Contacts of the helix formed by residues 11 - 31 (chain L) in PDB entry 1Q0K
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 PRO 11 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10L ASP* 1.3 88.5 - - - +
12L ALA* 1.3 56.2 + - - -
13L GLN 3.1 0.7 - - - -
14L ALA* 3.0 10.6 + - + +
15L ARG* 3.0 26.4 + - - +
54L HIS* 6.4 0.2 - - + -
55L LEU* 5.9 0.4 - - + -
58L LEU* 3.8 27.4 - - + -
104L ILE* 4.4 7.7 - - + +
107L ILE* 5.1 2.2 - - + +
108L ASP* 3.4 31.4 - - + +
111L PHE* 3.4 47.6 - - + -
112L TRP* 5.0 0.7 - - - +
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Residues in contact with ALA 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ALA* 6.1 1.8 - - + -
16J ILE* 4.5 7.9 - - + -
10L ASP* 2.8 26.0 + - - +
11L PRO* 1.3 76.7 - - - +
13L GLN* 1.3 65.2 - - - +
15L ARG* 3.8 33.8 - - - +
16L ILE* 2.9 36.2 + - + +
108L ASP* 4.8 1.2 + - - -
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Residues in contact with GLN 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J GLN* 5.5 5.8 + - - +
16J ILE* 3.9 33.1 - - + +
17J GLU* 3.3 24.9 + - - +
1L HIS* 3.6 32.3 + - - +
10L ASP* 3.0 20.5 + - + +
12L ALA* 1.3 79.9 - - - +
14L ALA* 1.3 62.5 + - - +
16L ILE* 3.6 7.0 + - - +
17L GLU* 3.5 17.0 + - - +
54L HIS* 3.4 46.2 + - + +
7012L THJ 4.7 0.2 + - - -
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Residues in contact with ALA 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L ASP 4.5 0.2 + - - -
11L PRO* 3.0 12.7 + - + +
13L GLN* 1.3 77.9 - - - +
15L ARG* 1.3 64.8 + - - +
17L GLU 3.3 1.9 + - - -
18L ALA* 3.0 22.7 + - - +
51L ALA* 3.8 14.2 - - - +
54L HIS* 3.7 26.8 - - + +
55L LEU* 3.9 27.8 - - + -
58L LEU* 5.5 0.4 - - + -
104L ILE* 4.3 9.0 - - + -
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Residues in contact with ARG 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J ASP* 4.8 7.1 + - - -
11L PRO 3.0 13.2 + - - +
12L ALA* 3.7 34.7 - - - +
14L ALA* 1.3 77.7 - - - +
16L ILE* 1.3 70.9 + - - +
18L ALA* 3.2 7.4 + - - +
19L GLU* 2.9 53.7 + - - +
101L LEU* 4.1 16.6 - - + +
104L ILE* 4.2 17.1 - - + +
108L ASP* 5.4 9.0 + - - -
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Residues in contact with ILE 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J HIS* 4.1 18.8 - - + +
8J VAL* 4.2 12.1 - - + +
10J ASP* 4.0 30.5 - - + +
12J ALA* 4.5 10.1 - - + -
13J GLN* 4.1 32.1 - - + +
16J ILE* 5.5 2.2 - - + -
12L ALA* 2.9 31.5 + - + +
13L GLN* 4.0 6.3 - - - +
15L ARG* 1.3 88.3 - - - +
17L GLU* 1.3 63.4 + - - +
19L GLU* 3.3 21.8 + - - +
20L SER* 3.4 13.3 + - - -
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Residues in contact with GLU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J HIS* 3.0 18.3 + - - -
13J GLN* 3.0 24.2 + - - +
13L GLN 3.5 13.6 + - - +
14L ALA 3.3 7.6 + - - +
16L ILE* 1.3 76.3 - - - +
18L ALA* 1.3 62.5 + - - +
20L SER* 3.1 14.8 + - - -
21L VAL* 3.2 16.6 + - - +
