Contacts of the helix formed by residues 14 - 32 (chain T) in PDB entry 6QX2
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 ILE 14 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12T ARG 3.5 1.0 + - - -
13T ASN* 1.3 71.9 - - - +
15T THR* 1.3 66.6 + - - +
17T GLU* 3.4 4.3 + - - +
18T MET* 3.0 36.7 + - + +
521U LEU* 4.6 13.0 - - + +
525U TYR* 4.2 6.7 - - + -
532U ILE* 3.5 34.8 - - + -
606U VAL* 3.6 27.4 - - + -
607U LYS 2.9 9.9 + - - +
608U LEU* 3.9 33.2 - - + -
614U ALA* 4.4 6.3 - - + -
618U PHE* 4.0 25.6 - - + -
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Residues in contact with THR 15 (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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13T ASN* 3.3 12.0 + - - +
14T ILE* 1.3 77.6 - - - +
16T SER* 1.3 59.4 + - - +
18T MET* 3.5 2.7 + - - +
19T ARG* 3.0 43.3 + - - +
610U ASP 4.8 0.9 + - - -
613U GLU* 3.0 35.8 + - - +
614U ALA* 3.2 34.3 + - - +
617U THR* 3.6 22.3 + - - +
618U PHE* 5.5 1.2 - - - -
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Residues in contact with SER 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T ARG* 3.3 24.1 + - - -
13T ASN* 3.2 29.1 + - - +
15T THR* 1.3 75.9 - - - +
17T GLU* 1.3 57.0 + - - +
19T ARG* 3.5 6.4 + - - +
20T GLU* 3.0 33.9 + - - +
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Residues in contact with GLU 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T ARG* 3.0 39.3 + - + +
13T ASN 3.0 16.4 + - - +
14T ILE* 3.6 8.3 - - - +
15T THR 3.3 0.2 - - - -
16T SER* 1.3 73.3 - - - +
18T MET* 1.3 58.7 - - - +
20T GLU* 4.2 0.5 - - - +
21T SER* 2.8 42.9 + - - +
517U ARG* 2.6 35.7 + - - -
521U LEU* 3.6 16.8 - - + -
539U ILE* 3.4 28.7 - - + +
604U LEU* 5.0 4.9 - - - +
606U VAL* 5.8 1.3 - - + -
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Residues in contact with MET 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T ILE* 3.0 21.0 + - + +
15T THR 3.6 4.7 - - - +
17T GLU* 1.3 76.3 - - - +
19T ARG* 1.3 55.9 + - - +
21T SER* 4.6 0.2 - - - -
22T PHE* 2.9 35.5 + - - +
518U THR* 3.5 30.8 - - + +
521U LEU* 3.5 26.7 - - + -
522U THR* 3.5 13.2 - - - +
617U THR* 4.1 7.2 - - + -
618U PHE* 3.3 50.0 - - + -
621U LEU* 3.7 15.5 - - + -
622U MET* 4.0 12.3 - - + -
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Residues in contact with ARG 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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15T THR* 3.0 41.9 + - - +
16T SER* 4.0 5.0 - - - +
17T GLU 3.4 0.2 - - - -
18T MET* 1.3 76.0 - - - +
20T GLU* 1.3 58.2 + - - +
23T LEU* 3.1 30.2 + - - +
613U GLU* 4.8 4.8 + - - -
616U GLN* 5.1 4.4 - - - +
617U THR* 3.4 23.3 + - + -
620U MET* 3.7 14.9 - - + +
621U LEU* 3.8 10.8 - - + -
632U PHE* 3.5 33.1 - - + -
636U ASN* 4.1 17.4 + - - +
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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
----------------------------------------------------------
12T ARG* 2.8 30.9 + - - +
16T SER* 3.0 15.4 + - - +
17T GLU 4.2 0.2 - - - +
19T ARG* 1.3 73.6 - - - +
21T SER* 1.3 61.7 + - - +
23T LEU* 3.6 9.7 + - + +
24T ASP* 3.1 28.2 + - - +
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Residues in contact with SER 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17T GLU* 2.8 44.0 + - - -
20T GLU* 1.3 74.2 - - - +
22T PHE* 1.3 64.6 + - - +
24T ASP* 3.3 3.3 + - - +
25T TYR* 3.2 11.4 + - - +
514U ALA* 3.2 31.3 - - - +
517U ARG* 3.0 19.8 + - - +
518U THR* 3.5 20.6 - - - -
521U LEU* 6.1 0.4 - - - -
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Residues in contact with PHE 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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18T MET 2.9 21.4 + - - +
19T ARG 4.3 0.4 - - - +
21T SER* 1.3 70.3 - - - +
23T LEU* 1.3 55.6 + - - +
25T TYR* 3.4 9.2 + + - +
26T ALA* 2.8 38.2 + - + +
177T VAL* 3.8 20.9 - - + -
515U HIS* 4.5 9.6 - + - -
518U THR* 3.3 17.2 - - + +
621U LEU* 3.3 48.9 - - + -
622U MET* 3.5 25.4 - - + -
629U ARG* 3.6 29.4 - - + -
632U PHE* 4.8 4.5 - + - -
633U ILE* 5.0 1.1 - - + -
2016V C 3.9 17.5 - - - -
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Residues in contact with LEU 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 ARG 3.1 21.1 + - - +
