Contacts of the helix formed by residues 20 - 37 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q ALA 3.3 15.9 - - - +
38Q PRO* 3.5 25.1 - - + -
16V PHE* 3.3 28.9 - - + +
17V ASP* 2.9 6.0 + - - +
19V GLY* 1.3 81.1 - - - +
21V ASP* 1.3 62.2 + - - +
22V ASN 3.1 3.4 - - - +
23V LEU* 3.1 27.6 + - + +
57V TYR* 3.2 39.9 - - + -
5b TRP* 3.6 15.5 - - + +
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Residues in contact with ASP 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V ASP* 2.5 22.6 + - - +
18V THR* 3.8 11.9 + - - +
19V GLY 3.7 1.6 - - - -
20V VAL* 1.3 74.0 - - - +
22V ASN* 1.3 69.5 + - - +
24V GLN* 3.9 12.0 + - - +
25V THR* 4.0 10.6 + - - -
57V TYR* 5.0 6.7 + - - -
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Residues in contact with ASN 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V VAL* 3.1 0.6 - - - +
21V ASP* 1.3 86.2 - - - +
23V LEU* 1.3 68.4 + - - +
24V GLN 3.2 0.4 - - - -
25V THR* 3.0 11.0 + - - -
26V GLN* 2.8 33.8 + - + +
3b THR 5.5 1.2 + - - -
4b PRO* 5.3 2.0 - - - +
5b TRP* 3.8 35.2 - - + +
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Residues in contact with LEU 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q PRO* 5.8 1.6 - - + -
20V VAL* 3.1 29.2 + - + +
22V ASN* 1.3 77.6 - - - +
24V GLN* 1.3 65.1 + - - +
26V GLN* 3.2 4.2 + - - +
27V VAL* 3.0 21.7 + - + +
50V LYS* 3.5 31.0 - - + +
53V GLU* 3.7 30.7 - - + +
54V TYR* 4.2 6.3 - - + +
57V TYR* 3.8 24.7 - - + -
5b TRP* 3.7 37.5 - - + -
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Residues in contact with GLN 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P ALA* 5.4 4.6 - - - +
20V VAL 3.7 2.4 + - - -
21V ASP* 4.2 7.6 - - - +
22V ASN 3.2 0.6 - - - -
23V LEU* 1.3 77.9 - - - +
25V THR* 1.3 56.3 + - - +
27V VAL* 3.3 8.2 - - - +
28V THR* 2.7 44.2 + - - +
54V TYR* 4.0 16.5 + - + +
57V TYR* 2.8 34.8 + - + +
58V ARG* 3.6 21.5 + - - +
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Residues in contact with THR 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V ASP 4.0 8.9 + - - -
22V ASN* 3.0 14.7 + - - -
24V GLN* 1.3 79.4 - - - +
26V GLN* 1.3 59.5 + - + +
28V THR* 3.7 5.4 - - - -
29V GLU* 3.0 50.8 + - + +
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Residues in contact with GLN 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V ASN* 2.8 25.8 + - + +
23V LEU* 3.6 3.8 - - - +
25V THR* 1.3 80.6 - - + +
27V VAL* 1.3 57.5 + - - +
29V GLU* 3.4 8.9 + - - +
30V ALA* 2.9 28.8 + - - +
50V LYS* 2.9 41.4 + - + +
4b PRO* 4.4 8.5 - - - +
5b TRP* 3.0 58.2 + - - +
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Residues in contact with VAL 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V LEU 3.0 13.7 + - - +
24V GLN 3.3 11.4 - - - +
26V GLN* 1.3 74.7 - - - +
28V THR* 1.3 67.2 + - - +
30V ALA* 4.0 4.5 - - - -
31V LEU* 3.0 21.7 + - - +
47V TYR* 3.4 30.0 - - + +
50V LYS* 3.8 13.9 - - + +
51V LEU* 3.7 35.9 - - + +
54V TYR* 3.8 29.2 - - + -
68a PHE* 6.1 3.3 - - + -
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Residues in contact with THR 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V GLN* 2.7 32.6 + - - +
25V THR* 3.7 7.0 - - - -
27V VAL* 1.3 79.1 - - - +
29V GLU* 1.3 61.4 + - + +
31V LEU* 3.2 10.9 + - + +
32V ASP* 2.9 40.6 + - - +
54V TYR* 6.0 0.5 - - - -
68a PHE* 6.5 0.9 - - - -
