Contacts of the helix formed by residues 2 - 19 (chain K) in PDB entry 2WQT
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 THR 2 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0K LEU 3.5 5.0 + - - -
1K MET* 1.3 82.7 - - + +
3K LYS* 1.3 65.2 + - - +
4K HIS 3.2 1.8 - - - -
5K THR* 3.1 15.8 + - + +
6K LEU* 2.9 41.3 + - - +
29K LEU 6.1 1.3 - - - +
30K ILE* 6.6 0.2 - - - -
34K ASN* 5.8 4.9 - - - +
37K ALA* 5.7 2.4 - - - +
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Residues in contact with LYS 3 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0K LEU* 3.7 32.9 - - + +
1K MET 3.2 2.8 - - - -
2K THR* 1.3 78.5 + - - +
4K HIS* 1.3 64.2 + - - +
6K LEU* 3.2 14.4 + - + +
7K GLU* 3.0 42.3 + - + +
44K ILE* 4.8 10.3 - - + -
52R GLN* 2.9 33.4 + - - +
53R GLY* 4.8 6.1 - - - +
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Residues in contact with HIS 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0K LEU 4.9 1.2 + - - -
1K MET 4.4 1.6 + - - +
2K THR 3.2 0.4 - - - -
3K LYS* 1.3 78.0 - - - +
5K THR* 1.3 66.0 + - - +
7K GLU* 3.3 9.2 + - - +
8K GLN* 3.1 48.0 + - + +
49R ASP* 3.4 33.2 + - - -
52R GLN* 4.2 9.2 + - - +
54R ARG* 3.5 51.7 + - + +
85R ASP* 4.0 13.5 - - - +
98R ARG* 5.5 3.6 - - - -
1263R K 4.3 10.1 - - - -
1318R NA 4.1 7.7 - - - -
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Residues in contact with THR 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K MET 4.4 3.5 + - - -
2K THR* 3.1 23.1 + - + +
4K HIS* 1.3 80.4 - - - +
6K LEU* 1.3 62.1 + - + +
8K GLN* 3.2 18.4 + - - +
9K LEU* 3.0 47.0 + - + +
29K LEU* 4.9 20.4 - - + +
30K ILE* 5.7 0.9 - - + -
98R ARG* 5.5 11.1 + - - -
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Residues in contact with LEU 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0K LEU 6.1 0.7 - - - +
2K THR* 2.9 34.7 + - - +
3K LYS* 3.4 17.9 - - + +
5K THR* 1.3 76.1 - - - +
7K GLU* 1.3 60.5 + - - +
9K LEU* 3.3 2.1 + - - +
10K ALA* 2.9 30.9 + - - +
30K ILE* 4.1 25.6 - - + -
37K ALA* 4.2 19.1 - - + +
40K ALA* 4.0 21.5 - - + -
41K ILE* 3.9 23.0 - - + +
44K ILE* 5.1 11.9 - - + -
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Residues in contact with GLU 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LYS* 3.0 45.1 + - + +
4K HIS* 3.5 7.9 - - - +
6K LEU* 1.3 75.5 - - - +
8K GLN* 1.3 62.1 + - - +
10K ALA* 3.5 5.4 + - - +
11K ALA* 3.0 24.3 + - - +
14K ARG* 5.2 2.6 + - - -
44K ILE* 3.6 31.7 - - + +
18R GLU* 5.5 0.2 - - - -
52R GLN* 3.3 48.5 - - + +
1263R K 4.6 1.8 - - - -
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Residues in contact with GLN 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K HIS* 3.1 44.8 + - + +
5K THR* 3.4 23.9 - - + +
6K LEU 3.2 0.4 - - - -
7K GLU* 1.3 77.2 - - - +
9K LEU* 1.3 58.6 + - + +
11K ALA* 3.2 4.3 + - - +
12K ASP* 3.0 34.1 + - - +
14R ARG 5.0 0.2 + - - -
17R ALA* 3.9 28.4 + - - +
18R GLU* 3.7 33.3 - - + +
1263R K 4.5 4.9 - - - -
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Residues in contact with LEU 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K THR* 3.0 28.0 + - + +
6K LEU 3.9 3.1 - - - +
8K GLN* 1.3 73.7 - - + +
10K ALA* 1.3 66.0 + - - +
12K ASP* 3.1 18.7 + - - +
13K LEU* 3.0 26.6 + - - +
26K LEU* 4.0 32.3 - - + +
29K LEU* 4.2 30.3 - - + -
30K ILE* 3.4 33.0 - - + -
41K ILE* 3.9 18.2 - - + -
18R GLU 5.6 0.9 - - - +
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Residues in contact with ALA 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU 2.9 17.7 + - - +
7K GLU 3.6 5.4 - - - +
9K LEU* 1.3 77.6 - - - +
11K ALA* 1.3 57.2 + - - +
13K LEU* 3.3 1.8 + - - -
14K ARG* 3.0 25.0 + - - +
41K ILE* 3.8 16.9 - - + +
44K ILE* 3.8 26.2 - - + -
45K ASN* 3.2 33.3 + - - +
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Residues in contact with ALA 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K GLU 3.0 14.3 + - - +
