Contacts of the helix formed by residues 14 - 32 (chain j) 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 j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12j ARG 3.5 4.7 + - - -
13j ASN* 1.3 77.5 + - - +
15j THR* 1.3 68.4 + - - +
17j GLU* 3.4 5.8 + - - +
18j MET* 3.0 37.7 + - + +
521k LEU* 4.8 13.5 - - + -
525k TYR* 4.8 5.4 - - + -
532k ILE* 4.5 22.9 - - + -
606k VAL* 3.7 26.0 - - + -
607k LYS 3.5 16.7 + - - +
608k LEU* 4.4 19.7 - - + -
609k GLU 5.1 1.1 - - - +
614k ALA* 4.7 7.6 - - + -
618k PHE* 4.0 31.4 - - + -
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Residues in contact with THR 15 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13j ASN* 3.2 12.5 + - - +
14j ILE* 1.3 83.3 - - - +
16j SER* 1.3 60.7 + - - +
18j MET* 3.4 5.5 + - - +
19j ARG* 3.0 62.7 + - - +
610k ASP 5.4 0.5 + - - -
613k GLU* 4.5 21.5 + - - +
614k ALA* 4.4 14.0 + - - +
617k THR* 4.1 15.9 + - - +
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Residues in contact with SER 16 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j ARG* 3.3 18.2 - - - -
13j ASN* 3.3 28.3 + - - +
15j THR* 1.3 77.2 - - - +
17j GLU* 1.3 57.2 + - - +
19j ARG* 3.5 5.8 + - - +
20j GLU* 3.0 39.0 + - - +
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Residues in contact with GLU 17 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j ARG* 2.9 43.6 + - + +
13j ASN 3.0 16.6 + - - +
14j ILE* 3.6 8.1 - - - +
15j THR 3.3 0.2 - - - -
16j SER* 1.3 73.2 - - - +
18j MET* 1.3 56.7 + - - +
20j GLU* 4.3 0.3 - - - +
21j SER* 2.8 54.1 + - - +
517k ARG* 2.5 36.3 + - + +
521k LEU* 4.2 14.1 - - + -
539k ILE* 4.0 25.3 - - + +
604k LEU* 5.2 1.7 - - - +
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Residues in contact with MET 18 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14j ILE* 3.0 24.4 + - + +
15j THR 3.6 4.3 - - - +
17j GLU* 1.3 76.3 - - - +
19j ARG* 1.3 57.7 + - - +
21j SER* 3.9 2.4 - - - -
22j PHE* 2.9 36.0 + - - +
518k THR* 3.8 42.3 - - + +
521k LEU* 4.4 13.0 - - + -
522k THR* 4.4 2.0 - - - +
617k THR* 4.0 9.9 - - + -
618k PHE* 4.3 31.6 - - + -
621k LEU* 3.5 28.3 - - + -
622k MET* 4.0 20.2 - - + -
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Residues in contact with ARG 19 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15j THR* 3.0 37.8 + - - +
16j SER* 4.0 5.4 - - - +
18j MET* 1.3 76.2 - - - +
20j GLU* 1.3 58.3 + - + +
23j LEU* 3.1 30.5 + - - +
613k GLU* 5.5 4.6 + - - +
617k THR* 3.2 32.2 + - + -
620k MET* 4.1 15.0 - - + +
621k LEU* 4.5 2.5 - - + -
632k PHE* 3.5 45.6 - - + -
636k ASN* 4.8 9.1 + - - +
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Residues in contact with GLU 20 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j ARG* 4.0 20.8 + - - +
16j SER* 3.0 21.6 + - - +
17j GLU 4.3 0.9 - - - +
19j ARG* 1.3 76.4 - - + +
21j SER* 1.3 60.8 + - - +
23j LEU* 3.6 7.8 + - + +
24j ASP* 3.1 39.0 + - - +
639k TYR* 4.4 18.9 - - - +
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Residues in contact with SER 21 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j ARG* 5.5 0.9 + - - +
17j GLU* 2.8 44.5 + - - -
20j GLU* 1.3 73.8 - - - +
22j PHE* 1.3 62.7 + - - +
24j ASP* 3.3 8.0 + - - +
25j TYR* 3.2 18.5 + - - +
514k ALA* 3.5 20.8 - - - +
517k ARG* 2.9 16.8 + - - +
518k THR* 3.9 18.8 - - - -
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Residues in contact with PHE 22 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18j MET 2.9 19.1 + - - +
19j ARG 4.3 1.3 - - - +
21j SER* 1.3 73.5 - - - +
23j LEU* 1.3 55.9 + - - +
25j TYR* 3.4 12.1 + + + +
26j ALA* 2.8 39.0 + - + +
177j VAL* 3.8 23.1 - - + -
515k HIS* 4.8 8.7 - + - -
518k THR* 4.1 15.6 - - + +
621k LEU* 3.8 37.5 - - + -
622k MET* 4.3 16.2 - - - -
629k ARG* 3.3 40.6 - - + -
632k PHE* 4.3 6.1 - + - -
633k ILE* 4.2 3.8 - - + -
2016o C 3.9 19.1 - - - -
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Residues in contact with LEU 23 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19j ARG 3.1 21.1 + - - +
20j GLU* 3.8 9.6 - - + +
21j SER 3.3 0.2 - - - -
22j PHE* 1.3 76.4 - - - +
24j ASP* 1.3 55.6 + - - +
