Contacts of the helix formed by residues 24 - 37 (chain e) in PDB entry 6QXT
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 ASP 24 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22e ILE* 3.2 4.5 - - - +
23e GLU* 1.3 78.1 - - - +
25e VAL* 1.3 60.8 + - - +
26e SER* 4.5 2.9 - - - +
27e VAL* 3.9 23.4 - - + +
28e PHE* 2.9 31.1 + - - +
208e LEU 4.7 0.6 + - - -
209e ASP 5.5 1.1 - - - +
210e LYS* 4.8 17.7 - - + +
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Residues in contact with VAL 25 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23e GLU 4.1 2.0 + - - -
24e ASP* 1.3 69.7 - - - +
26e SER* 1.3 60.0 + - - +
28e PHE* 3.8 5.5 - - - +
29e ALA* 2.9 32.1 + - - +
197e PRO* 6.6 0.2 - - - -
171f SER 4.5 11.0 - - - +
172f TYR* 3.7 17.8 - - - +
173f PHE 4.8 6.5 - - - +
174f SER* 4.9 12.3 - - - +
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Residues in contact with SER 26 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24e ASP* 3.3 2.6 - - - +
25e VAL* 1.3 80.5 - - - +
27e VAL* 1.3 56.5 + - - +
29e ALA* 4.3 3.0 - - - +
30e GLN* 2.9 32.8 + - - +
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Residues in contact with VAL 27 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7e LEU* 6.1 4.5 - - + -
22e ILE* 5.1 4.9 - - + -
24e ASP* 3.5 21.9 + - + +
25e VAL 3.4 0.4 - - - -
26e SER* 1.3 78.9 - - - +
28e PHE* 1.3 58.7 + - - +
30e GLN* 4.2 4.6 - - - +
31e LEU* 2.9 30.1 + - - +
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Residues in contact with PHE 28 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22e ILE* 4.0 22.4 - - + +
24e ASP 2.9 17.8 + - - +
25e VAL* 3.8 7.0 - - - +
27e VAL* 1.3 75.4 - - - +
29e ALA* 1.3 59.6 + - - +
31e LEU* 3.1 6.5 + - - +
32e VAL* 2.9 28.9 + - - +
196e GLU 5.9 0.7 - - - +
197e PRO* 5.4 9.6 - - + -
171f SER 5.9 2.5 - - - +
172f TYR* 6.0 2.5 - - - -
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Residues in contact with ALA 29 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25e VAL 2.9 17.6 + - - +
26e SER* 4.3 3.1 - - - +
28e PHE* 1.3 75.2 - - - +
30e GLN* 1.3 58.5 + - - +
32e VAL* 3.4 6.5 + - - +
33e LYS* 2.9 27.9 + - - +
144f VAL* 5.0 15.0 + - + +
172f TYR* 3.8 30.9 - - + +
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Residues in contact with GLN 30 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26e SER 2.9 21.7 + - - +
27e VAL* 4.2 5.2 - - - +
29e ALA* 1.3 76.7 - - - +
31e LEU* 1.3 56.6 + - - +
33e LYS* 3.6 7.5 - - - +
34e GLU* 2.9 27.4 + - - +
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Residues in contact with LEU 31 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27e VAL 2.9 21.7 + - - +
28e PHE* 3.1 7.8 + - - +
30e GLN* 1.3 75.0 - - - +
32e VAL* 1.3 60.3 + - - +
34e GLU* 3.2 9.8 + - - +
35e PHE* 2.9 25.5 + - - +
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Residues in contact with VAL 32 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28e PHE 2.9 15.6 + - - +
29e ALA* 3.8 6.5 - - - +
31e LEU* 1.3 72.6 - - - +
33e LYS* 1.3 61.7 + - - +
35e PHE* 2.9 23.5 + - - +
36e TYR* 2.9 16.6 + - - +
167e VAL* 5.6 10.1 - - + -
144f VAL* 6.5 0.9 - - + -
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Residues in contact with LYS 33 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29e ALA 2.9 18.0 + - - +
30e GLN* 3.6 10.3 - - - +
32e VAL* 1.3 76.4 - - - +
34e GLU* 1.3 56.8 + - - +
36e TYR* 3.9 4.7 - - - +
37e GLN* 2.9 34.1 + - - +
142f CYS 5.4 3.6 - - - +
143f THR* 5.3 13.9 - - - -
144f VAL* 5.4 4.3 - - + +
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Residues in contact with GLU 34 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30e GLN 2.9 15.6 + - - +
31e LEU* 3.2 11.6 + - - +
33e LYS* 1.3 76.3 - - - +
35e PHE* 1.3 56.6 + - - +
37e GLN* 4.5 4.3 - - - +
38e TYR* 3.0 29.0 + - - +
41e GLN* 5.3 9.7 - - + +
43e ASN* 5.8 3.6 - - + -
44e LEU* 4.0 29.0 - - + +
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Residues in contact with PHE 35 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31e LEU 2.9 11.9 + - - +
32e VAL* 2.9 13.9 + - - +
34e GLU* 1.3 75.6 - - - +
36e TYR* 1.3 64.2 + - - +
38e TYR* 3.5 17.0 - - - +
61e LEU* 5.4 14.9 - - + +
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Residues in contact with TYR 36 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32e VAL 2.9 14.0 + - - +
33e LYS* 4.2 4.3 - - - +
35e PHE* 1.3 76.5 - - - +
37e GLN* 1.3 58.4 + - - +
38e TYR 3.3 1.0 + - - -
39e ASP* 4.9 2.3 + - - +
66f LEU* 4.3 24.9 - - + +
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Residues in contact with GLN 37 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33e LYS* 2.9 19.6 + - + +
34e GLU* 3.8 1.8 - - - -
36e TYR* 1.3 73.6 - - - +
38e TYR* 1.3 51.8 + - - +
39e ASP 3.1 3.6 - - - -
40e GLU* 2.6 39.5 + - + +
41e GLN* 2.7 26.5 + - + -
140f LYS 4.9 12.1 - - - +
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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
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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