Contacts of the helix formed by residues 17 - 37 (chain K) in PDB entry 1L0N
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 TRP 17 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A THR* 4.2 12.8 - - - -
348A SER* 3.1 35.8 - - - +
443A TRP* 4.3 15.3 - + - -
445A ARG* 4.0 42.8 - - + -
446A PHE* 4.5 8.7 - + - -
13K LEU* 3.3 25.0 - - + +
14K ALA* 3.2 10.1 + - - +
15K ARG 3.2 0.4 - - - -
16K ASN* 1.3 87.6 - - + +
18K VAL* 1.3 58.1 + - - +
19K PRO* 3.6 0.9 - - - -
20K THR* 3.5 20.9 + - + -
21K ALA* 2.8 34.2 + - + +
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Residues in contact with VAL 18 (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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14K ALA* 3.2 20.5 + - + +
15K ARG* 4.0 7.6 - - + +
16K ASN 3.5 0.2 - - - -
17K TRP* 1.3 72.6 - - - +
19K PRO* 1.3 79.4 - - + +
20K THR 3.0 1.5 + - - -
21K ALA* 3.2 4.6 + - + -
22K GLN* 2.9 33.4 + - + +
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Residues in contact with PRO 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG* 4.6 17.3 - - - +
15K ARG 3.5 15.3 - - - +
16K ASN* 4.0 7.4 - - - +
17K TRP 3.8 1.1 - - - -
18K VAL* 1.3 93.8 - - + +
20K THR* 1.3 62.7 + - - +
22K GLN* 3.9 13.9 - - - +
23K LEU* 3.1 31.1 + - + +
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Residues in contact with THR 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ARG 3.8 20.4 - - - +
446A PHE* 3.5 35.8 - - + +
16J ARG* 4.3 7.7 + - - +
18J SER* 3.6 20.5 + - - +
16K ASN 4.0 9.4 + - - -
17K TRP* 3.5 21.3 + - + -
18K VAL 3.0 0.6 - - - -
19K PRO* 1.3 75.6 - - - +
21K ALA* 1.3 61.7 + - - +
23K LEU* 3.1 5.6 + - - +
24K TRP* 2.8 32.0 + - + +
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Residues in contact with ALA 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K TRP* 2.8 24.1 + - + +
18K VAL* 4.0 5.4 - - + +
20K THR* 1.3 73.2 - - - +
22K GLN* 1.3 63.2 + - - +
24K TRP* 3.3 8.2 + - - +
25K GLY* 3.0 19.9 + - - -
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Residues in contact with GLN 22 (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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18K VAL* 2.9 20.4 + - + +
19K PRO* 3.9 16.2 - - - +
21K ALA* 1.3 75.9 - - - +
23K LEU* 1.3 71.3 + - + +
25K GLY* 3.0 13.3 + - - -
26K ALA* 3.1 13.5 + - + +
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Residues in contact with LEU 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG* 4.3 11.4 - - - +
18J SER* 4.0 21.3 - - - +
19J THR* 3.8 29.2 - - + +
22J LEU* 4.2 22.4 - - + +
19K PRO* 3.1 18.0 + - + +
20K THR 3.1 5.0 + - - +
22K GLN* 1.3 85.6 - - + +
24K TRP* 1.3 63.9 + - - +
26K ALA* 3.2 10.8 + - + +
27K VAL* 3.2 24.1 + - - +
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Residues in contact with TRP 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LEU 3.8 22.4 - - - -
445A ARG* 4.8 10.5 - - - -
17J THR* 3.6 16.8 - - + -
18J SER* 3.4 43.5 - - - -
21J ALA* 4.2 12.8 - - + -
20K THR* 2.8 16.6 + - + +
21K ALA* 3.5 9.4 - - - +
23K LEU* 1.3 73.8 - - - +
25K GLY* 1.3 65.9 + - - +
27K VAL* 3.0 29.2 + - + +
28K GLY* 3.2 4.9 + - - -
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Residues in contact with GLY 25 (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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21K ALA 3.0 14.6 + - - -
22K GLN* 3.0 3.6 + - - -
24K TRP* 1.3 76.6 - - - +
26K ALA* 1.3 55.9 + - - +
28K GLY* 3.2 3.5 + - - -
29K ALA* 2.8 29.2 + - - +
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Residues in contact with ALA 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LEU* 4.1 14.1 - - + -
22K GLN* 3.1 12.1 + - + +
23K LEU* 3.4 17.7 - - + +
24K TRP 3.1 0.2 - - - -
25K GLY* 1.3 72.5 - - - +
27K VAL* 1.3 65.6 + - - +
29K ALA* 3.1 7.4 + - - +
30K VAL* 2.9 32.3 + - + +
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Residues in contact with VAL 27 (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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18J SER 3.9 9.6 - - - +
21J ALA* 3.9 18.4 - - + -
22J LEU* 3.6 35.2 - - + +
25J VAL* 4.2 18.1 - - + +
23K LEU 3.2 15.5 + - - +
