Contacts of the helix formed by residues 31 - 49 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ARG* 4.0 12.3 - - - +
69A GLU* 4.2 14.6 - - - -
73A ILE* 3.5 10.2 - - - +
29B PRO 3.7 3.0 + - - -
30B LEU* 1.3 75.4 - - - +
32B ASP* 1.3 66.3 + - - +
33B ALA* 3.5 8.3 + - - +
34B LEU* 3.2 27.3 + - - +
35B LEU* 2.9 23.9 + - - +
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Residues in contact with ASP 32 (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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69A GLU* 4.9 2.2 + - - +
72A ALA* 4.9 17.3 - - + +
73A ILE* 3.7 23.1 - - + +
106A SER* 4.5 19.0 - - - +
107A GLN* 6.3 0.7 - - - -
31B SER* 1.3 72.3 - - - +
33B ALA* 1.3 60.2 + - - +
35B LEU* 3.6 5.5 - - - +
36B ASN* 2.9 59.6 + - - +
74B GLN* 5.3 5.7 + - - +
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Residues in contact with ALA 33 (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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102A GLN* 5.8 1.6 - - + +
144A GLN* 3.5 37.5 - - + +
31B SER* 3.2 9.0 + - - +
32B ASP* 1.3 81.2 + - - +
34B LEU* 1.3 60.1 + - + +
36B ASN* 3.4 9.8 + - - +
37B LYS* 3.0 26.9 + - - +
52C ASP* 4.7 2.8 - - - +
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Residues in contact with LEU 34 (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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148A GLU* 5.4 12.1 - - + -
26B ASN 5.3 2.7 - - - +
27B SER* 3.8 37.3 + - - +
28B VAL 5.1 1.8 - - - -
29B PRO* 3.3 26.2 - - + +
30B LEU* 4.5 3.4 - - + -
31B SER* 3.2 19.9 + - - +
33B ALA* 1.3 79.0 - - + +
35B LEU* 1.3 60.9 + - - +
37B LYS* 3.3 21.7 + - + +
38B LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 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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73A ILE* 3.8 32.8 - - + -
30B LEU* 4.0 23.7 - - + +
31B SER 2.9 17.5 + - - +
32B ASP* 3.6 6.5 - - - +
34B LEU* 1.3 75.3 - - - +
36B ASN* 1.3 60.9 + - - +
38B LEU* 3.2 4.6 + - + +
39B ILE* 2.9 44.7 + - + +
70B LEU* 3.7 32.1 - - + +
73B ILE* 3.9 15.7 - - + -
74B GLN* 4.2 20.4 - - + +
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Residues in contact with ASN 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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143A LYS* 5.7 5.0 - - - +
144A GLN* 6.1 0.6 - - - +
32B ASP* 2.9 46.2 + - - +
33B ALA* 3.7 7.2 - - - +
34B LEU 3.3 0.2 - - - -
35B LEU* 1.3 76.6 - - - +
37B LYS* 1.3 58.2 + - - +
39B ILE* 3.5 2.9 + - - +
40B GLY* 2.9 24.4 + - - -
74B GLN* 2.2 41.2 + - - +
52C ASP* 3.6 21.7 - - + +
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Residues in contact with LYS 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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23B LEU* 4.4 28.9 - - + +
27B SER* 6.0 0.9 - - - +
33B ALA 3.0 14.2 + - - +
34B LEU* 3.5 24.1 - - + +
35B LEU 3.2 0.4 - - - -
36B ASN* 1.3 77.0 - - - +
38B LEU* 1.3 61.7 + - - +
40B GLY* 3.3 1.7 + - - -
41B ARG* 3.0 24.9 + - + +
50C PRO* 6.3 0.4 - - + -
52C ASP* 3.7 29.0 - - - +
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Residues in contact with LEU 38 (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 LEU* 4.2 2.0 - - + +
23B LEU* 3.7 33.2 - - + +
24B GLU* 3.5 49.1 - - + +
27B SER* 4.7 11.4 - - - +
30B LEU* 5.1 10.5 - - + -
34B LEU 2.9 15.6 + - - +
35B LEU* 3.6 5.8 - - + +
37B LYS* 1.3 73.8 - - - +
39B ILE* 1.3 64.5 + - - +
41B ARG* 3.1 4.2 + - - +
42B TYR* 3.0 37.8 + - + -
70B LEU* 4.0 25.6 - - + -
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Residues in contact with ILE 39 (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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35B LEU* 2.9 27.0 + - + +
36B ASN* 3.9 4.7 - - - +
38B LEU* 1.3 75.4 - - - +
40B GLY* 1.3 63.0 + - - +
42B TYR* 3.3 6.1 + - - +
43B SER* 3.0 18.7 + - - -
67B PHE* 3.6 17.7 - - + +
70B LEU* 3.6 43.3 - - + +
71B LYS* 3.7 25.4 - - + +
74B GLN* 3.5 36.8 - - + +
88C ALA* 6.2 0.4 - - + -
89C ASN* 5.5 4.0 - - - +
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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
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36B ASN 2.9 16.0 + - - -
37B LYS 3.7 4.0 - - - -
39B ILE* 1.3 75.4 - - - +
41B ARG* 1.3 61.6 + - - +
43B SER* 2.7 26.8 + - - -
44B GLN* 3.1 10.9 + - - +
51C PRO* 3.6 27.8 - - - +
52C ASP* 4.8 2.7 - - - -
89C ASN* 4.7 2.0 - - - -
