Contacts of the helix formed by residues 25 - 47 (chain H) in PDB entry 5W97
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 GLN 25 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 5.6 0.7 + - - -
153B LEU* 4.0 16.2 - - + -
179B LEU* 2.7 23.6 + - + +
181B GLN* 3.7 35.4 - - + +
20H PHE* 2.7 31.2 + - - +
21H PRO 4.4 0.4 - - - -
22H ASN 2.8 20.0 + - - -
23H GLN 3.6 10.8 - - - +
24H ASN* 1.3 75.5 + - - +
26H THR* 1.3 64.2 + - - +
27H ARG 3.2 2.5 - - - -
28H ASN* 3.0 46.1 + - + +
29H CYS 3.3 8.7 + - - -
63H LEU* 5.0 4.8 - - + +
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Residues in contact with THR 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLY 3.5 21.5 - - - +
178B ARG* 3.3 5.7 - - - +
179B LEU* 2.9 27.6 + - - -
110C PRO* 4.2 21.3 - - + +
24H ASN* 2.4 28.8 + - - -
25H GLN* 1.3 78.5 - - - +
27H ARG* 1.3 61.8 - - - +
29H CYS* 3.4 7.1 + - - +
30H TRP* 3.2 18.4 + - - +
68H TRP* 4.0 16.0 - - + -
72H TRP* 5.5 0.2 - - - -
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Residues in contact with ARG 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PRO* 3.4 22.9 + - - -
109C THR* 4.9 0.2 - - - +
110C PRO* 4.7 10.0 - - - +
114C GLY* 3.1 33.4 + - - -
304C PGV 6.0 1.6 - - - +
20H PHE* 3.7 25.6 - - + -
24H ASN* 4.9 2.3 + - - +
25H GLN 3.2 0.6 - - - -
26H THR* 1.3 77.3 - - - +
28H ASN* 1.3 56.0 + - - +
29H CYS 3.4 0.2 - - - -
30H TRP* 3.6 29.2 - - + +
31H GLN* 2.7 45.9 + - + +
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Residues in contact with ASN 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 6.0 2.2 - - - +
14H ALA* 5.9 0.4 - - - +
15H PRO 5.3 4.2 + - - -
17H ASP* 4.3 15.5 - - - +
20H PHE* 3.4 37.9 + - + +
25H GLN* 3.0 36.6 + - - +
27H ARG* 1.3 74.1 - - - +
29H CYS* 1.3 64.3 + - - +
32H ASN* 2.8 53.4 + - - +
59H VAL* 4.4 1.8 - - - +
63H LEU* 3.4 22.0 - - + +
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Residues in contact with CYS 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.9 19.7 - - + -
25H GLN 3.3 3.2 + - - -
26H THR 3.5 8.7 - - - +
28H ASN* 1.3 80.7 - - - +
30H TRP* 1.3 63.3 + - - +
32H ASN* 4.2 0.8 - - - -
33H TYR* 3.1 18.2 + - - +
60H TYR* 4.2 1.7 - - - +
63H LEU* 4.3 8.7 - - + +
64H CYS* 2.1 59.8 - - - +
68H TRP* 4.0 9.9 - - + -
72H TRP* 3.6 22.2 - - - -
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Residues in contact with TRP 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PRO* 3.5 45.5 - - + -
113C GLY* 3.8 23.9 + - - -
114C GLY* 4.3 2.8 - - - -
26H THR 3.2 11.3 + - - +
27H ARG* 3.2 49.8 + - + +
29H CYS* 1.3 78.3 - - - +
31H GLN* 1.3 69.9 + - - +
33H TYR* 3.2 4.3 + + - +
34H LEU* 3.0 49.0 + - + +
72H TRP* 3.7 27.8 - + + -
81H PHE* 3.5 39.0 - + - -
82H PRO* 4.9 1.8 - - + -
83H GLY* 4.1 11.4 - - - -
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Residues in contact with GLN 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ARG* 4.0 20.6 - - - +
20H PHE* 3.9 18.6 - - + -
27H ARG* 2.7 37.6 + - - +
28H ASN 4.4 0.7 - - - +
29H CYS 3.5 0.2 - - - -
30H TRP* 1.3 77.4 - - - +
32H ASN* 1.3 60.4 + - - +
34H LEU* 3.2 8.5 + - - +