24K TRP* 3.0 23.0 + - + +
26K ALA* 1.3 76.5 - - - +
28K GLY* 1.3 54.5 + - - +
30K VAL* 3.3 2.6 + - - +
31K GLY* 2.7 32.9 + - - -
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Residues in contact with GLY 28 (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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24K TRP 3.2 8.1 + - - -
25K GLY* 3.6 3.6 - - - -
27K VAL* 1.3 82.1 - - - +
29K ALA* 1.3 52.6 + - - +
31K GLY* 3.4 2.4 - - - -
32K LEU* 2.7 35.2 + - - +
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Residues in contact with ALA 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K GLY 2.8 14.7 + - - +
26K ALA* 3.5 12.1 - - - +
27K VAL 3.1 0.2 - - - -
28K GLY* 1.3 73.1 - - - +
30K VAL* 1.3 68.3 + - + +
32K LEU* 2.9 17.9 + - - +
33K VAL* 2.9 21.2 + - + +
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Residues in contact with VAL 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LEU* 4.5 11.0 - - + -
25J VAL* 3.7 21.3 - - + +
26J VAL* 4.2 23.1 - - + -
29J LEU* 5.0 13.0 - - + -
26K ALA* 2.9 24.0 + - + +
27K VAL* 3.7 3.8 - - - +
29K ALA* 1.3 76.1 - - + +
31K GLY* 1.3 55.6 - - - +
33K VAL* 3.7 7.6 - - + +
34K SER* 3.0 29.7 + - - -
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Residues in contact with GLY 31 (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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52E LYS* 4.7 1.6 + - - -
25J VAL* 3.6 17.2 - - - +
27K VAL 2.7 15.2 + - - -
28K GLY* 3.4 6.1 - - - -
30K VAL* 1.3 75.2 - - - +
32K LEU* 1.3 63.8 + - - +
34K SER* 3.9 1.2 - - - -
35K ALA* 3.0 25.7 + - - +
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Residues in contact with LEU 32 (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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28K GLY 2.7 18.3 + - - +
29K ALA* 2.9 6.8 + - - +
31K GLY* 1.3 72.1 - - - -
33K VAL* 1.3 66.5 + - + +
35K ALA* 3.1 15.2 + - + +
36K THR* 3.2 32.5 + - + +
40K LEU 6.0 0.2 - - - +
41K ILE* 4.2 30.5 - - + -
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Residues in contact with VAL 33 (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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29J LEU* 5.8 6.7 - - + -
29K ALA* 2.9 20.9 + - + +
30K VAL* 3.7 10.1 - - + +
32K LEU* 1.3 77.6 - - + +
34K SER* 1.3 60.1 + - - +
36K THR* 3.2 1.5 + - - -
37K ASP* 2.9 32.4 + - - +
38K SER* 4.4 6.7 - - - +
41K ILE* 3.6 23.3 - - + +
42K LEU* 3.5 46.2 - - + +
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Residues in contact with SER 34 (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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52E LYS* 2.7 34.9 + - - +
25J VAL* 4.9 7.5 + - - -
28J ALA* 4.9 0.3 - - - +
29J LEU* 3.4 46.2 + - - +
32J GLU* 4.6 5.7 + - - +
30K VAL* 3.0 15.7 + - - -
31K GLY* 4.1 3.4 - - - -
33K VAL* 1.3 80.7 - - - +
35K ALA* 1.3 60.9 + - - +
37K ASP* 3.5 15.7 - - - +
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Residues in contact with ALA 35 (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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52E LYS* 3.0 29.3 - - + +
56E SER* 5.0 5.4 + - - -
31K GLY 3.0 21.2 + - - +
32K LEU* 3.1 10.5 + - + +
34K SER* 1.3 77.7 - - - +
36K THR* 1.3 66.4 + - + +
37K ASP* 4.9 1.2 - - - +
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Residues in contact with THR 36 (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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32K LEU* 3.2 29.0 + - + +
33K VAL* 4.0 2.3 + - - -
35K ALA* 1.3 84.6 - - + +
37K ASP* 1.3 72.1 + - - +
39K ARG* 5.0 1.4 - - - +
40K LEU* 3.4 51.2 + - + +
41K ILE* 5.4 0.3 - - - +
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Residues in contact with ASP 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J LEU* 5.9 1.9 - - - +
32J GLU* 4.8 10.0 - - - +
33K VAL 2.9 16.1 + - - +
34K SER* 3.5 14.8 + - - +
35K ALA 4.9 0.7 - - - -
36K THR* 1.3 85.0 + - - +
38K SER* 1.3 58.8 + - - +
39K ARG* 2.9 15.5 + - + +
40K LEU 3.3 5.4 + - - -
41K ILE 3.3 12.7 + - - +
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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