Contacts of the helix formed by residues 24 - 37 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G ILE* 3.2 3.5 - - - +
23G GLU* 1.3 78.3 - - - +
25G VAL* 1.3 60.7 + - - +
26G SER* 4.5 3.1 - - - +
27G VAL* 3.9 23.2 - - + +
28G PHE* 2.9 31.0 + - - +
208G LEU 4.7 0.6 + - - -
209G ASP 5.5 1.3 - - - +
210G LYS* 4.8 17.0 - - + +
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Residues in contact with VAL 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLU 4.1 1.8 + - - -
24G ASP* 1.3 70.2 - - - +
26G SER* 1.3 61.9 + - - +
28G PHE* 3.8 5.7 - - - +
29G ALA* 2.9 31.7 + - - +
197G PRO* 6.6 0.2 - - - -
171H SER 4.5 11.4 - - - +
172H TYR 3.7 16.9 - - - +
173H PHE 4.8 6.5 - - - +
174H SER* 4.9 11.7 - - - +
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Residues in contact with SER 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ASP* 3.3 2.8 - - - +
25G VAL* 1.3 80.5 - - - +
27G VAL* 1.3 57.6 + - - +
29G ALA* 4.3 3.0 - - - +
30G GLN* 2.9 32.3 + - - +
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Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 6.1 4.7 - - + -
22G ILE* 5.1 5.8 - - + -
24G ASP* 3.5 21.4 + - + +
25G VAL 3.4 0.2 - - - -
26G SER* 1.3 78.9 - - - +
28G PHE* 1.3 58.5 + - - +
30G GLN* 4.2 4.4 - - - +
31G LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G ILE* 4.0 21.7 - - + +
24G ASP 2.9 19.9 + - - +
25G VAL* 3.8 7.0 - - - +
26G SER 3.2 0.2 - - - -
27G VAL* 1.3 75.1 - - - +
29G ALA* 1.3 60.2 + - - +
31G LEU* 3.1 6.5 + - - +
32G VAL* 2.9 28.9 + - - +
196G GLU 5.9 0.7 - - - +
197G PRO* 5.4 9.6 - - + -
171H SER 5.9 2.2 - - - +
172H TYR* 6.0 2.7 - - - -
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Residues in contact with ALA 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G VAL 2.9 18.7 + - - +
26G SER* 4.3 2.9 - - - +
28G PHE* 1.3 75.8 - - - +
30G GLN* 1.3 58.9 + - - +
32G VAL* 3.4 6.6 + - - +
33G LYS* 2.9 28.8 + - - +
144H VAL* 5.0 14.7 + - + +
172H TYR* 3.7 31.8 - - + +
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Residues in contact with GLN 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G SER 2.9 21.9 + - - +
27G VAL* 4.2 4.5 - - - +
29G ALA* 1.3 76.5 - - - +
31G LEU* 1.3 57.6 + - - +
33G LYS* 3.5 7.9 + - - +
34G GLU* 2.9 27.4 + - - +
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Residues in contact with LEU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G VAL 2.9 21.7 + - - +
28G PHE* 3.1 7.6 + - - +
30G GLN* 1.3 74.1 - - - +
32G VAL* 1.3 60.4 + - - +
34G GLU* 3.2 9.5 + - - +
35G PHE* 2.9 25.8 + - - +
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Residues in contact with VAL 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G PHE 2.9 14.9 + - - +
29G ALA* 3.8 6.7 - - - +
31G LEU* 1.3 73.1 - - - +
33G LYS* 1.3 61.0 + - - +
35G PHE* 2.9 23.1 + - - +
36G TYR* 2.9 17.0 + - - +
167G VAL* 5.6 9.4 - - + -
144H VAL* 6.5 1.3 - - + -
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Residues in contact with LYS 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ALA 2.9 18.3 + - - +
30G GLN* 3.6 9.4 - - - +
31G LEU 3.3 0.2 - - - -
32G VAL* 1.3 77.2 - - - +
34G GLU* 1.3 57.2 + - - +
36G TYR* 3.5 4.2 + - - +
37G GLN* 2.9 34.9 + - + +
142H CYS 5.4 2.9 - - - +
143H THR* 5.3 14.8 - - - -
144H VAL* 5.4 3.8 - - + +
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Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G GLN 2.9 15.6 + - - +
31G LEU* 3.2 12.1 + - - +
33G LYS* 1.3 77.2 - - - +
35G PHE* 1.3 56.9 + - - +
37G GLN* 4.5 4.0 - - - +
38G TYR* 3.0 27.4 + - - +
41G GLN* 5.3 9.3 - - + +
43G ASN* 5.8 3.8 - - + -
44G LEU* 4.0 30.0 - - + +
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Residues in contact with PHE 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G LEU 2.9 12.8 + - - +
32G VAL* 2.9 12.5 + - - +
34G GLU* 1.3 76.7 - - - +
36G TYR* 1.3 64.0 + - - +
38G TYR* 3.5 17.7 - - - +
61G LEU* 5.4 14.7 - - + +
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Residues in contact with TYR 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G VAL 2.9 14.2 + - - +
33G LYS* 4.2 4.5 - - - +
35G PHE* 1.3 77.2 - - - +
37G GLN* 1.3 58.0 + - - +
38G TYR 3.3 1.1 + - - -
39G ASP* 4.9 2.3 + - - +
66H LEU* 4.3 24.0 - - + +
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Residues in contact with GLN 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G LYS 2.9 20.7 + - - +
34G GLU* 3.8 1.8 - - - -
36G TYR* 1.3 75.3 - - - +
38G TYR* 1.3 51.1 + - - +
39G ASP* 3.1 4.3 - - - -
40G GLU* 2.6 38.0 + - + +
41G GLN* 2.7 26.0 + - + -
140H LYS 4.9 11.7 - - - +
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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
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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