Contacts of the helix formed by residues 24 - 37 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ILE* 3.3 3.1 - - + +
23H GLU* 1.3 77.8 - - - +
25H VAL* 1.3 60.9 + - - +
26H SER* 4.4 3.6 - - - +
27H VAL* 4.2 20.5 - - + +
28H PHE* 3.0 31.3 + - - +
208H LEU 4.5 1.0 + - - -
209H ASP 5.2 2.0 - - - +
210H LYS* 4.6 21.5 - - + +
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Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G SER 4.3 12.8 - - - +
172G TYR* 3.8 16.9 - - - +
173G PHE 4.8 9.2 - - - +
174G SER* 4.9 9.4 - - - +
23H GLU 3.9 3.4 + - - -
24H ASP* 1.3 70.1 - - - +
26H SER* 1.3 59.5 + - - +
28H PHE* 3.8 5.7 - - - +
29H ALA* 2.9 32.9 + - - +
197H PRO* 6.4 1.6 - - - -
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Residues in contact with SER 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ASP* 3.3 3.9 - - - +
25H VAL* 1.3 79.2 - - - +
27H VAL* 1.3 57.1 + - - +
29H ALA* 3.9 3.1 - - - +
30H GLN* 2.9 31.8 + - - +
27M SER* 5.4 10.3 - - - -
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LEU* 6.0 6.3 - - + -
22H ILE* 5.2 5.6 - - + -
24H ASP* 3.5 19.5 + - + +
25H VAL 3.4 0.2 - - - -
26H SER* 1.3 78.7 - - - +
28H PHE* 1.3 57.3 + - - +
30H GLN* 3.9 5.6 - - - +
31H LEU* 2.9 30.5 + - - +
27M SER* 5.1 15.3 - - - -
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Residues in contact with PHE 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G SER 6.0 1.6 - - - +
172G TYR* 6.3 1.3 - - - -
22H ILE* 3.9 24.4 - - + +
24H ASP 3.0 19.9 + - - +
25H VAL* 3.8 6.7 - - - +
26H SER 3.2 0.2 - - - -
27H VAL* 1.3 74.6 - - - +
29H ALA* 1.3 60.3 + - - +
31H LEU* 3.2 5.4 + - - +
32H VAL* 2.9 29.7 + - - +
196H GLU 6.2 0.4 - - - -
197H PRO* 5.5 9.0 - - + -
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Residues in contact with ALA 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G VAL* 5.6 8.2 - - + +
172G TYR* 3.8 30.0 - - + +
25H VAL 2.9 17.9 + - - +
26H SER* 4.1 3.4 - - - +
28H PHE* 1.3 75.7 - - - +
30H GLN* 1.3 58.2 + - - +
32H VAL* 3.4 6.1 + - - +
33H LYS* 2.9 29.9 + - - +
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Residues in contact with GLN 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H SER 2.9 20.8 + - - +
27H VAL* 4.0 5.4 - - - +
29H ALA* 1.3 76.3 - - - +
31H LEU* 1.3 58.0 + - - +
33H LYS* 3.8 6.4 - - - +
34H GLU* 2.9 28.4 + - - +
27M SER 6.1 0.7 - - - +
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H VAL 2.9 20.7 + - - +
28H PHE* 3.2 6.7 + - - +
30H GLN* 1.3 75.2 - - - +
32H VAL* 1.3 58.7 + - - +
34H GLU* 3.3 8.4 + - - +
35H PHE* 2.9 25.8 + - - +
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Residues in contact with VAL 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H PHE 2.9 15.8 + - - +
29H ALA* 3.9 7.0 - - - +
31H LEU* 1.3 75.6 - - - +
33H LYS* 1.3 59.2 + - - +
35H PHE* 2.9 23.0 + - - +
36H TYR* 2.9 15.4 + - - +
167H VAL* 5.8 8.7 - - + -
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Residues in contact with LYS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G LEU* 6.4 1.8 - - - -
142G CYS 4.8 12.3 - - - +
143G THR* 5.5 4.9 - - - -
144G VAL 5.8 2.2 - - - +
29H ALA 2.9 17.7 + - - +
30H GLN* 3.8 7.2 - - - +
32H VAL* 1.3 76.0 - - - +
34H GLU* 1.3 58.1 + - - +
36H TYR* 3.4 5.7 + - - +
37H GLN* 2.9 33.1 + - - +
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H GLN 2.9 19.0 + - - +
31H LEU* 3.5 8.5 - - - +
32H VAL 3.2 0.2 - - - -
33H LYS* 1.3 75.9 - - - +
35H PHE* 1.3 57.7 + - - +
37H GLN* 4.6 4.0 - - - +
38H TYR* 3.1 28.8 - - - +
41H GLN* 5.1 12.4 - - + +
43H ASN* 5.5 4.7 - - + -
44H LEU* 4.2 28.1 - - + +
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Residues in contact with PHE 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU 2.9 11.6 + - - +
32H VAL* 2.9 16.4 + - - +
34H GLU* 1.3 76.3 - - - +
36H TYR* 1.3 61.4 + - - +
38H TYR* 3.6 15.3 - - - +
61H LEU* 5.0 14.6 - - + +
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Residues in contact with TYR 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G LEU* 4.6 20.4 - - + +
32H VAL 2.9 13.1 + - - +
33H LYS* 4.0 5.2 - - - +
35H PHE* 1.3 77.0 - - - +
37H GLN* 1.3 60.6 + - + +
38H TYR 3.3 1.8 + - - -
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Residues in contact with GLN 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LYS 2.9 17.8 + - - +
34H GLU* 4.0 3.6 - - - -
36H TYR* 1.3 75.1 - - - +
38H TYR* 1.3 50.8 + - - +
39H ASP* 3.1 3.1 - - - -
40H GLU* 2.6 40.9 + - + +
41H GLN* 3.2 12.9 + - + -
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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