47L ARG* 3.0 53.3 + - - +
50L LEU* 3.9 20.9 - - + +
51L ALA* 3.9 5.8 - - + -
54L HIS* 4.1 10.5 + - + +
7010L THJ 4.4 4.5 - - - -
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Residues in contact with ALA 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L ALA 3.0 13.7 + - - +
15L ARG 3.5 7.6 - - - +
17L GLU* 1.3 76.0 - - - +
19L GLU* 1.3 63.9 + - - +
21L VAL* 3.1 21.6 + - - +
22L LYS* 3.1 13.3 + - - +
51L ALA* 4.2 3.3 - - + +
85L LEU* 4.5 12.1 - - + -
97L GLY 5.0 2.1 - - - +
100L ALA* 5.1 1.6 - - + -
101L LEU* 3.5 24.7 - - + +
104L ILE* 3.6 17.5 - - + -
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Residues in contact with GLU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J VAL* 4.1 21.6 - - + +
15L ARG* 2.9 41.0 + - + +
16L ILE* 3.6 16.1 - - - +
17L GLU 3.2 0.4 - - - -
18L ALA* 1.3 76.5 - - - +
20L SER* 1.3 63.0 + - - +
22L LYS* 3.3 3.3 + - - +
23L ALA* 3.0 24.4 + - - +
101L LEU* 4.1 22.4 - - + -
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Residues in contact with SER 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J HIS* 3.0 30.1 - - - -
2J CYS* 5.0 0.2 - - - -
6J CYS* 3.4 20.5 - - - -
8J VAL* 3.6 12.1 - - - +
16L ILE 3.4 1.9 + - - -
17L GLU 3.1 10.6 + - - -
19L GLU* 1.3 76.7 - - - +
21L VAL* 1.3 67.0 + - - +
23L ALA* 3.8 1.2 - - - +
24L ILE* 2.8 32.0 + - - +
47L ARG* 4.0 19.3 - - - -
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Residues in contact with VAL 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L GLU 3.5 14.1 - - - +
18L ALA* 3.1 13.4 + - - +
20L SER* 1.3 78.2 - - - +
22L LYS* 1.3 62.8 + - - +
24L ILE* 3.3 8.9 + - - +
25L GLN* 3.0 33.0 + - - +
44L LYS* 3.9 23.9 - - + +
47L ARG* 3.9 4.7 - - + -
48L ALA* 3.6 34.8 - - + +
85L LEU* 5.2 4.7 - - + -
88L ALA* 3.9 26.7 - - + -
97L GLY* 4.7 4.0 - - - -
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Residues in contact with LYS 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ALA 3.1 9.1 + - - +
19L GLU 3.8 6.3 - - - +
21L VAL* 1.3 78.4 - - - +
23L ALA* 1.3 65.7 + - - +
25L GLN* 3.0 12.9 + - - +
26L GLU* 2.9 47.0 + - - +
94L PRO* 3.7 33.9 - - + +
97L GLY* 4.4 6.3 - - - -
98L GLN* 2.5 38.0 + - - +
101L LEU* 4.2 15.0 - - + -
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Residues in contact with ALA 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J CYS 3.8 20.6 - - - +
8J VAL* 4.0 12.6 - - + -
19L GLU 3.0 17.7 + - - +
20L SER 3.8 3.8 - - - +
22L LYS* 1.3 76.5 - - - +
24L ILE* 1.3 61.7 + - - +
26L GLU* 3.3 17.7 + - - +
27L LYS* 3.1 29.6 + - - +
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Residues in contact with ILE 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J CYS* 4.3 0.2 - - - -
4J LEU* 3.9 15.5 - - + -
6J CYS* 3.9 17.5 - - + -
20L SER 2.8 30.0 + - - +
21L VAL 3.5 4.0 - - - +
23L ALA* 1.3 75.6 - - - +
25L GLN* 1.3 64.4 + - - +
27L LYS* 3.2 9.6 + - - +