20T GLU* 3.8 9.0 - - + +
22T PHE* 1.3 73.1 - - - +
24T ASP* 1.3 57.5 + - - +
26T ALA* 4.3 3.8 - - - -
27T MET* 2.8 55.8 + - + +
632U PHE* 4.1 17.2 - - + -
633U ILE* 4.1 18.4 - - + +
636U ASN* 3.5 45.5 - - + +
638U VAL* 5.7 3.6 - - + +
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Residues in contact with ASP 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T GLU* 3.1 15.8 + - + +
21T SER* 3.4 10.3 - - - +
22T PHE 3.3 0.2 - - - -
23T LEU* 1.3 75.8 - - - +
25T TYR* 1.3 61.5 - - - +
27T MET* 4.2 3.4 - - - +
28T SER* 3.2 22.2 + - - -
510U ASP 3.7 5.5 - - - +
511U VAL* 3.5 24.2 - - - +
514U ALA* 3.5 18.4 - - + +
517U ARG* 5.4 0.5 + - - -
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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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21T SER 3.2 8.7 + - - +
22T PHE* 3.5 15.7 - + - +
24T ASP* 1.3 78.2 + - - +
26T ALA* 1.3 68.2 + - - +
28T SER* 3.1 6.1 + - - -
29T VAL* 2.9 47.2 + - + +
33T ARG* 4.1 3.8 + - - -
177T VAL* 3.6 25.1 - - + +
460U LYS* 3.6 6.6 + - - -
511U VAL* 3.6 25.8 - - + +
512U ASP* 3.5 23.1 - - - -
515U HIS* 3.2 63.5 + + + +
2015V A 4.6 9.7 + - - -
2016V C 4.6 7.4 + - - -
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Residues in contact with ALA 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 PHE* 2.8 27.0 + - + +
23T LEU* 3.9 3.8 - - - +
25T TYR* 1.3 73.5 - - - +
27T MET* 1.3 62.8 + - - +
29T VAL* 3.4 2.4 + - - +
30T ILE* 3.1 30.9 + - - +
177T VAL* 3.7 34.4 - - + +
633U ILE* 3.8 23.3 - - + -
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Residues in contact with MET 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 LEU* 2.8 39.7 + - + +
24T ASP* 4.2 3.8 - - - +
26T ALA* 1.3 72.8 - - - +
28T SER* 1.3 58.0 + - - +
30T ILE* 3.2 8.5 + - - +
31T VAL* 3.0 51.6 + - + +
633U ILE* 3.8 18.2 - - + +
637U ALA* 3.6 37.2 - - + -
638U VAL 4.6 8.7 - - - +
701U JK8 4.0 19.3 - - + -
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Residues in contact with SER 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 ASP 3.2 17.4 + - - -
25T TYR 3.1 5.5 + - - -
27T MET* 1.3 76.6 - - - +
29T VAL* 1.3 59.6 + - - +
31T VAL* 4.6 4.9 - - - -
32T ALA* 3.0 41.9 + - - +
33T ARG* 4.9 2.8 + - - -
511U VAL* 3.3 36.7 - - - +
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Residues in contact with VAL 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 56.2 + - + +
26T ALA 3.7 4.9 - - - +
28T SER* 1.3 75.8 - - - +
30T ILE* 1.3 58.6 + - - +
33T ARG* 3.5 28.5 + - - +
34T ALA* 3.1 34.1 + - + +
175T ILE 4.4 2.0 - - - +
176T ALA* 3.6 34.5 - - - -
177T VAL* 3.8 6.5 - - + +
511U VAL* 5.9 0.2 - - + -
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Residues in contact with ILE 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 ALA 3.1 20.7 + - - +
27T MET* 3.6 6.3 - - - +
28T SER 3.2 0.4 - - - -
29T VAL* 1.3 77.9 - - - +
31T VAL* 1.3 70.9 + - + +
32T ALA 3.8 0.3 + - - -
35T LEU* 3.4 38.3 + - + +
176T ALA* 4.3 5.4 - - + -
177T VAL 3.3 33.0 - - - +
179T MET* 4.4 10.3 - - + -
338T LEU* 3.8 3.9 - - + +
343T PRO* 3.7 29.6 - - + -
633U ILE* 3.7 31.0 - - + -
701U JK8 4.8 3.1 - - + -
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Residues in contact with VAL 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T MET* 3.0 34.6 + - + +
28T SER* 4.4 2.5 - - - +
30T ILE* 1.3 89.7 - - + +
32T ALA* 1.3 67.1 + - + +
33T ARG 4.0 0.7 - - - -
35T LEU 5.6 0.2 - - - -
44T PRO* 5.0 2.6 - - - +
338T LEU* 3.8 23.4 - - + +
341T GLY* 3.6 23.3 - - - +
701U JK8 4.3 13.2 - - + -
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Residues in contact with ALA 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 SER* 3.0 21.6 + - - +
31T VAL* 1.3 88.1 - - + +
33T ARG* 1.3 63.8 + - - +
44T PRO* 3.6 22.8 - - + +
48T ARG* 5.7 4.7 + - - +
79T HIS* 6.1 0.2 - - - -
81T HIS* 5.8 1.9 + - - -
7W A 4.9 1.7 + - - -
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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
------------------------------------------------------------
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