Contacts of the helix formed by residues 31 - 47 (chain A) in PDB entry 4IP9
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 GLY 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR 3.7 0.4 + - - -
30A ILE* 1.4 73.7 - - - +
32A SER* 1.3 68.7 + - - +
33A ASP* 2.9 9.0 + - - -
34A LYS* 3.4 12.3 + - - +
35A TYR 3.8 4.7 + - - -
95A PHE 4.8 2.8 - - - +
97A PRO* 4.6 10.1 - - - +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 4.4 10.5 + - - +
27A ALA* 6.1 0.7 - - - -
29A TYR* 2.4 34.2 + - - -
30A ILE 3.6 1.0 + - - -
31A GLY* 1.3 74.7 + - - +
33A ASP* 1.3 75.4 + - - +
34A LYS 2.7 1.6 + - - -
35A TYR* 2.8 13.4 + - - +
36A PHE* 3.1 30.3 + - - -
97A PRO* 4.4 12.3 - - - +
100A LEU* 5.6 1.3 - - - -
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 3.5 29.7 - - - +
31A GLY* 2.9 6.3 + - - +
32A SER* 1.3 83.2 + - - +
34A LYS* 1.3 63.5 + - + +
36A PHE* 3.1 8.7 + - - +
37A HIS* 3.2 34.3 + - + +
66A GLN* 5.8 1.6 + - - -
71A HIS* 5.7 4.3 - - - -
79A ASP* 4.6 8.7 - - - +
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 3.4 7.1 + - - +
32A SER 2.7 1.0 + - - -
33A ASP* 1.3 79.8 - - + +
35A TYR* 1.3 72.4 + - - +
36A PHE 2.6 2.8 + - - -
37A HIS* 3.9 2.9 - - - +
38A ALA* 3.2 17.2 + - - +
78A ALA* 4.0 40.1 + - + +
79A ASP* 4.7 5.4 - - - +
81A ALA* 6.1 1.3 - - - +
82A ALA* 3.9 18.9 - - + +
95A PHE* 3.7 35.4 - - + +
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 3.8 2.8 + - - -
32A SER* 2.8 13.6 + - - +
34A LYS* 1.3 78.0 - - - +
36A PHE* 1.3 78.9 + + - +
38A ALA* 3.1 3.8 + - - +
39A ARG* 3.1 32.9 + - + +
92A PRO* 3.4 35.1 - - + +
93A ASN* 3.6 12.0 + - - -
95A PHE* 3.3 26.7 + - - +
96A ARG* 3.2 29.9 + - + -
97A PRO* 4.2 7.2 - - + -
100A LEU* 3.8 20.0 - - + -
104A TYR* 3.0 27.7 + - - -
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 3.7 30.6 - - + +
21A TYR* 4.8 3.3 + - + -
23A ASP* 4.1 7.2 - - + -
24A MET* 3.3 53.6 - - + -
27A ALA* 4.8 5.8 - - + -
32A SER* 3.1 19.7 + - - -
33A ASP 3.1 5.8 + - - +
34A LYS 2.6 2.4 + - - -
35A TYR* 1.3 100.2 - + - +
37A HIS* 1.3 70.4 + - - +
38A ALA 2.6 2.1 + - - -
39A ARG* 3.4 32.0 + - + +
40A GLY* 3.5 10.4 + - - -
100A LEU* 4.9 5.2 - - + -
104A TYR* 4.5 12.6 - + + -
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Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 6.1 0.2 - - - -
21A TYR* 2.9 42.7 - + - -
24A MET* 5.1 4.9 - - + +
33A ASP* 3.2 32.6 + - + +
34A LYS* 3.9 4.4 - - - +
36A PHE* 1.3 78.8 - - - +
38A ALA* 1.3 57.4 + - - +
40A GLY 4.7 0.2 - - - -
41A ASN* 3.1 10.3 + - - -
62A ARG* 3.5 23.6 + - - -
66A GLN* 4.6 3.1 + - - -
79A ASP* 3.6 42.9 + - + +
82A ALA* 4.3 9.0 - - + -
83A ASN* 3.0 26.9 + - - +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS 3.2 7.3 + - - +
35A TYR 3.1 8.1 + - - +
36A PHE 2.6 3.4 - - - -
37A HIS* 1.3 80.4 - - - +
39A ARG* 1.2 60.2 + - - +
40A GLY 3.5 0.2 - - - -
41A ASN* 4.0 4.7 - - - -
42A TYR* 3.5 15.6 + - - +
82A ALA 3.0 28.5 - - - +
86A GLY* 3.6 14.2 - - - +
92A PRO* 4.0 8.1 - - + +
