Contacts of the helix formed by residues 18 - 35 (chain t) 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 THR 18 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16t THR 3.2 7.8 - - - +
17t ASP* 1.3 80.4 - - - +
19t ALA* 1.3 59.7 + - - +
20t GLU* 4.2 6.3 - - - -
21t GLU* 3.3 18.4 + - - +
22t ARG* 3.0 23.2 + - - +
250u SER* 5.2 17.3 - - - -
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Residues in contact with ALA 19 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17t ASP 3.8 0.8 + - - -
18t THR* 1.3 70.2 - - - +
20t GLU* 1.3 61.9 + - - +
22t ARG* 3.2 8.0 + - - +
23t LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 20 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18t THR* 3.3 5.5 - - - -
19t ALA* 1.3 77.9 - - - +
21t GLU* 1.3 58.6 + - - +
23t LYS* 3.4 6.5 + - - +
24t ALA* 2.9 29.5 + - - +
250u SER* 6.4 2.5 - - - -
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Residues in contact with GLU 21 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14t MET* 6.1 1.2 - - - +
15t PRO* 3.1 28.1 - - + +
16t THR* 4.3 2.6 - - - -
18t THR* 3.3 24.4 + - - +
19t ALA 3.2 0.6 - - - -
20t GLU* 1.3 76.5 - - - +
22t ARG* 1.3 60.3 + - - +
24t ALA* 3.4 6.5 + - - +
25t TYR* 2.9 28.2 + - - +
68t LYS 6.1 0.4 - - - +
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Residues in contact with ARG 22 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16t THR* 4.3 14.3 + - - +
18t THR 3.0 12.9 + - - +
19t ALA* 3.6 10.8 - - - +
21t GLU* 1.3 75.2 - - - +
23t LYS* 1.3 60.2 + - - +
25t TYR* 3.1 8.6 + - - +
26t ARG* 2.9 28.6 + - - +
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Residues in contact with LYS 23 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19t ALA 2.9 17.3 + - - +
20t GLU* 3.7 7.9 - - - +
21t GLU 3.3 0.2 - - - -
22t ARG* 1.3 75.4 - - - +
24t ALA* 1.3 58.2 + - - +
26t ARG* 3.3 6.8 + - - +
27t LYS* 2.9 29.0 + - - +
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Residues in contact with ALA 24 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20t GLU 2.9 18.3 + - - +
21t GLU* 3.7 7.2 - - - +
22t ARG 3.3 0.2 - - - -
23t LYS* 1.3 76.9 - - - +
25t TYR* 1.3 58.3 + - - +
27t LYS* 3.7 6.1 - - - +
28t PHE* 2.9 30.5 + - - +
67t PRO* 3.9 26.2 - - + +
68t LYS 5.6 1.6 - - - +
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Residues in contact with TYR 25 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14t MET* 5.9 6.7 - - + -
16t THR* 6.0 5.4 - - - -
21t GLU 2.9 17.6 + - - +
22t ARG* 3.1 8.7 + - - +
24t ALA* 1.3 73.9 - - - +
26t ARG* 1.3 60.0 + - - +
28t PHE* 3.4 4.9 + - - +
29t ARG* 2.9 30.5 + - - +
67t PRO* 5.3 0.2 - - - +
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Residues in contact with ARG 26 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22t ARG 2.9 16.6 + - - +
23t LYS* 3.7 7.2 - - - +
25t TYR* 1.3 75.4 - - - +
27t LYS* 1.3 58.1 + - - +
29t ARG* 3.4 5.8 + - - +
30t LYS* 2.9 30.7 + - - +
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Residues in contact with LYS 27 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23t LYS 2.9 17.4 + - - +
24t ALA* 3.7 7.4 - - - +
26t ARG* 1.3 77.2 - - - +
28t PHE* 1.3 57.3 + - - +
30t LYS* 3.4 6.6 + - - +
31t PHE* 2.9 28.8 + - - +
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Residues in contact with PHE 28 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24t ALA 2.9 17.5 + - - +
25t TYR* 3.9 5.2 - - - +
27t LYS* 1.3 77.3 - - - +
29t ARG* 1.3 58.4 + - - +
31t PHE* 3.2 7.5 + - - +
32t LEU* 2.9 27.9 + - - +
65t ASN* 4.7 15.5 - - - +
66t ASN* 6.0 0.4 - - - -
67t PRO* 5.0 9.9 - - + -
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Residues in contact with ARG 29 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25t TYR 2.9 19.1 + - - +
26t ARG* 3.8 5.8 - - - +
28t PHE* 1.3 76.4 - - - +
30t LYS* 1.3 57.3 + - - +
32t LEU* 3.1 8.6 + - - +
33t LEU* 2.9 28.2 + - - +
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Residues in contact with LYS 30 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26t ARG 2.9 17.0 + - - +
27t LYS* 3.7 6.5 - - - +
29t ARG* 1.3 76.9 - - - +
31t PHE* 1.3 57.2 + - - +
33t LEU* 3.4 6.9 + - - +
34t SER* 2.9 29.8 + - - -
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Residues in contact with PHE 31 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27t LYS 2.9 17.2 + - - +
28t PHE* 3.5 9.9 - - - +
29t ARG 3.2 0.2 - - - -
30t LYS* 1.3 78.2 - - - +
32t LEU* 1.3 60.6 + - - +
34t SER* 3.3 7.1 + - - -
35t GLU* 3.1 24.3 + - - +
65t ASN* 5.2 14.4 - - + -
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Residues in contact with LEU 32 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28t PHE 2.9 13.6 + - - +
29t ARG* 3.1 11.2 + - - +
31t PHE* 1.3 77.3 - - - +
33t LEU* 1.3 59.1 + - - +
35t GLU* 3.3 9.9 + - - +
37t PHE* 3.0 40.8 + - + +
45t TYR* 5.8 4.7 - - + -
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Residues in contact with LEU 33 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29t ARG 2.9 15.6 + - - +
30t LYS* 3.8 7.6 - - - +
32t LEU* 1.3 75.9 - - - +
34t SER* 1.3 62.9 + - - +
36t GLY* 3.3 12.1 + - - -
37t PHE 3.7 14.0 + - - +
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Residues in contact with SER 34 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30t LYS 2.9 18.1 + - - -
31t PHE* 3.8 7.2 - - - -
32t LEU 3.3 0.4 - - - -
33t LEU* 1.3 76.5 - - - +
35t GLU* 1.3 60.0 + - - +
36t GLY 3.3 0.9 + - - -
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Residues in contact with GLU 35 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31t PHE 3.1 15.9 + - - +
32t LEU* 3.3 8.0 + - - +
33t LEU 3.2 0.4 - - - -
34t SER* 1.3 76.2 - - - +
36t GLY* 1.3 57.7 + - - +
37t PHE* 3.6 1.8 - - + +
47t LYS* 5.5 2.8 - - - +
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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