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Residues in contact with GLU 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V THR* 3.0 39.2 + - + +
26V GLN* 3.8 7.8 - - - +
28V THR* 1.3 75.9 - - + +
30V ALA* 1.3 60.3 + - - +
32V ASP* 3.3 13.6 + - - +
33V LYS* 3.0 44.5 + - - +
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Residues in contact with ALA 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26V GLN 2.9 18.6 + - - +
27V VAL* 3.7 8.7 - - - +
28V THR 3.3 0.2 - - - -
29V GLU* 1.3 77.3 - - - +
31V LEU* 1.3 56.6 + - - +
33V LYS* 3.9 7.0 - - - +
34V LEU* 2.9 30.7 + - - +
43V LEU* 4.8 6.7 - - + +
46V ALA* 4.8 5.8 - - + -
47V TYR* 3.8 32.4 - - + +
50V LYS* 4.9 4.7 - - + -
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Residues in contact with LEU 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V VAL 3.0 15.1 + - - +
28V THR* 3.2 15.2 + - + +
30V ALA* 1.3 74.0 - - - +
32V ASP* 1.3 63.1 + - - +
34V LEU* 3.2 6.2 + - + -
35V ALA* 2.8 34.5 + - + +
47V TYR* 3.6 30.0 - - + +
12a VAL* 5.1 7.4 - - + +
15a LYS* 5.0 21.8 - - + -
16a PHE* 5.3 12.8 - - + +
64a THR* 4.4 14.6 - - + +
68a PHE* 3.8 31.9 - - + -
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Residues in contact with ASP 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28V THR* 2.9 31.5 + - - +
29V GLU* 3.5 17.0 - - - +
31V LEU* 1.3 82.0 - - - +
33V LYS* 1.3 63.9 + - + +
35V ALA* 3.5 15.2 - - - +
36V ALA* 3.7 6.6 + - - +
15a LYS* 5.3 13.5 + - - +
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Residues in contact with LYS 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V GLU* 3.0 30.0 + - - +
30V ALA* 4.0 3.6 - - - +
32V ASP* 1.3 75.7 - - + +
34V LEU* 1.3 65.4 + - - +
36V ALA* 2.9 19.8 + - - +
37V LYS 3.2 7.6 + - - -
43V LEU* 3.5 32.2 - - + +
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Residues in contact with LEU 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V ALA 2.9 20.6 + - - +
31V LEU* 3.7 8.1 - - + +
33V LYS* 1.3 76.3 - - - +
35V ALA* 1.3 58.8 + - - +
37V LYS 3.0 13.2 - - - +
38V PRO* 2.8 55.4 - - + +
43V LEU* 3.5 29.3 - - + +
44V LEU* 3.6 25.4 - - + +
47V TYR* 3.3 38.8 - - + -
16a PHE* 5.4 5.8 - - + -
60a ALA* 6.2 2.2 - - + -
64a THR* 5.4 4.9 - - + -
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Residues in contact with ALA 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31V LEU* 2.8 19.7 + - + +
32V ASP* 3.5 10.5 - - - +
34V LEU* 1.3 77.3 - - - +
36V ALA* 1.3 59.3 + - - +
38V PRO* 3.6 1.0 - - - +
15a LYS 3.4 26.0 - - - +
16a PHE* 3.6 26.4 - - + +
19a GLY* 3.2 22.6 - - - +
20a VAL* 3.3 11.8 - - - +
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Residues in contact with ALA 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V ASP 3.7 4.6 + - - +
33V LYS* 2.9 14.1 + - - +
35V ALA* 1.3 81.7 - - - +
37V LYS* 1.3 69.7 + - + +
38V PRO* 3.6 4.0 - - - +
19a GLY* 3.5 24.7 - - - +
20a VAL* 4.1 2.1 - - - +
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Residues in contact with LYS 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V LYS 3.2 2.6 + - - -
34V LEU* 3.0 12.0 + - - +
36V ALA* 1.3 89.7 - - + +
38V PRO* 1.3 67.3 - - - +
39V SER* 3.0 7.6 + - - +
40V ASP* 3.1 29.6 + - + +
43V LEU* 3.7 14.0 - - + +
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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