8K GLN 3.5 8.5 - - - +
9K LEU 3.2 0.2 - - - -
10K ALA* 1.3 74.9 - - - +
12K ASP* 1.3 59.6 + - - +
14K ARG* 3.2 26.9 + - - +
15K ARG* 2.9 36.1 + - - +
1262K PO4 5.2 3.9 + - - +
18R GLU* 3.7 24.7 - - - +
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Residues in contact with ASP 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K GLN* 3.0 17.2 + - - +
9K LEU* 3.3 25.7 - - + +
11K ALA* 1.3 77.0 - - - +
13K LEU* 1.3 56.5 + - - +
15K ARG* 2.7 36.5 + - - +
16K ALA* 2.9 28.9 + - - +
23K ILE* 3.9 26.7 - - + +
26K LEU* 5.7 0.2 - - - +
18R GLU* 3.0 32.1 - - - +
19R GLN* 4.4 3.0 - - - +
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Residues in contact with LEU 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LEU 3.0 9.5 + - - +
10K ALA 3.4 8.5 - - - +
11K ALA 3.2 0.2 - - - -
12K ASP* 1.3 72.7 - - - +
14K ARG* 1.3 65.1 + - - +
16K ALA* 3.4 4.8 + - - +
17K ALA* 3.2 22.2 + - - +
23K ILE* 3.7 23.6 - - + -
26K LEU* 3.7 27.8 - - + -
41K ILE* 3.8 17.3 - - + -
45K ASN* 3.8 9.0 - - - +
143K ARG* 3.9 23.4 - - + +
144K ILE* 4.7 4.5 - - + -
156K ALA 3.6 25.6 - - - +
157K ASP* 4.0 18.4 - - - +
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Residues in contact with ARG 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I GLN* 5.2 0.2 + - - -
7K GLU* 5.2 2.0 + - - -
10K ALA* 3.0 18.5 + - - +
11K ALA* 3.6 28.8 - - - +
13K LEU* 1.3 75.0 - - - +
15K ARG* 1.3 63.4 + - - +
17K ALA* 3.2 7.8 + - - +
18K GLU* 3.0 36.8 + - - +
44K ILE* 4.5 7.5 - - - +
45K ASN* 2.8 47.9 + - - +
48K HIS* 3.7 51.8 + - - +
49K ASP* 4.8 4.5 - - - -
1265K K 4.5 7.9 - - - -
1305K NA 4.4 8.1 - - - -
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Residues in contact with ARG 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I ARG* 3.6 18.2 - - - +
11K ALA 2.9 14.7 + - - +
12K ASP* 2.7 37.6 + - - +
14K ARG* 1.3 73.5 - - - +
16K ALA* 1.3 66.3 + - - +
18K GLU* 3.3 10.1 + - - +
19K GLN* 2.9 42.1 + - - +
1262K PO4 2.8 46.0 + - - +
1263K PO4 3.8 19.1 - - - -
15R ARG* 3.7 10.9 - - - +
18R GLU* 3.2 19.4 + - - +
19R GLN* 3.3 27.2 - - - +
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Residues in contact with ALA 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ASP 2.9 18.7 + - - +
13K LEU* 3.5 9.2 - - - +
15K ARG* 1.3 76.6 - - - +
17K ALA* 1.3 56.6 + - - +
19K GLN* 5.0 1.8 - - - -
20K GLY* 3.0 24.9 + - - -
21K GLU 3.2 31.0 + - - +
23K ILE* 4.1 10.5 - - + +
100K LEU* 4.1 2.3 - - - +
143K ARG* 3.8 28.7 - - + +
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Residues in contact with ALA 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLN* 3.8 21.2 + - - +
13K LEU 3.2 10.4 + - - +
14K ARG* 3.6 9.0 - - - +
16K ALA* 1.3 76.7 - - - +
18K GLU* 1.3 66.3 + - - +
19K GLN 3.3 0.7 + - - -
20K GLY* 3.4 9.6 + - - -
100K LEU* 5.4 2.9 - - - +
143K ARG* 3.8 20.4 - - + +
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Residues in contact with GLU 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLN* 3.9 34.9 - - + +
9I LEU* 5.7 0.2 - - - +
11I ALA* 3.5 23.3 - - - +
12I ASP* 2.9 34.3 - - - +
15I ARG* 3.1 27.5 + - - +
14K ARG* 3.0 30.4 + - - +
15K ARG* 3.7 7.0 - - - +
17K ALA* 1.3 75.9 - - - +
19K GLN* 1.3 58.9 + - - +
1262K PO4 3.9 4.7 + - - -
1265K K 3.6 16.6 - - - -
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Residues in contact with GLN 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ASP* 4.3 3.6 - - - +
15I ARG* 3.0 38.5 - - - +
19I GLN* 5.2 0.4 + - - -
15K ARG* 2.9 26.9 + - - +
16K ALA* 5.2 0.9 - - - -
18K GLU* 1.3 76.7 - - - +
20K GLY* 1.3 62.8 + - - +
21K GLU* 3.4 35.8 + - + +
1263K PO4 2.8 40.3 + - - -
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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
------------------------------------------------------------
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