Contacts of the helix formed by residues 9 - 26 (chain K) in PDB entry 3J9X
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 SER 9 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ARG* 1.3 75.4 - - - +
10K TYR* 1.3 60.0 + - - +
11K SER* 3.6 9.5 + - - -
12K GLN* 2.8 34.3 + - - +
13K ARG* 2.8 27.3 + - - +
53L THR* 4.3 3.4 - - - -
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Residues in contact with TYR 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K SER* 1.3 72.9 - - - +
11K SER* 1.3 74.0 + - - +
13K ARG* 3.0 4.6 + - + -
14K TYR* 2.9 47.2 + + + +
45L PHE* 4.1 1.3 - + - -
46L GLN* 3.3 35.2 + - - +
49L VAL* 3.8 15.3 - - + -
50L PRO* 3.5 46.7 - - + -
53L THR* 3.5 33.3 - - + +
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Residues in contact with SER 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K SER* 3.2 9.2 + - - -
10K TYR* 1.3 89.1 - - - +
12K GLN* 1.3 60.2 + - - +
14K TYR* 4.0 3.4 - - - +
15K ALA* 3.0 30.2 + - - +
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Residues in contact with GLN 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2847 T 4.5 3.2 + - - -
40J VAL* 5.2 1.9 - - - +
43J GLN* 5.3 9.3 - - + +
44J ASN* 2.9 33.5 + - - +
47J THR* 4.6 18.7 + - - +
48J ASN* 5.2 1.8 - - - +
7K SER 4.2 5.3 + - - +
8K ARG* 3.6 28.9 - - - +
9K SER* 2.8 40.0 + - - +
11K SER* 1.3 77.4 - - - +
13K ARG* 1.3 67.5 + - - +
15K ALA* 3.7 5.9 - - - +
16K LYS* 3.2 23.9 + - - +
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Residues in contact with ARG 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2837 A 3.4 53.4 + - + +
2847 T 3.6 41.5 + - - -
668 T 4.1 7.7 + - - -
678 A 5.3 5.7 + - - -
8K ARG* 4.1 6.0 - - + +
9K SER 2.8 22.9 + - - +
10K TYR* 3.4 10.1 - - + +
12K GLN* 1.3 73.0 - - - +
14K TYR* 1.3 62.9 + - - +
17K TRP* 3.1 23.3 + - - +
45L PHE* 4.6 7.4 - - + -
49L VAL* 3.7 20.6 + - - +
52L PHE* 4.6 4.6 - - - +
53L THR* 2.8 44.6 + - - +
56L ASN* 4.3 11.0 - - - +
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Residues in contact with TYR 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K TYR* 2.9 35.8 + + + +
11K SER* 4.1 3.6 - - - +
13K ARG* 1.3 76.5 - - - +
15K ALA* 1.3 70.1 + - - +
17K TRP* 3.1 17.1 + + - +
18K GLN* 2.7 55.9 + - + +
42L GLN* 3.7 9.2 + - - +
45L PHE* 3.4 34.5 - + + -
46L GLN* 2.9 36.8 + - + -
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Residues in contact with ALA 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J VAL* 4.0 22.2 - - + +
11K SER 3.0 20.1 + - - +
12K GLN* 3.4 7.6 + - - +
14K TYR* 1.3 82.2 - - - +
16K LYS* 1.3 62.0 + - - +
18K GLN* 3.3 6.5 + - - +
19K ALA* 3.2 19.8 + - - +
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Residues in contact with LYS 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2837 A 3.3 41.8 + - - +
2847 T 4.3 13.9 + - - +
578 A 3.8 37.4 + - - +
588 T 2.8 35.0 + - - +
37J VAL* 4.9 7.6 - - + -
40J VAL* 3.9 19.2 - - + +
44J ASN* 5.0 2.5 - - - +
8K ARG* 6.0 0.4 - - - +
12K GLN 3.2 12.8 + - - +
15K ALA* 1.3 76.8 - - - +
17K TRP* 1.3 66.5 + - - +
19K ALA* 3.1 4.3 + - - +
20K LYS* 3.0 25.2 + - + +
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Residues in contact with TRP 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2817 A 5.3 0.2 - - - -
2827 T 3.6 19.8 + - + +
2837 A 3.5 28.9 - - - +
678 A 5.0 0.4 - + - -
688 T 2.9 37.1 + - + -
698 A 5.4 0.2 - - - -
13K ARG 3.1 18.6 + - - +
14K TYR* 3.1 21.9 + + - +
16K LYS* 1.3 77.1 - - - +
18K GLN* 1.3 94.3 + - - +
20K LYS* 3.4 1.6 + - - +
21K PHE* 2.9 50.9 + + + +
41L ALA* 4.1 22.2 - - + -
42L GLN* 4.3 4.9 - - + -
45L PHE* 3.5 44.0 - + + -
