Contacts of the helix formed by residues 24 - 39 (chain W) in PDB entry 5L4K
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 24 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O TRP* 4.7 13.4 - - + -
17W ARG* 4.0 33.2 - - + -
18W ASN 3.8 2.9 - - - -
19W GLY* 4.7 0.2 - - - -
22W LEU 2.6 8.6 + - - +
23W PRO* 1.3 80.1 + - - +
25W ARG* 1.3 69.4 + - - +
26W LEU* 3.0 21.0 + - + +
27W GLN* 3.2 21.7 + - - +
28W ALA 3.1 17.8 + - - -
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Residues in contact with ARG 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W ASP* 3.1 30.5 + - - -
15W TYR* 3.8 25.1 + - - -
16W MET* 3.3 35.1 - - - +
18W ASN* 2.8 30.7 + - + +
20W ASP* 4.6 1.3 - - - -
21W PHE* 4.1 18.4 - - + -
22W LEU 3.9 1.3 + - - -
24W THR* 1.3 73.6 - - - +
26W LEU* 1.3 56.2 + - - +
28W ALA* 3.9 6.7 - - - -
29W GLN* 2.9 42.9 + - - +
113W VAL 3.8 0.8 + - - +
114W GLY* 3.4 14.2 + - - -
143W PHE* 2.8 53.0 + - + +
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Residues in contact with LEU 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W MET* 3.5 49.1 + - + +
17W ARG* 6.0 1.8 - - + -
24W THR* 3.0 13.6 + - + -
25W ARG* 1.3 73.1 - - - +
27W GLN* 1.3 74.8 + - + +
29W GLN* 3.0 14.9 + - - +
30W GLN* 3.1 23.9 + - - +
76W HIS 5.9 0.9 - - - +
78W VAL* 3.9 22.7 - - + +
80W PRO* 4.2 20.0 - - + -
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Residues in contact with GLN 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W PRO* 3.3 33.0 - - + +
24W THR* 3.2 21.0 + - - +
26W LEU* 1.3 86.2 - - + +
28W ALA* 1.3 64.0 + - - +
30W GLN* 2.9 32.4 + - - +
31W ASP* 3.1 19.7 + - - +
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Residues in contact with ALA 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W PHE* 4.8 0.4 - - + -
22W LEU* 3.9 35.8 + - + +
24W THR 3.1 16.1 + - - +
25W ARG* 3.8 6.5 - - - +
27W GLN* 1.3 76.3 - - - +
29W GLN* 1.3 63.5 + - - +
31W ASP* 3.1 14.2 + - - +
32W ALA* 3.0 22.3 + - - +
143W PHE* 4.1 21.2 - - + -
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Residues in contact with GLN 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W VAL* 3.8 23.5 - - + +
11W ASP* 3.6 10.6 - - - +
16W MET* 4.2 15.5 - - + -
25W ARG* 2.9 30.2 + - - +
26W LEU 3.0 10.1 + - - +
28W ALA* 1.3 75.1 - - - +
30W GLN* 1.3 64.6 + - + +
32W ALA* 3.2 5.9 + - - +
33W VAL* 3.1 27.4 + - + +
75W LEU* 5.3 1.1 - - + -
112W PHE* 3.4 40.6 - - - +
143W PHE* 3.4 26.3 - - - -
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Residues in contact with GLN 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W LEU* 3.1 23.7 + - + +
27W GLN* 2.9 27.9 + - - +
29W GLN* 1.3 77.1 - - + +
31W ASP* 1.3 67.8 + - - +
33W VAL* 3.3 2.8 + - - +
34W ASN* 3.0 23.0 + - - +
72W LEU* 4.8 5.0 - - + +
75W LEU* 3.8 34.6 - - + +
76W HIS* 3.8 40.6 + - - +
78W VAL* 5.5 2.7 - - + -
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Residues in contact with ASP 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22W LEU* 5.5 7.2 - - + +
27W GLN* 3.1 17.8 + - - +
28W ALA* 3.1 12.5 + - - +
30W GLN* 1.3 77.5 - - - +
32W ALA* 1.3 63.6 + - - +
34W ASN* 3.0 18.8 + - - +
35W ILE* 3.1 20.7 + - + +
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Residues in contact with ALA 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W ALA 3.0 12.0 + - - +
29W GLN* 3.2 18.6 + - - +