35H ASP* 2.8 63.3 + - - +
38H ARG* 3.9 13.7 + - - -
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Residues in contact with ASN 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASP* 4.9 1.2 + - - +
19H ARG* 4.5 16.6 + - - +
20H PHE* 4.8 0.2 - - - -
28H ASN* 2.8 43.9 + - - +
30H TRP 3.3 0.2 - - - -
31H GLN* 1.3 80.9 - - - +
33H TYR* 1.3 60.1 + - - +
35H ASP* 4.3 5.9 - - - +
36H PHE* 3.0 25.6 + - - +
55H TRP* 5.0 2.4 + - - -
56H TYR* 3.8 32.4 - - - +
59H VAL* 3.4 33.1 - - + +
60H TYR* 3.9 9.6 - - + -
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Residues in contact with TYR 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H CYS 3.1 18.5 + - - +
30H TRP* 3.2 5.4 + + - +
32H ASN* 1.3 78.6 - - - +
34H LEU* 1.3 62.3 - - + +
36H PHE* 3.8 0.3 - - - +
37H HIS* 3.1 56.5 + + + -
60H TYR* 3.7 36.7 - + + +
69H VAL* 4.2 6.7 - - + -
72H TRP* 3.2 44.6 - + + +
73H ASP* 2.5 38.0 + - - -
76H ARG* 2.9 18.0 + - - -
81H PHE* 3.8 24.7 - + - -
85H ILE* 5.2 0.2 - - + -
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLY 5.7 0.4 - - - +
30H TRP* 3.0 50.8 + - + +
31H GLN* 3.6 14.6 - - - +
33H TYR* 1.3 73.9 - - + +
35H ASP* 1.3 60.8 + - - +
37H HIS* 3.3 4.1 + - - +
38H ARG* 2.8 63.4 + - - +
81H PHE* 3.6 37.9 - - + -
83H GLY* 4.4 6.7 - - - -
84H LYS 4.4 3.6 - - - +
85H ILE* 4.3 11.7 - - + +
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Residues in contact with ASP 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ARG* 4.5 8.3 + - - -
31H GLN* 2.8 49.7 + - - +
32H ASN* 4.0 3.3 - - - +
34H LEU* 1.3 71.6 - - - +
36H PHE* 1.3 64.8 + - - +
38H ARG* 3.6 16.1 + - - +
39H CYS* 2.8 26.0 + - - +
56H TYR* 3.9 39.5 - - + -
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Residues in contact with PHE 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H ASN 3.0 20.2 + - - +
33H TYR 3.8 2.2 - - - +
35H ASP* 1.3 79.7 - - - +
37H HIS* 1.3 93.1 + + - +
39H CYS* 3.1 2.3 + - - +
40H GLU* 2.8 54.1 + - + +
50H VAL* 5.3 6.1 - - + -
53H CYS* 3.4 34.1 - - + -
54H GLU* 5.0 2.5 - - - -
56H TYR* 3.8 14.7 - - + +
57H ARG* 3.5 37.2 - - + -
60H TYR* 3.7 17.5 - + + -
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Residues in contact with HIS 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H TYR* 3.1 62.3 + + - +
34H LEU 4.2 0.4 - - - +
36H PHE* 1.3 106.4 - + - +
38H ARG* 1.3 57.0 + - - +
40H GLU* 3.8 17.8 + - - +
41H LYS* 3.0 27.2 + - - +
60H TYR* 3.8 8.5 + - - -
73H ASP* 4.0 1.3 - - - -
76H ARG* 3.1 40.3 + - - +
85H ILE* 3.8 27.5 - - + +
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Residues in contact with ARG 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H GLN* 3.9 19.6 + - - -
34H LEU* 2.8 43.4 + - - +
35H ASP* 3.6 13.3 + - - +
37H HIS* 1.3 73.6 - - - +
39H CYS* 1.3 67.7 + - - +
41H LYS* 3.3 8.0 + - - +
42H ALA* 3.3 21.1 + - - +
84H LYS* 2.7 36.9 + - - +
85H ILE* 4.1 24.9 + - + +
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Residues in contact with CYS 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ASP 2.8 20.6 + - - +
36H PHE 3.5 2.7 - - - +
38H ARG* 1.3 73.7 - - - +
