Contacts of the helix formed by residues 24 - 37 (chain f) in PDB entry 6QY3
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 f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22f ILE* 3.2 3.5 - - + +
23f GLU* 1.3 78.4 - - - +
25f VAL* 1.3 60.5 + - - +
26f SER* 4.5 2.7 - - - +
27f VAL* 4.2 21.8 - - + +
28f PHE* 3.0 30.7 + - - +
208f LEU 4.5 1.8 + - - -
209f ASP 5.2 2.5 - - - +
210f LYS* 4.6 19.5 - - + +
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Residues in contact with VAL 25 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171e SER 4.3 12.3 - - - +
172e TYR* 3.9 14.9 - - - +
173e PHE 4.8 7.6 - - - +
174e SER* 4.9 12.3 - - - +
23f GLU 3.9 3.0 + - - -
24f ASP* 1.3 70.5 - - - +
26f SER* 1.3 61.1 + - - +
28f PHE* 3.8 5.5 - - - +
29f ALA* 2.9 32.4 + - - +
197f PRO* 6.4 2.2 - - - -
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Residues in contact with SER 26 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24f ASP* 3.3 3.5 - - - +
25f VAL* 1.3 79.4 - - - +
27f VAL* 1.3 57.5 + - - +
29f ALA* 4.0 2.4 - - - +
30f GLN* 2.9 31.4 + - - +
27s SER* 4.2 21.9 - - - -
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Residues in contact with VAL 27 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22f ILE* 5.2 5.4 - - + -
24f ASP* 3.5 20.9 + - + +
26f SER* 1.3 79.1 - - - +
28f PHE* 1.3 56.9 + - - +
30f GLN* 4.0 5.5 - - - +
31f LEU* 2.9 30.5 + - - +
27s SER* 5.1 7.1 - - - +
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Residues in contact with PHE 28 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171e SER 6.0 1.8 - - - +
172e TYR* 6.3 1.3 - - - -
22f ILE* 3.9 25.1 - - + +
24f ASP 3.0 19.5 + - - +
25f VAL* 3.8 6.7 - - - +
27f VAL* 1.3 74.7 - - - +
29f ALA* 1.3 60.0 + - - +
31f LEU* 3.2 6.2 + - - +
32f VAL* 2.9 29.3 + - - +
196f GLU 6.2 0.7 - - - -
197f PRO* 5.5 8.3 - - + -
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Residues in contact with ALA 29 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144e VAL* 5.7 8.4 - - + +
172e TYR* 3.8 30.2 - - + +
25f VAL 2.9 17.7 + - - +
26f SER* 4.1 3.4 - - - +
28f PHE* 1.3 76.3 - - - +
30f GLN* 1.3 57.8 + - - +
32f VAL* 3.4 6.0 + - - +
33f LYS* 2.9 30.5 + - - +
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Residues in contact with GLN 30 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26f SER 2.9 21.0 + - - +
27f VAL* 4.0 5.4 - - - +
29f ALA* 1.3 77.3 - - - +
31f LEU* 1.3 57.9 + - - +
33f LYS* 3.8 6.3 - - - +
34f GLU* 2.9 28.6 + - - +
27s SER* 5.5 10.1 - - - +
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Residues in contact with LEU 31 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27f VAL 2.9 21.2 + - - +
28f PHE* 3.2 6.7 + - - +
30f GLN* 1.3 75.2 - - - +
32f VAL* 1.3 59.1 + - - +
34f GLU* 3.3 8.7 + - - +
35f PHE* 2.9 25.5 + - - +
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Residues in contact with VAL 32 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28f PHE 2.9 16.1 + - - +
29f ALA* 3.9 6.3 - - - +
31f LEU* 1.3 74.1 - - - +
33f LYS* 1.3 60.7 + - - +
35f PHE* 2.9 23.5 + - - +
36f TYR* 2.9 14.9 + - - +
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Residues in contact with LYS 33 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142e CYS 4.8 13.2 - - - +
143e THR* 5.4 6.1 - - - -
144e VAL 5.7 2.2 - - - +
29f ALA 2.9 18.5 + - - +
30f GLN* 3.9 6.7 - - - +
32f VAL* 1.3 74.4 - - - +
34f GLU* 1.3 58.4 + - - +
36f TYR* 3.5 5.9 + - - +
37f GLN* 3.0 31.9 + - - +
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Residues in contact with GLU 34 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30f GLN 2.9 18.8 + - - +
31f LEU* 3.5 9.0 - - - +
32f VAL 3.2 0.4 - - - -
33f LYS* 1.3 75.7 - - - +
35f PHE* 1.3 57.4 + - - +
37f GLN* 4.6 3.8 - - - +
38f TYR* 3.2 28.4 - - - +
41f GLN* 5.1 11.5 - - + +
43f ASN* 5.5 4.9 - - + -
44f LEU* 4.2 29.1 - - + +
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Residues in contact with PHE 35 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31f LEU 2.9 12.4 + - - +
32f VAL* 2.9 14.6 + - - +
34f GLU* 1.3 78.4 - - - +
36f TYR* 1.3 63.2 + - - +
38f TYR* 3.6 15.9 - - - +
44f LEU* 6.1 0.2 - - - -
61f LEU* 5.1 14.8 - - + +
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Residues in contact with TYR 36 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66e LEU* 4.6 21.1 - - + -
32f VAL 2.9 13.3 + - - +
33f LYS* 4.1 6.3 - - - +
35f PHE* 1.3 77.0 - - - +
37f GLN* 1.3 58.6 + - - +
38f TYR 3.3 1.4 + - - -
39f ASP 5.2 0.2 + - - -
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Residues in contact with GLN 37 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33f LYS 3.0 18.5 + - - +
34f GLU* 4.0 3.1 - - - -
36f TYR* 1.3 74.4 - - + +
38f TYR* 1.3 52.2 + - - +
39f ASP* 3.1 2.9 - - - -
40f GLU* 2.6 39.7 + - + +
41f GLN* 3.1 13.2 + - + -
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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