Contacts of the helix formed by residues 24 - 41 (chain X) in PDB entry 1YHQ
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 LYS 24 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17270 G 5.9 1.0 + - - -
20440 G 4.1 4.6 + - - +
20X GLU* 3.7 29.6 + - + +
21X PRO* 3.0 22.0 + - + +
23X HIS* 1.3 120.1 - - + +
25X ARG* 1.3 64.8 + - - +
26X ALA 3.4 2.7 - - - -
27X ASP* 3.4 16.4 + - + +
28X LYS 3.5 7.3 + - - -
63X ARG* 4.0 29.4 - - - +
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Residues in contact with ARG 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27270 A 5.0 8.3 + - - -
27280 C 4.2 19.4 + - - -
14X LEU 5.5 3.2 + - - -
17X ALA* 4.0 27.4 + - + +
18X ARG* 3.7 29.3 - - - +
20X GLU* 4.8 0.7 - - - +
21X PRO 3.6 2.4 + - - +
22X ASN* 3.4 34.4 + - - +
24X LYS* 1.3 75.7 - - - +
26X ALA* 1.3 53.7 + - - +
28X LYS* 2.9 9.5 + - - +
29X ALA* 2.7 34.5 + - - +
63X ARG 3.2 6.6 + - - +
64X ALA 2.9 26.6 + - - +
65X ASN* 4.4 9.3 + - - +
66X THR* 3.7 34.6 + - - +
67X PRO 6.0 0.4 - - - -
68X SER* 6.0 2.6 - - - +
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Residues in contact with ALA 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25X ARG* 1.3 75.6 - - - +
27X ASP* 1.3 63.0 + - - +
29X ALA* 3.2 4.2 + - - +
30X MET* 3.1 27.2 + - - +
58X ALA 4.3 3.8 - - - +
59X TRP* 3.5 39.7 - - + +
62X GLY 4.2 2.5 - - - +
63X ARG* 3.0 27.7 + - + +
66X THR* 3.3 14.3 + - - +
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Residues in contact with ASP 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13820 G 2.6 26.4 + - - +
13830 U 3.5 28.5 + - - +
24X LYS* 3.7 9.8 - - + +
25X ARG 3.2 0.8 - - - -
26X ALA* 1.3 73.2 - - - +
28X LYS* 1.3 63.3 + - - +
30X MET* 3.2 14.0 + - - +
31X ILE* 3.2 20.3 + - + +
59X TRP* 3.5 10.9 - - - -
63X ARG* 2.8 37.9 + - - +
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Residues in contact with LYS 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17280 G 4.1 23.2 + - - +
17290 A 2.7 35.7 + - - -
17310 C 5.3 2.0 - - - +
16X ASP 4.8 4.7 - - - +
17X ALA* 4.2 16.8 - - + -
19X ALA* 6.5 0.7 - - - -
20X GLU* 3.8 45.2 + - + +
24X LYS 3.5 1.4 + - - -
25X ARG 2.9 8.1 + - - +
27X ASP* 1.3 80.1 - - - +
29X ALA* 1.3 63.8 + - - +
31X ILE* 3.1 22.4 + - + +
32X LEU* 3.0 37.6 + - + +
35X GLU* 5.5 3.2 + - - -
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Residues in contact with ALA 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X LEU* 4.1 10.7 - - + +
17X ALA* 4.4 9.8 - - + +
25X ARG 2.7 16.5 + - - +
26X ALA* 3.4 10.3 - - - +
27X ASP 3.2 0.2 - - - -
28X LYS* 1.3 73.4 - - - +
30X MET* 1.3 63.8 + - - +
32X LEU* 3.0 9.8 + - - +
33X ILE* 3.0 28.4 + - + +
58X ALA* 4.6 7.4 - - + -
66X THR* 3.7 29.2 - - + +
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Residues in contact with MET 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13830 U 3.7 10.1 - - - +
13840 C 3.4 34.8 + - - +
26X ALA 3.1 6.7 + - - +
27X ASP* 3.2 10.7 + - - +
29X ALA* 1.3 79.5 - - - +
31X ILE* 1.3 60.8 + - + +
33X ILE* 3.7 7.4 + - - +
34X ARG* 3.4 20.8 + - - +
50X LEU* 4.0 12.4 - - + +
54X ILE* 4.2 17.7 - - - -
55X ASN* 3.6 34.3 - - - +
58X ALA* 3.2 32.3 - - + -
59X TRP* 3.7 11.7 - - + +
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Residues in contact with ILE 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13840 C 5.6 4.9 - - - +
17270 G 5.1 0.2 - - - +
17280 G 3.4 35.0 - - - +
27X ASP* 3.2 16.1 + - + +
28X LYS* 3.1 28.0 + - + +
29X ALA 3.1 0.8 - - - -
30X MET* 1.3 77.2 - - + +
32X LEU* 1.3 66.4 + - - +
34X ARG* 3.1 10.4 + - + +
35X GLU* 3.0 50.2 + - + +
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Residues in contact with LEU 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X ILE* 4.9 1.6 - - + -
13X PRO 4.9 4.0 - - - +
14X LEU* 4.2 19.7 - - + -
16X ASP* 3.8 24.7 - - + +
17X ALA* 3.5 39.9 - - + +
28X LYS* 3.0 28.9 + - + +
29X ALA* 3.4 8.1 - - - +
31X ILE* 1.3 76.7 - - - +
33X ILE* 1.3 56.5 + - - +