26j ALA* 4.4 4.3 - - - -
27j MET* 2.8 54.3 + - + +
632k PHE* 4.7 5.6 - - + -
633k ILE* 3.8 23.1 - - + +
636k ASN* 3.3 47.1 - - + +
637k ALA* 3.9 2.2 - - - +
639k TYR* 3.7 27.4 - - + +
640k ALA* 4.3 7.4 - - + -
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Residues in contact with ASP 24 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20j GLU* 3.1 23.7 + - - +
21j SER* 3.4 12.6 - - - +
22j PHE 3.3 0.2 - - - -
23j LEU* 1.3 76.8 - - - +
25j TYR* 1.3 60.6 + - - +
27j MET* 4.1 3.2 - - - +
28j SER* 3.2 25.1 + - - -
511k VAL* 4.1 11.7 - - + +
514k ALA* 5.0 5.8 - - + -
639k TYR 5.2 0.5 - - - +
640k ALA* 3.7 23.3 - - - +
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Residues in contact with TYR 25 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21j SER 3.2 9.1 + - - +
22j PHE* 3.5 18.2 - + - +
24j ASP* 1.3 76.1 - - - +
26j ALA* 1.3 67.0 + - - +
28j SER* 3.0 5.4 + - - -
29j VAL* 2.9 46.3 + - + +
33j ARG* 4.1 7.6 + - - -
177j VAL* 3.8 23.1 - - + +
460k LYS* 3.7 12.6 + - - -
511k VAL* 3.5 36.9 + - + +
512k ASP* 3.8 19.1 - - - -
515k HIS* 3.8 45.6 + + + +
2015o A 4.6 10.7 + - - -
2016o C 4.6 7.8 + - - -
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Residues in contact with ALA 26 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22j PHE* 2.8 23.8 + - + +
23j LEU* 3.9 3.4 - - - +
25j TYR* 1.3 72.9 - - - +
27j MET* 1.3 63.8 + - - +
29j VAL* 3.4 2.9 + - - +
30j ILE* 3.1 29.9 + - - +
177j VAL* 3.7 22.1 - - + +
633k ILE* 3.6 39.3 - - + -
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Residues in contact with MET 27 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23j LEU* 2.8 41.9 + - + +
24j ASP* 4.1 4.0 - - - +
26j ALA* 1.3 73.0 - - - +
28j SER* 1.3 57.0 + - - +
30j ILE* 3.2 7.1 + - - +
31j VAL* 3.0 50.7 + - + +
633k ILE* 4.7 4.5 - - + -
637k ALA* 3.7 23.6 - - + -
638k VAL 5.6 2.2 - - - +
640k ALA* 5.1 11.0 - - + -
701k JK8 3.2 49.1 - - + -
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Residues in contact with SER 28 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24j ASP 3.2 17.6 + - - -
25j TYR 3.0 4.9 + - - -
27j MET* 1.3 77.0 - - - +
29j VAL* 1.3 59.1 + - - +
31j VAL* 4.6 5.2 - - - -
32j ALA* 3.0 42.6 + - - +
33j ARG* 4.9 3.6 + - - -
511k VAL* 3.7 31.1 - - - +
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Residues in contact with VAL 29 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25j TYR* 2.9 55.4 + - + +
26j ALA 3.7 4.7 - - - +
28j SER* 1.3 75.1 - - - +
30j ILE* 1.3 59.2 + - - +
33j ARG* 3.5 26.1 + - + +
34j ALA* 3.1 33.9 + - + +
175j ILE 4.5 2.2 - - - +
176j ALA* 3.6 35.4 - - - -
177j VAL* 3.8 6.3 - - + +
511k VAL* 5.8 0.4 - - + -
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Residues in contact with ILE 30 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26j ALA 3.1 24.6 + - - +
27j MET* 3.6 7.0 - - - +
28j SER 3.2 0.2 - - - -
29j VAL* 1.3 78.1 - - - +
31j VAL* 1.3 71.1 + - + +
32j ALA 3.8 0.2 + - - -
35j LEU* 3.4 37.7 + - + +
176j ALA* 4.3 10.3 - - + -
177j VAL 3.3 26.9 - - - +
179j MET* 4.4 6.3 - - + -
338j LEU* 3.7 4.1 - - + +
343j PRO* 3.7 30.1 - - + -
633k ILE* 4.0 21.1 - - + -
701k JK8 4.1 12.8 - - + -
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Residues in contact with VAL 31 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27j MET* 3.0 30.5 + - + +
28j SER* 4.4 2.7 - - - +
30j ILE* 1.3 80.7 - - + +
32j ALA* 1.3 66.0 + - + +
33j ARG 4.0 0.4 - - - -
35j LEU 5.6 0.4 - - - -
44j PRO* 4.9 3.4 - - - +
338j LEU* 3.8 21.5 - - + +
341j GLY 3.6 21.8 - - - +
701k JK8 3.5 29.4 - - + -
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Residues in contact with ALA 32 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28j SER* 3.0 21.3 + - - +
31j VAL* 1.3 88.3 - - + +
33j ARG* 1.3 65.2 + - - +
44j PRO* 3.6 22.4 - - + +
48j ARG* 5.7 3.7 + - - +
81j HIS* 5.9 0.7 + - - -
7n A 4.9 1.9 + - - -
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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
------------------------------------------------------------
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