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Residues in contact with ARG 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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16B TRP* 3.6 17.8 - - - -
19B LEU* 3.7 27.6 - - + +
20B LEU* 3.6 21.1 - - + +
23B LEU* 3.7 27.1 - - + -
37B LYS* 3.0 13.1 + - - +
38B LEU 3.1 7.6 + - - +
40B GLY* 1.3 73.2 - - - +
42B TYR* 1.3 65.0 - - - +
44B GLN* 2.9 41.6 + - - +
45B ALA* 3.2 9.5 + - - +
47C GLU* 2.9 38.5 + - - -
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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
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17B LEU* 4.7 2.5 - - + +
20B LEU* 3.7 43.6 - - + +
21B LEU* 4.1 6.9 - - - +
24B GLU* 2.5 31.8 + - - +
38B LEU* 3.0 38.6 + - + -
39B ILE* 3.3 4.4 + - - +
41B ARG* 1.3 76.1 - - - +
43B SER* 1.3 62.9 + - - +
45B ALA* 3.1 5.1 + - - +
46B ILE* 3.0 26.0 + - - +
63B ILE* 3.6 29.1 - - + +
66B ARG* 3.4 28.2 - - + +
67B PHE* 3.7 22.9 - - + -
70B LEU* 3.6 20.4 - - + -
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Residues in contact with SER 43 (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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39B ILE 3.0 13.8 + - - -
40B GLY 2.7 19.0 + - - -
42B TYR* 1.3 75.4 - - - +
44B GLN* 1.3 57.4 + - - +
46B ILE* 3.1 2.8 + - - +
47B GLU* 2.8 33.4 + - - +
67B PHE* 3.9 7.9 - - - -
51C PRO* 3.5 5.9 - - - +
64C GLN* 5.5 0.3 + - - -
85C MET* 3.7 26.0 - - - +
89C ASN* 3.1 34.5 + - - -
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Residues in contact with GLN 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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16B TRP* 4.0 4.3 - - + -
40B GLY 3.1 8.1 + - - +
41B ARG* 2.9 52.5 + - - +
43B SER* 1.3 80.6 + - - +
45B ALA* 1.3 63.3 + - - +
47B GLU* 3.5 10.1 + - - +
48B ALA* 3.2 21.5 + - - +
46C ILE* 2.9 34.8 + - + +
47C GLU* 3.2 25.1 + - - +
49C LEU 3.6 15.6 + - - -
50C PRO* 4.1 5.6 - - - +
51C PRO* 3.7 19.7 - - + +
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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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16B TRP* 3.4 41.2 - - + -
20B LEU* 3.8 18.8 - - + -
41B ARG 3.2 6.1 + - - +
42B TYR 3.1 8.8 + - - +
44B GLN* 1.3 75.2 - - - +
46B ILE* 1.3 64.6 + - - +
48B ALA* 3.0 9.9 + - - -
49B LEU* 3.1 24.4 + - + +
63B ILE* 4.1 9.9 - - + -
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Residues in contact with ILE 46 (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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42B TYR 3.0 14.6 + - - +
43B SER 3.6 7.0 - - - +
45B ALA* 1.3 78.9 - - - +
47B GLU* 1.3 60.3 + - - +
48B ALA 3.2 0.7 + - - -
49B LEU* 3.5 17.9 + - - +
60B PHE* 5.6 1.3 - - + -
63B ILE* 4.0 15.5 - - + +
64B GLN* 4.0 20.0 - - + +
67B PHE* 3.7 40.2 - - + -
85B MET* 4.2 10.1 - - + -
81C ASP* 4.0 25.9 - - + +
82C TYR* 3.9 8.7 - - - -
85C MET* 3.7 31.2 - - + -
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Residues in contact with GLU 47 (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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43B SER* 2.8 25.1 + - - +
44B GLN* 3.7 6.3 - - - +
45B ALA 3.3 0.2 - - - -
46B ILE* 1.3 76.0 - - - +
48B ALA* 1.3 60.4 + - + +
43C SER* 5.2 1.2 + - - -
46C ILE* 3.6 34.0 - - + +
64C GLN* 3.6 28.6 + - - +
67C PHE* 3.6 33.4 - - + -
71C LYS* 5.7 0.3 - - - -
82C TYR* 3.4 42.7 + - - +
85C MET* 3.5 17.7 - - + +
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Residues in contact with ALA 48 (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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11B ASN* 3.0 38.0 - - - +
16B TRP* 3.9 11.0 - - + +
44B GLN 3.2 14.2 + - - +
45B ALA 3.0 6.5 + - - +
47B GLU* 1.3 79.0 - - + +
49B LEU* 1.3 59.7 + - - +
50B PRO* 3.5 9.9 - - - +
43C SER* 6.0 1.8 - - - -
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Residues in contact with LEU 49 (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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11B ASN* 3.7 17.9 - - - +
12B ASN* 3.8 7.9 - - - +
13B PRO* 3.8 23.3 - - + -
16B TRP* 3.9 16.2 - - + -
45B ALA 3.1 20.0 + - - +
46B ILE* 3.5 12.6 + - - +
47B GLU 3.5 0.4 - - - -
48B ALA* 1.3 79.6 - - - +
50B PRO* 1.3 67.7 - - - +
51B PRO* 3.5 5.0 - - - +
54B TYR* 3.8 22.0 - - + -
60B PHE* 3.3 32.3 - - + -
63B ILE* 3.8 30.1 - - + -
81C ASP* 4.8 0.9 - - - +
82C TYR* 4.5 1.3 - - - -
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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