
37B HIS* 3.4 2.2 + - - +
38B ALA* 3.0 25.3 + - - +
71B HIS* 6.1 1.4 - - - -
75B ASP* 4.6 5.2 + - - +
78B ALA* 3.8 37.7 - - - +
79B ASP* 3.2 28.6 + - - +
82B ALA* 3.7 18.2 - - + +
95B PHE* 4.1 22.3 - - + +
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B SER 3.0 9.4 + - - +
34B LYS* 1.3 78.7 - - - +
36B PHE* 1.3 74.0 + + - +
38B ALA* 3.3 2.6 + - - +
39B ARG* 2.8 48.9 + - + +
92B PRO* 3.2 33.8 - - + +
93B ASN* 3.3 22.8 + - - -
95B PHE* 3.6 25.2 + - - +
96B ARG* 3.1 25.1 + - + -
97B PRO* 4.2 4.9 - - + -
100B LEU* 3.6 22.2 - - + -
104B TYR* 2.4 36.6 + - - -
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA* 3.4 33.0 - - + +
23B ASP* 3.6 30.5 - - + -
24B MET* 3.8 29.6 - - + -
27B ALA* 4.0 11.4 - - + -
32B SER* 3.1 47.9 + - - -
33B ASP 3.1 5.4 + - - +
35B TYR* 1.3 88.5 - + - +
37B HIS* 1.3 62.7 + - + +
39B ARG* 3.9 21.1 - - - -
40B GLY* 2.9 23.0 + - - -
100B LEU* 4.2 5.8 - - + -
104B TYR* 3.9 23.6 - - + -
203B P4C 5.1 1.6 + - - +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B MET* 5.4 0.4 - - - +
24B MET* 4.7 11.3 - - + +
33B ASP* 3.1 35.2 + - - -
34B LYS* 3.7 8.7 - - - +
36B PHE* 1.3 75.7 - - - +
38B ALA* 1.3 65.4 + - - +
40B GLY* 4.0 0.5 - - - -
41B ASN* 2.9 32.1 + - - +
62B ARG* 3.3 35.3 + - - +
66B GLN* 4.3 5.3 + - - -
79B ASP* 3.2 42.3 + - + +
82B ALA* 4.1 8.5 - - + -
83B ASN* 3.5 16.6 - - - +
203B P4C 3.5 13.6 + - - -
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS 3.0 17.3 + - - +
35B TYR 3.7 3.6 - - - +
37B HIS* 1.3 77.8 - - - +
39B ARG* 1.3 51.9 + - - +
41B ASN 3.3 0.7 + - - -
42B TYR* 2.8 36.9 + - - +
82B ALA 3.4 21.7 + - - +
85B TRP* 4.4 0.2 - - + -
86B GLY* 3.4 10.8 - - - +
92B PRO* 3.7 18.4 - - + -
95B PHE* 3.8 19.5 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP 4.9 0.6 + - - -
19B ARG* 3.5 25.2 + - - +
20B ALA* 3.5 28.0 - - - +
23B ASP* 2.8 32.9 + - - -
35B TYR* 2.8 38.3 + - + +
36B PHE* 3.9 16.2 - - - +
38B ALA* 1.3 73.5 - - - +
40B GLY* 1.3 58.3 + - - +
42B TYR* 3.2 0.9 + - - +
43B ASP* 2.8 55.3 + - - +
92B PRO* 3.7 19.5 - - + -
103B LYS 4.9 1.0 + - - -
104B TYR* 3.0 34.4 + - - +
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 4.2 8.0 - - - +
17B MET* 3.4 21.6 - - - +
20B ALA* 3.6 24.1 - - - +
36B PHE 2.9 13.1 + - - -
37B HIS 4.0 0.7 - - - -
39B ARG* 1.3 76.1 - - - +
41B ASN* 1.3 59.5 + - - +
43B ASP* 3.9 4.4 - - - +
44B ALA* 3.1 19.4 + - - +
203B P4C 6.2 0.2 - - - -
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B MET* 3.8 14.4 - - - +
37B HIS 2.9 28.1 + - - +
38B ALA 3.8 1.3 - - - +
40B GLY* 1.3 72.6 - - - +
42B TYR* 1.3 60.9 + - - +
44B ALA* 3.8 1.0 - - - +
45B ALA* 2.9 32.2 + - - +
55B ALA* 3.4 9.6 - - - +
59B SER* 3.1 12.7 + - - -
62B ARG* 4.3 0.2 - - - +
83B ASN* 3.1 44.4 + - - +
87B ARG* 2.7 41.7 + - + +
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 2.8 21.9 + - - +
39B ARG* 3.5 6.1 - - + +
41B ASN* 1.3 73.6 - - - +
43B ASP* 1.3 77.8 + - - +
45B ALA* 3.3 1.9 + - - +
46B LYS* 3.0 58.7 + - + +
86B GLY* 3.3 22.6 - - - +
89B GLY* 3.6 26.0 - - - -
90B LYS 3.5 19.3 - - - -
91B ASP* 4.9 1.8 - - - -
92B PRO* 3.8 20.4 - - + -
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 3.2 28.6 - - + +
19B ARG* 3.3 21.2 + - - +
39B ARG* 2.8 48.0 + - - +
40B GLY* 3.9 4.5 - - - +
42B TYR* 1.3 88.6 - - - +
44B ALA* 1.3 62.1 + - - +
46B LYS* 3.4 21.1 + - - +
47B ARG* 3.7 5.9 + - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY* 3.5 29.4 - - - +
16B ASP* 3.8 8.9 + - + +
17B MET* 4.2 2.7 - - + -
40B GLY 3.1 18.2 + - - +
41B ASN 3.9 2.7 - - - +
43B ASP* 1.3 74.2 - - - +
45B ALA* 1.3 67.5 + - - +
47B ARG* 3.0 13.5 + - - +
51B GLY* 3.1 31.6 - - - +
55B ALA* 3.9 10.3 - - + -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASN 2.9 19.0 + - - +
42B TYR* 3.8 4.0 - - - +
44B ALA* 1.3 76.3 - - - +
46B LYS* 1.3 63.1 + - - +
48B GLY* 3.1 15.9 + - - +
51B GLY 4.3 0.4 + - - -
52B VAL* 3.9 27.1 - - + +
86B GLY 4.6 0.4 - - - +
87B ARG* 3.3 31.6 - - + +
89B GLY* 5.6 1.3 - - - +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 3.0 48.8 + - + +
43B ASP* 3.4 16.9 + - - +
44B ALA 3.1 0.4 - - - -
45B ALA* 1.3 77.2 - - - +
47B ARG* 1.3 63.3 + - - +
48B GLY* 3.3 0.8 + - - -
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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