31W ASP* 1.3 76.0 - - - +
33W VAL* 1.3 64.4 + - - +
35W ILE* 3.0 14.9 + - - +
36W VAL* 3.0 20.4 + - + +
112W PHE* 4.5 12.3 - - + -
143W PHE* 5.6 6.3 - - + -
182W ALA* 4.9 22.0 - - + +
183W LEU* 6.2 3.8 - - - -
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Residues in contact with VAL 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W VAL* 3.7 27.4 - - + -
10W VAL* 4.8 9.4 - - + -
29W GLN* 3.1 22.2 + - + +
30W GLN 3.7 0.7 - - - +
32W ALA* 1.3 74.9 - - - +
34W ASN* 1.3 67.5 + - - +
35W ILE 2.9 1.4 + - - -
36W VAL* 2.9 12.4 + - - +
37W CYS* 3.0 32.6 + - - -
51W LEU* 5.0 0.2 - - + -
71W ILE* 4.4 9.0 - - + +
72W LEU* 6.1 0.7 - - - -
75W LEU* 3.6 31.2 - - + -
112W PHE* 3.8 19.5 - - + -
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Residues in contact with ASN 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W GLN 3.0 13.2 + - - +
31W ASP* 3.0 12.8 + - - +
33W VAL* 1.3 78.9 - - - +
35W ILE* 1.3 75.6 + - - +
37W CYS* 4.6 3.5 - - - +
38W HIS* 3.4 23.7 + - - +
68W THR* 4.8 8.6 - - - +
72W LEU* 3.5 42.3 - - + +
75W LEU* 5.0 0.2 - - - +
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Residues in contact with ILE 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31W ASP* 3.1 15.0 + - + +
32W ALA* 3.0 8.3 + - - +
33W VAL 3.0 1.0 - - - -
34W ASN* 1.3 94.5 - - - +
36W VAL* 1.3 60.9 + - + +
37W CYS 3.3 0.4 - - - -
38W HIS* 3.9 8.9 - - - +
39W SER* 2.9 44.6 + - - +
183W LEU* 4.9 22.9 - - + +
186W SER* 5.2 9.0 - - - +
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Residues in contact with VAL 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W THR* 5.9 3.0 - - + +
8W VAL* 5.7 4.3 - - + -
32W ALA* 3.0 14.8 + - + +
33W VAL* 2.9 5.5 + - - +
35W ILE* 1.3 79.1 - - + +
37W CYS* 1.3 64.1 + - - +
39W SER* 3.8 6.0 + - - -
40W LYS* 3.5 19.2 + - + +
110W ILE* 3.9 20.2 - - + -
112W PHE* 4.2 18.2 - - + -
182W ALA 5.9 1.1 - - - +
186W SER* 4.1 14.8 - - - +
187W PRO* 3.9 38.8 - - + -
188W ILE* 5.0 8.7 - - + +
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Residues in contact with CYS 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6W THR* 6.3 1.1 - - - -
8W VAL* 3.7 13.7 - - - -
33W VAL* 3.0 38.8 + - - +
34W ASN* 4.6 1.3 - - - +
36W VAL* 1.3 74.7 - - - +
38W HIS* 1.3 66.6 + - - +
39W SER 3.1 1.3 - - - -
40W LYS* 2.9 15.5 + - - +
41W THR* 3.0 14.7 + - - +
49W VAL* 3.7 35.3 - - + +
68W THR* 3.7 22.5 + - + +
71W ILE* 3.8 10.8 - - + -
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Residues in contact with HIS 38 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W ASN* 3.4 20.4 + - - +
35W ILE* 3.6 10.7 + - + +
37W CYS* 1.3 78.3 - - - +
39W SER* 1.3 60.6 + - - +
41W THR* 3.1 23.6 + - - -
42W ARG* 3.5 44.7 + - + +
68W THR* 4.0 13.8 - - + +
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Residues in contact with SER 39 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35W ILE* 2.9 30.2 + - - +
36W VAL* 4.2 5.4 - - - -
37W CYS 3.1 0.4 - - - -
38W HIS* 1.3 76.2 - - - +
40W LYS* 1.3 58.1 + - - +
42W ARG* 3.6 25.7 + - - +
43W SER* 3.1 20.6 + - - -
188W ILE* 4.2 30.3 - - - +
196W MET 3.3 10.4 - - - +
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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
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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