35X GLU* 3.2 20.5 + - - +
36X HIS* 2.8 32.0 + - - +
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Residues in contact with ILE 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X ILE* 4.3 16.2 - - + -
14X LEU* 3.9 18.6 - - + -
29X ALA 3.0 17.8 + - - +
30X MET* 3.8 17.3 - - + +
32X LEU* 1.3 76.5 - - - +
34X ARG* 1.3 61.3 + - - +
36X HIS* 3.3 2.1 + - - +
37X LEU* 3.1 42.7 + - + +
50X LEU* 4.0 15.5 - - + -
54X ILE* 3.7 29.8 - - + -
58X ALA* 5.0 4.5 - - + -
70X ILE* 4.2 23.6 - - + -
72X VAL* 5.3 3.4 - - + -
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Residues in contact with ARG 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13840 C 3.8 22.2 + - - -
13850 G 3.0 26.3 + - - -
30X MET 3.4 9.9 + - - +
31X ILE* 3.1 13.1 + - - +
33X ILE* 1.3 79.9 - - - +
35X GLU* 1.3 58.7 + - + +
38X ALA* 3.1 27.0 + - - +
45X GLU* 3.0 40.7 + - + +
46X ASP* 5.0 1.4 + - - +
48X VAL* 2.4 44.5 + - + +
50X LEU* 4.2 14.3 - - + +
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Residues in contact with GLU 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17280 G 5.4 2.4 + - - +
17290 A 5.5 4.0 + - - -
28X LYS* 5.5 3.9 + - - -
31X ILE* 3.0 34.3 + - + +
32X LEU* 3.7 24.2 - - + +
34X ARG* 1.3 75.5 - - + +
36X HIS* 1.3 64.7 + - - +
38X ALA* 3.5 2.1 + - - +
39X LYS* 3.1 25.3 + - - +
45X GLU* 3.5 29.8 - - - +
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Residues in contact with HIS 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28550 G 4.2 8.0 + - - -
10X VAL* 3.5 21.1 - - + +
11X THR 4.1 2.4 + - - -
12X ILE* 3.0 44.9 - - + +
13X PRO* 3.9 20.2 - - + +
32X LEU 2.8 17.1 + - - +
33X ILE 3.6 4.9 - - - +
35X GLU* 1.3 77.8 - - - +
37X LEU* 1.3 60.3 + - - +
39X LYS* 3.3 2.8 + - - +
40X HIS* 3.0 70.2 + + + +
41X PHE* 6.2 0.2 - - - -
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Residues in contact with LEU 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X VAL* 5.4 1.6 - - + -
12X ILE* 4.6 8.7 - - + -
33X ILE* 3.1 23.9 + - + +
34X ARG 4.1 0.2 - - - +
36X HIS* 1.3 76.4 - - - +
38X ALA* 1.3 62.4 + - - +
41X PHE* 3.0 48.1 + - + +
48X VAL* 3.9 16.1 - - + +
50X LEU* 3.6 22.0 - - + -
72X VAL* 3.8 23.3 - - + -
74X ALA* 4.0 17.5 - - + -
83X ALA* 5.6 2.9 - - + +
85X VAL* 3.2 31.9 - - + -
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Residues in contact with ALA 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X ARG 3.1 19.5 + - - +
35X GLU 3.8 4.3 - - - +
36X HIS 3.2 0.2 - - - -
37X LEU* 1.3 78.7 - - - +
39X LYS* 1.3 61.1 + - - +
42X SER* 3.2 2.9 + - - -
43X VAL* 2.9 45.9 + - - +
45X GLU* 3.8 31.0 - - + +
48X VAL* 4.0 8.0 - - + +
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Residues in contact with LYS 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28340 G 3.2 35.6 + - - +
28350 C 3.2 31.5 + - - -
29050 A 3.5 33.1 - - - +
35X GLU 3.1 18.1 + - - +
36X HIS* 3.8 2.7 - - - +
38X ALA* 1.3 77.6 - - - +
40X HIS* 1.3 85.3 + - + +
41X PHE 3.2 0.4 - - - -
42X SER* 3.2 15.8 + - - -
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Residues in contact with HIS 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28540 A 5.2 4.9 - + - -
28550 G 5.2 10.5 + - - -
29040 U 2.8 42.3 + - - +
29050 A 3.4 31.9 + - - +
8X ARG* 3.6 19.4 + - - +
10X VAL* 5.8 2.2 - - + -
36X HIS* 3.0 65.2 + + + +
39X LYS* 1.3 91.8 + - + +
41X PHE* 1.3 72.6 + - + +
42X SER 3.5 0.2 - - - -
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Residues in contact with PHE 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X GLU* 5.1 3.1 - - - -
8X ARG* 3.7 47.8 - - + +
10X VAL* 4.2 13.9 - - + -
36X HIS* 6.2 0.2 - - - -
37X LEU* 3.0 39.9 + - + +
40X HIS* 1.3 88.0 - - + +
42X SER* 1.3 75.4 + - - +
43X VAL* 3.0 16.9 - - + +
74X ALA* 3.7 37.2 - - + -
75X ALA 4.5 2.7 - - - -
76X ARG* 3.4 36.7 + - + +
83X ALA* 4.6 13.5 - - + -
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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