95A PHE* 4.3 16.6 - - + -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP 4.9 0.4 + - - -
19A ARG* 3.4 25.9 + - - +
20A ALA* 3.7 28.0 - - - +
23A ASP* 2.8 33.5 + - - +
35A TYR* 3.1 29.8 + - + +
36A PHE* 3.4 11.7 + - + +
38A ALA* 1.2 74.1 - - - +
40A GLY* 1.3 60.6 + - - +
42A TYR* 3.2 1.5 + - - +
43A ASP* 2.9 53.7 + - - +
92A PRO* 3.9 20.1 - - + +
103A LYS 4.7 1.8 + - - -
104A TYR* 3.1 37.3 + - - +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.8 12.4 - - - +
17A MET* 3.3 14.2 - - - +
20A ALA* 3.6 23.5 - - - +
36A PHE 3.5 8.4 + - - -
37A HIS 5.2 0.2 - - - -
38A ALA 3.5 0.4 - - - -
39A ARG* 1.3 78.1 - - - +
41A ASN* 1.4 57.2 + - - +
43A ASP* 4.0 3.1 - - - +
44A ALA* 3.0 31.9 + - - +
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.6 14.5 - - - +
37A HIS 3.1 11.5 + - - +
38A ALA 3.9 3.9 + - - +
39A ARG 3.3 0.4 - - - -
40A GLY* 1.4 73.7 - - - +
42A TYR* 1.3 56.8 + - - +
44A ALA* 4.0 0.9 - - - +
45A ALA* 3.0 30.7 + - - +
55A ALA* 3.4 10.2 - - - +
59A SER* 3.1 11.4 + - - -
83A ASN* 2.8 53.6 - - - +
87A ARG* 2.9 41.7 + - - +
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA 3.5 12.1 + - - +
39A ARG 3.2 7.4 + - - +
41A ASN* 1.3 75.7 - - - +
43A ASP* 1.3 79.2 + - - +
45A ALA* 3.4 3.6 + - - +
46A LYS* 3.1 59.8 + - + +
86A GLY* 3.4 23.3 - - - +
89A GLY* 3.3 26.5 - - - -
90A LYS 3.3 20.2 - - - -
91A ASP* 4.8 2.5 - - - -
92A PRO* 3.8 26.9 - - + -
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASP* 3.6 27.7 - - + +
19A ARG* 2.9 30.3 + - - +
39A ARG* 2.9 38.2 + - - +
40A GLY* 4.0 1.1 - - - +
42A TYR* 1.3 89.4 - - - +
44A ALA* 1.4 61.4 + - - +
46A LYS* 3.2 21.3 + - - +
47A ARG* 3.5 7.3 + - - +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY* 3.5 25.6 - - - +
16A ASP* 3.8 10.9 + - - +
17A MET* 4.3 1.3 - - + -
40A GLY 3.0 19.8 + - - +
41A ASN 4.0 0.2 - - - +
43A ASP* 1.4 75.0 - - - +
45A ALA* 1.4 61.5 + - - +
47A ARG* 3.1 13.5 + - - +
51A GLY* 3.1 35.4 - - - +
55A ALA* 3.8 14.4 - - + -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN 3.0 20.3 + - - +
42A TYR* 3.7 4.9 - - - +
44A ALA* 1.4 75.8 - - - +
46A LYS* 1.4 61.1 + - - +
48A GLY* 3.3 18.2 + - - +
51A GLY 4.1 0.6 + - - -
52A VAL* 3.8 26.6 - - + +
86A GLY 4.6 0.7 - - - +
87A ARG* 3.3 29.6 - - + +
89A GLY* 5.2 3.4 - - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.1 47.6 + - + +
43A ASP* 3.2 15.6 + - - +
45A ALA* 1.4 72.9 - - - +
47A ARG* 1.3 63.2 + - - +
48A GLY* 3.2 1.4 + - - -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU* 3.3 39.0 - - + +
12A ASP* 3.6 33.4 + - + +
13A GLY 4.1 4.3 - - - +
15A ARG* 4.1 18.6 - - - +
16A ASP* 2.7 41.9 + - - +
19A ARG* 5.0 1.0 - - - +
43A ASP 3.7 4.8 + - - +
44A ALA 3.1 15.0 + - - +
46A LYS* 1.3 77.3 - - - +
48A GLY* 1.3 54.3 + - - +
51A GLY* 4.4 0.2 - - - -
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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
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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