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Residues in contact with GLN 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K TYR* 2.7 52.9 + - + +
15K ALA* 3.5 7.4 - - - +
17K TRP* 1.3 88.0 - - - +
19K ALA* 1.3 62.9 + - - +
21K PHE* 3.2 6.5 + - - -
22K ASN* 2.9 63.4 + - - +
42L GLN* 3.2 36.6 - - - +
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Residues in contact with ALA 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ASN* 3.4 35.8 - - - +
37J VAL* 3.7 17.5 - - + -
40J VAL* 4.3 6.5 - - + -
15K ALA 3.2 9.8 + - - +
16K LYS* 3.1 9.5 + - - +
18K GLN* 1.3 80.3 - - - +
20K LYS* 1.3 58.9 + - - +
22K ASN* 3.5 8.7 + - - +
23K ALA* 3.1 26.5 + - - +
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Residues in contact with LYS 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2827 T 3.5 41.2 + - + +
2837 A 3.1 30.2 + - - +
588 T 2.8 31.1 + - - +
598 A 3.2 27.0 + - - -
33J ILE* 4.0 21.1 - - + -
37J VAL* 3.7 15.0 - - + -
16K LYS* 3.0 20.2 + - + +
17K TRP 3.9 3.1 - - - +
19K ALA* 1.3 73.9 - - - +
21K PHE* 1.3 66.6 + - - +
23K ALA* 3.3 3.9 + - - +
24K PHE* 3.0 24.3 + - - +
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Residues in contact with PHE 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2817 A 6.1 4.0 - + - -
2827 T 5.6 2.6 - - - +
688 T 5.8 0.4 - - - -
698 A 4.5 23.6 - - - -
17K TRP* 2.9 46.0 + + + +
18K GLN* 3.6 10.8 - - - +
20K LYS* 1.3 77.0 - - - +
22K ASN* 1.3 73.7 + - - +
24K PHE* 3.3 12.6 + + - +
25K SER* 3.1 23.4 + - - -
34L LEU* 4.1 31.0 - - + -
37L VAL* 4.6 4.9 - - + -
38L SER* 3.6 36.6 - - - -
41L ALA* 4.3 12.6 - - + -
42L GLN* 5.8 0.2 - - + -
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Residues in contact with ASN 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ASN* 4.0 12.2 - - - +
18K GLN* 2.9 52.4 + - - +
19K ALA* 3.6 7.9 - - - +
21K PHE* 1.3 81.7 - - - +
23K ALA* 1.3 62.9 + - - +
25K SER* 2.6 26.4 + - - -
26K ASN* 3.6 3.5 + - - +
38L SER* 5.5 2.4 + - - -
42L GLN* 4.7 3.3 + - - -
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Residues in contact with ALA 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J THR* 3.6 14.2 - - + +
33J ILE* 3.8 28.5 - - + -
36J ASN* 3.4 17.0 - - - +
19K ALA 3.1 11.9 + - - +
20K LYS* 3.5 11.4 - - + +
22K ASN* 1.3 78.8 - - - +
24K PHE* 1.3 63.8 + - - +
26K ASN* 3.1 22.3 + - - +
29K VAL* 3.5 9.7 - - - +
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Residues in contact with PHE 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2817 A 3.7 51.1 - - + -
2827 T 4.6 7.9 - - - +
20K LYS 3.0 17.4 + - - +
21K PHE* 3.7 12.3 - + - +
23K ALA* 1.3 77.2 - - - +
25K SER* 1.3 62.4 + - - +
26K ASN 3.0 1.6 + - - -
29K VAL* 4.0 6.0 - - - +
30K ALA* 3.3 45.3 + - + +
33K ILE* 4.3 14.6 - - + -
34K LEU* 4.0 23.1 - - + -
24L PHE* 4.4 9.9 - + - -
34L LEU* 3.4 30.3 - - + -
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Residues in contact with SER 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K PHE* 3.1 15.2 + - - -
22K ASN* 2.6 24.1 + - - -
24K PHE* 1.3 76.6 - - - +
26K ASN* 1.3 60.6 + - - +
27K PRO* 3.2 4.5 - - - +
30K ALA* 5.0 0.6 - - - +
31L SER* 3.5 21.5 - - - +
34L LEU* 3.9 35.2 - - - -
35L SER* 4.6 6.4 - - - -
38L SER* 4.6 7.7 + - - -
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Residues in contact with ASN 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J THR* 4.9 3.4 - - - +
32J THR* 4.0 19.6 + - + +
22K ASN 3.6 2.0 + - - +
23K ALA 3.1 15.8 + - - +
24K PHE 3.0 1.0 + - - -
25K SER* 1.3 78.8 + - - +
27K PRO* 1.4 67.6 - - - +
28K THR* 2.7 33.0 + - - +
29K VAL* 2.7 34.6 + - + -
30K ALA* 2.9 11.5 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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