Contacts of the helix formed by residues 20 - 37 (chain K) in PDB entry 2LPZ
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 VAL 20 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ALA 3.3 15.9 - - - +
38F PRO* 3.5 24.9 - - + -
16K PHE* 3.3 29.2 - - + +
17K ASP* 3.1 5.8 - - - +
19K GLY* 1.3 81.7 - - - +
21K ASP* 1.3 63.0 + - - +
22K ASN 3.1 3.4 - - - +
23K LEU* 3.1 28.7 + - + +
57K TYR* 3.2 39.1 - - + -
5Q TRP* 3.6 15.3 - - + +
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Residues in contact with ASP 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ASP* 2.5 23.3 + - - +
18K THR* 3.8 10.7 + - - +
19K GLY 3.7 1.6 - - - -
20K VAL* 1.3 74.1 - - - +
22K ASN* 1.3 68.6 + - - +
24K GLN* 3.9 11.8 + - - +
25K THR* 4.0 10.4 + - - -
57K TYR* 5.0 6.6 + - - -
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Residues in contact with ASN 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K VAL* 3.1 0.6 - - - +
21K ASP* 1.3 86.0 - - - +
23K LEU* 1.3 66.5 + - - +
24K GLN 3.2 0.7 - - - -
25K THR* 3.0 10.5 + - - -
26K GLN* 2.8 34.7 + - + +
3Q THR 5.5 1.0 + - - -
4Q PRO* 5.3 2.2 - - - +
5Q TRP* 3.8 34.6 - - + +
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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
----------------------------------------------------------
38F PRO* 5.8 1.3 - - + -
20K VAL* 3.1 29.9 + - + +
22K ASN* 1.3 77.1 - - - +
24K GLN* 1.3 65.3 + - - +
26K GLN* 3.2 4.6 + - - +
27K VAL* 3.0 21.9 + - + +
50K LYS* 3.5 30.7 - - + +
53K GLU* 3.7 31.6 - - + +
54K TYR* 4.2 5.8 - - + +
57K TYR* 3.8 23.8 - - + -
5Q TRP* 3.7 36.2 - - + -
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Residues in contact with GLN 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ALA* 5.4 4.6 - - - +
20K VAL 3.7 2.6 + - - -
21K ASP* 4.2 8.1 - - - +
23K LEU* 1.3 78.9 - - - +
25K THR* 1.3 56.8 + - - +
27K VAL* 3.3 7.9 - - - +
28K THR* 2.7 43.7 + - - +
54K TYR* 4.0 17.6 + - + +
57K TYR* 2.8 33.5 + - + +
58K ARG* 3.6 22.2 - - - +
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Residues in contact with THR 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ASP 4.0 8.2 + - - -
22K ASN* 3.0 15.8 + - - -
24K GLN* 1.3 79.4 - - - +
26K GLN* 1.3 59.7 + - + +
28K THR* 3.4 5.9 + - - -
29K GLU* 3.0 51.7 + - + +
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Residues in contact with GLN 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ASN* 2.8 25.3 + - + +
23K LEU* 3.6 3.8 - - - +
25K THR* 1.3 79.7 - - + +
27K VAL* 1.3 57.2 + - - +
29K GLU* 3.4 9.2 + - - +
30K ALA* 2.9 28.6 + - - +
50K LYS* 2.9 40.3 + - + +
4Q PRO* 4.4 9.1 - - - +
5Q TRP* 3.0 58.5 + - - +
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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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23K LEU 3.0 14.6 + - - +
24K GLN 3.3 11.2 - - - +
26K GLN* 1.3 74.9 - - - +
28K THR* 1.3 67.8 + - - +
30K ALA* 4.0 4.7 - - - -
31K LEU* 3.0 21.8 + - - +
47K TYR* 3.4 29.5 - - + +
50K LYS* 3.8 13.9 - - + +
51K LEU* 3.7 36.6 - - + +
54K TYR* 3.8 29.4 - - + -
68P PHE* 6.1 2.9 - - + -
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Residues in contact with THR 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN* 2.7 32.5 + - - +
25K THR* 3.7 6.7 - - - -
27K VAL* 1.3 78.0 - - - +
29K GLU* 1.3 62.2 + - + +
31K LEU* 3.2 11.2 + - + +
32K ASP* 2.9 40.6 + - - +
54K TYR* 5.8 0.7 - - - -
68P PHE* 6.5 0.9 - - - -
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Residues in contact with GLU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K THR* 3.0 39.5 + - + +