28L MET* 2.9 33.2 + - - +
40L ALA* 3.7 33.7 - - + +
43L ILE* 3.7 29.8 - - + -
44L LYS* 3.9 23.6 - - + -
47L ARG* 4.1 6.5 - - + -
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Residues in contact with GLN 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L VAL* 3.0 20.2 + - - +
22L LYS* 3.0 12.2 + - - +
24L ILE* 1.3 75.8 - - - +
26L GLU* 1.3 62.8 + - - +
28L MET* 3.3 9.9 + - - +
29L ALA* 3.2 18.7 + - - +
44L LYS* 3.5 14.9 - - + +
88L ALA* 3.3 14.5 + - - +
91L SER 2.9 24.7 + - - +
92L THR 3.4 22.9 - - - +
93L ASP 3.4 9.1 + - - +
94L PRO* 3.5 12.5 - - + +
96L THR* 2.9 21.4 + - - -
97L GLY* 3.2 27.0 + - - -
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Residues in contact with GLU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L LYS* 2.9 41.8 + - - +
23L ALA* 3.5 16.9 - - - +
24L ILE 3.2 0.2 - - - -
25L GLN* 1.3 77.8 - - - +
27L LYS* 1.3 61.8 + - + +
29L ALA* 3.1 20.1 + - - +
30L ALA* 3.7 6.1 + - - +
94L PRO* 4.0 21.7 - - + +
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Residues in contact with LYS 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 4.5 11.9 - - + -
5J PRO* 3.6 20.4 + - - +
6J CYS* 3.4 28.3 - - - +
7J GLY* 5.0 2.6 - - - -
9010J SO4 5.7 1.2 + - - -
23L ALA* 3.1 18.8 + - - +
24L ILE* 3.6 8.1 - - - +
26L GLU* 1.3 77.0 - - + +
28L MET* 1.3 57.4 + - - +
30L ALA* 3.0 7.1 + - - +
31L ASN* 2.9 30.8 + - + +
36L PHE* 3.7 18.4 - - + -
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Residues in contact with MET 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I HIS* 4.2 2.1 - - + +
24L ILE* 2.9 22.6 + - - +
25L GLN* 3.6 9.2 - - - +
26L GLU 3.3 0.2 - - - -
27L LYS* 1.3 75.6 - - - +
29L ALA* 1.3 60.6 + - - +
30L ALA 3.2 0.8 + - - -
31L ASN 3.7 3.4 + - - +
36L PHE* 3.9 5.6 - - + -
37L GLN* 3.2 54.3 + - - +
40L ALA* 3.5 23.8 - - + -
41L THR* 3.3 28.0 - - - +
44L LYS* 3.9 25.8 - - - -
92L THR* 3.8 28.8 - - + -
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Residues in contact with ALA 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L GLN 3.2 10.1 + - - +
26L GLU* 3.1 15.8 + - - +
27L LYS 3.1 1.0 - - - -
28L MET* 1.3 80.0 - - - +
30L ALA* 1.3 56.5 + - - +
92L THR* 5.4 3.1 - - - +
94L PRO* 5.3 8.1 - - + -
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Residues in contact with ALA 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L GLU 3.7 5.8 + - - +
27L LYS* 3.0 7.4 + - - +
29L ALA* 1.3 81.7 - - - +
31L ASN* 1.3 60.9 + - + +
32L ASP* 3.6 9.5 + - - +
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Residues in contact with ASN 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L LYS* 2.9 8.8 + - + +
28L MET 3.7 2.2 - - - +
30L ALA* 1.3 76.8 - - + +
32L ASP* 1.3 51.4 + - - +
33L ASP* 3.0 27.1 + - - +
36L PHE* 3.3 48.1 - - + +
37L GLN* 2.7 30.4 + - - -
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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