40H GLU* 1.3 60.6 + - - +
42H ALA* 3.3 4.6 + - - +
43H MET* 3.0 42.9 + - - +
52H VAL* 4.2 7.6 - - - -
53H CYS* 2.0 58.1 - - + -
56H TYR* 4.5 13.5 - - + -
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Residues in contact with GLU 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H PHE* 2.8 45.1 + - + +
37H HIS* 3.8 23.6 + - - +
39H CYS* 1.3 73.4 - - - +
41H LYS* 1.3 55.3 + - - +
43H MET* 4.6 2.5 - - - +
44H THR* 3.0 34.6 + - - +
50H VAL* 4.0 23.9 - - + +
53H CYS* 3.2 8.3 - - - -
76H ARG* 5.1 2.9 + - - -
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Residues in contact with LYS 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H HIS 3.0 19.3 + - - +
38H ARG* 3.3 6.9 + - - +
40H GLU* 1.3 71.9 + - - +
42H ALA* 1.3 69.6 + - - +
44H THR* 3.4 19.7 - - + +
45H ALA* 3.9 6.9 + - - +
46H LYS* 5.2 0.2 + - - -
85H ILE* 3.7 41.9 + - + +
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Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG 3.3 9.1 + - - +
39H CYS* 3.6 8.3 - - - +
41H LYS* 1.3 83.4 - - + +
43H MET* 1.3 74.5 + - + +
44H THR 3.2 0.5 + - - -
45H ALA 3.4 7.4 + - - -
46H LYS* 3.5 32.9 + - + +
52h VAL* 6.2 0.9 - - + -
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Residues in contact with MET 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H CYS* 3.0 31.7 + - - +
40H GLU* 4.5 1.8 - - - +
42H ALA* 1.3 85.1 - - + +
44H THR* 1.3 61.7 + - - +
45H ALA 3.3 0.2 - - - -
46H LYS 5.0 0.2 - - - +
47H GLY* 3.3 22.7 + - - +
48H GLY 3.6 20.6 + - - +
49H ASP 3.4 28.1 + - - +
50H VAL* 4.2 8.6 + - - -
52H VAL* 4.8 3.4 - - + -
53H CYS* 3.9 12.6 - - - -
39h CYS* 5.6 2.9 - - - -
43h MET* 3.4 33.0 - - + +
52h VAL* 4.0 23.1 - - + -
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Residues in contact with THR 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H GLU* 3.0 24.2 + - + +
41H LYS* 3.4 19.5 - - + +
43H MET* 1.3 77.6 - - - +
45H ALA* 1.3 69.0 + - + +
47H GLY* 4.3 2.9 + - - -
50H VAL* 5.9 3.7 - - - +
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LYS 4.3 6.7 - - - +
42H ALA 3.4 3.4 + - - +
43H MET 3.3 0.2 - - - -
44H THR* 1.3 84.6 - - + +
46H LYS* 1.3 88.0 + - - +
47H GLY* 3.0 3.9 + - - -
8h ILE* 5.3 6.1 - - + -
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Residues in contact with LYS 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H LYS 5.2 0.2 + - - -
42H ALA* 3.5 25.9 + - + +
45H ALA* 1.3 105.3 - - - +
47H GLY* 1.3 61.1 + - - +
48H GLY 4.6 0.2 - - - +
7h LYS 5.7 4.7 - - - +
8h ILE* 4.0 23.6 - - - +
51h SER* 5.4 4.5 + - - +
52h VAL* 3.7 44.3 - - + +
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Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H MET 3.3 10.6 + - - -
44H THR 4.8 2.7 - - - -
45H ALA 3.0 6.9 + - - -
46H LYS* 1.3 77.7 - - - +
48H GLY* 1.3 57.0 + - - +
49H ASP 3.4 7.4 + - - -
49h ASP* 5.0 5.1 - - - +
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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
------------------------------------------------------------
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