26K GLN* 3.8 7.4 - - - +
28K THR* 1.3 75.8 - - + +
30K ALA* 1.3 61.1 + - - +
32K ASP* 3.3 13.3 + - - +
33K LYS* 3.0 45.7 + - - +
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Residues in contact with ALA 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K GLN 2.9 18.6 + - - +
27K VAL* 3.7 8.7 - - - +
28K THR 3.3 0.2 - - - -
29K GLU* 1.3 76.6 - - - +
31K LEU* 1.3 55.9 + - - +
33K LYS* 3.6 7.2 + - - +
34K LEU* 2.9 30.3 + - - +
43K LEU* 4.8 5.8 - - + +
46K ALA* 4.8 6.5 - - + -
47K TYR* 3.8 32.2 - - + +
50K LYS* 4.9 4.7 - - + -
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K VAL 3.0 14.9 + - - +
28K THR* 3.2 14.8 + - + +
30K ALA* 1.3 74.1 - - - +
32K ASP* 1.3 63.1 + - - +
34K LEU* 3.7 6.0 - - + -
35K ALA* 2.8 34.5 + - + +
47K TYR* 3.6 29.8 - - + +
12P VAL* 5.1 7.9 - - + +
15P LYS* 5.0 22.4 - - + -
16P PHE* 5.3 12.3 - - + +
64P THR* 4.4 14.8 - - + +
68P PHE* 3.8 30.5 - - + -
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Residues in contact with ASP 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 THR* 2.9 31.4 + - - +
29K GLU* 3.3 17.8 + - - +
31K LEU* 1.3 81.4 - - - +
33K LYS* 1.3 64.3 + - + +
35K ALA* 3.5 15.4 - - - +
36K ALA* 3.7 6.1 + - - +
15P LYS* 5.3 13.2 + - - +
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Residues in contact with LYS 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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29K GLU* 3.0 30.0 + - - +
30K ALA* 4.0 3.6 - - - +
32K ASP* 1.3 76.2 - - + +
34K LEU* 1.3 65.7 + - - +
36K ALA* 2.9 19.0 + - - +
37K LYS 3.2 8.5 + - - -
43K LEU* 3.5 34.2 - - + +
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Residues in contact with LEU 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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30K ALA 2.9 19.3 + - - +
31K LEU* 3.7 8.3 - - + +
33K LYS* 1.3 75.7 - - - +
35K ALA* 1.3 58.8 + - - +
37K LYS 3.0 13.2 - - - +
38K PRO* 2.8 55.0 - - + +
43K LEU* 3.5 29.5 - - + +
44K LEU* 3.6 26.0 - - + +
47K TYR* 3.3 38.1 - - + -
16P PHE* 5.4 6.1 - - + -
60P ALA* 6.2 2.2 - - + -
64P THR* 5.4 4.7 - - + -
79V PHE* 5.6 1.1 - - + -
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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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31K LEU* 2.8 19.4 + - + +
32K ASP* 3.5 10.1 - - - +
33K LYS 3.1 0.4 - - - -
34K LEU* 1.3 76.9 - - - +
36K ALA* 1.3 59.7 + - - +
38K PRO* 3.6 0.9 - - - +
15P LYS 3.4 26.5 - - - +
16P PHE* 3.6 25.5 - - + +
19P GLY* 3.2 22.6 - - - +
20P VAL* 3.3 12.3 - - - +
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Residues in contact with ALA 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 ASP 3.7 5.5 + - - +
33K LYS* 2.9 13.9 + - - +
35K ALA* 1.3 80.5 - - - +
37K LYS* 1.3 67.1 + - + +
38K PRO* 3.6 0.2 - - - -
19P GLY* 3.5 14.5 - - - +
5V TRP* 2.7 36.3 + - + +
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Residues in contact with LYS 37 (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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33K LYS 3.2 2.8 + - - +
34K LEU* 3.0 12.6 + - - +
36K ALA* 1.3 89.7 - - + +
38K PRO* 1.3 66.8 - - - +
39K SER 3.0 4.1 + - - -
40K ASP* 3.1 26.3 + - + +
43K LEU* 3.7 14.6 - - + +
6V SER 3.5 22.7 - - - +
7V GLY* 4.2 1.6 - - - -
8V TYR* 4.0 25.3 - - + +
11V ASP* 2.8 22.0 + - - +
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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