Contacts of the helix formed by residues 9 - 26 (chain g) 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 g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 5.5 12.8 - - - +
51C LYS* 6.0 4.7 - - - -
8g ARG* 1.3 74.9 - - - +
10g TYR* 1.3 60.3 + - - +
11g SER* 3.6 9.7 + - - -
12g GLN* 2.8 34.6 + - - +
13g ARG* 2.8 27.6 + - - +
53h THR* 4.3 3.6 - - - -
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Residues in contact with TYR 10 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PRO* 4.9 12.3 - - + -
10D TYR* 2.8 44.7 + + - -
11D SER* 5.5 0.2 - - - -
9g SER* 1.3 72.5 - - - +
11g SER* 1.3 71.1 + - - +
13g ARG* 3.0 4.2 + - + -
14g TYR* 2.9 45.5 + + + +
45h PHE* 4.1 1.1 - + - -
46h GLN* 3.3 35.5 + - - +
49h VAL* 3.8 15.7 - - + -
50h PRO* 3.5 40.4 - - + -
53h THR* 3.5 32.2 - - + +
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Residues in contact with SER 11 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLN* 5.1 9.2 - - - -
46C GLN* 2.8 48.2 + - - +
47C THR* 4.1 4.5 - - - -
50C PRO* 4.8 0.5 - - - +
10D TYR* 5.0 2.2 + - - -
9g SER* 3.2 9.5 + - - -
10g TYR* 1.3 87.5 - - - +
12g GLN* 1.3 60.4 + - - +
14g TYR* 4.1 3.7 - - - +
15g ALA* 3.0 30.4 + - - +
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Residues in contact with GLN 12 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1527 T 4.5 3.8 + - - -
43C GLN* 6.1 2.5 - - - +
40f VAL* 5.2 1.5 - - - +
43f GLN* 5.3 8.4 - - + +
44f ASN* 2.9 34.9 + - - +
47f THR* 4.6 18.0 + - - +
48f ASN* 5.2 1.4 - - - +
7g SER 4.2 5.1 + - - +
8g ARG* 3.6 28.6 - - - +
9g SER* 2.8 38.9 + - - +
11g SER* 1.3 76.8 - - - +
13g ARG* 1.3 68.5 + - - +
15g ALA* 3.7 6.0 - - - +
16g LYS* 3.2 23.6 + - - +
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Residues in contact with ARG 13 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517 A 3.4 52.5 + - + +
1527 T 3.6 41.6 + - - -
1988 T 4.1 7.1 + - - -
1998 A 5.3 5.7 + - - -
8g ARG* 4.1 5.8 - - + +
9g SER 2.8 22.1 + - - +
10g TYR* 3.0 10.5 + - + +
12g GLN* 1.3 71.3 - - - +
14g TYR* 1.3 63.1 + - - +
17g TRP* 3.1 23.6 + - - +
45h PHE* 4.6 8.7 - - + -
49h VAL* 3.7 20.8 + - - +
52h PHE* 4.6 4.4 - - - +
53h THR* 2.8 44.4 + - - +
56h ASN* 4.3 10.7 - - - +
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Residues in contact with TYR 14 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLN* 6.2 2.0 - - - -
10D TYR* 5.5 1.6 - - - -
10g TYR* 2.9 36.5 + + + +
11g SER* 4.1 3.8 - - - +
13g ARG* 1.3 77.0 - - - +
15g ALA* 1.3 68.3 + - - +
17g TRP* 3.1 16.6 + + - -
18g GLN* 2.7 57.3 + - + +
42h GLN* 3.7 9.4 + - - +
45h PHE* 3.4 35.9 - + + -
46h GLN* 2.9 36.9 + - + -
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Residues in contact with ALA 15 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40f VAL* 4.0 22.0 - - + +
11g SER 3.0 20.1 + - - +
12g GLN* 3.4 8.0 + - - +
14g TYR* 1.3 82.0 - - - +
16g LYS* 1.3 62.5 + - - +
18g GLN* 3.3 6.5 + - - +
19g ALA* 3.2 19.2 + - - +
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Residues in contact with LYS 16 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517 A 3.3 41.4 + - - +
1527 T 4.3 14.5 + - - +
1898 A 3.8 38.1 + - - +
1908 T 2.8 35.2 + - - +
37f VAL* 4.9 7.9 - - + -
40f VAL* 3.9 17.5 - - + -
44f ASN* 5.0 3.4 - - - +
8g ARG* 6.0 0.2 - - - +
12g GLN 3.2 13.1 + - - +
15g ALA* 1.3 76.2 - - - +
17g TRP* 1.3 67.1 + - - +
19g ALA* 3.1 4.7 + - - +
20g LYS* 3.0 25.9 + - + +
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Residues in contact with TRP 17 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1507 T 3.6 19.6 + - + +
1517 A 3.5 27.5 - - - +
1998 A 5.0 0.2 - + - -
2008 T 2.9 36.7 + + + -
13g ARG 3.1 18.6 + - - +
14g TYR* 3.1 22.6 + + - +
16g LYS* 1.3 76.8 - - - +
18g GLN* 1.3 95.1 + - - +
20g LYS* 3.4 2.4 + - - +
21g PHE* 2.9 52.8 + + + +
41h ALA* 4.1 21.5 - - + -
42h GLN* 4.3 5.4 - - + -
45h PHE* 3.5 45.6 - + + -
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Residues in contact with GLN 18 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14g TYR* 2.7 53.5 + - + +
15g ALA* 3.5 7.0 - - - +
17g TRP* 1.3 88.6 - - - +
19g ALA* 1.3 62.5 + - - +
21g PHE* 3.2 6.3 + - - -
22g ASN* 2.9 63.3 + - - +
42h GLN* 3.2 36.1 - - - +
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Residues in contact with ALA 19 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36f ASN* 3.4 34.1 - - - +
37f VAL* 3.7 17.9 - - + -
40f VAL* 4.3 7.2 - - + -
15g ALA 3.2 9.4 + - - +
16g LYS 3.1 9.5 + - - +
18g GLN* 1.3 81.5 - - - +
20g LYS* 1.3 57.9 + - - +
22g ASN* 3.5 8.0 + - - +
23g ALA* 3.1 26.5 + - - +
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Residues in contact with LYS 20 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1507 T 3.5 41.1 + - + +
1517 A 3.1 30.8 + - - +
1908 T 2.8 32.2 + - - +
1918 A 3.2 26.8 + - - -
33f ILE* 4.0 21.8 - - + -
37f VAL* 3.7 15.3 - - + -
16g LYS* 3.0 16.6 + - + +
17g TRP 3.9 3.4 - - - +
19g ALA* 1.3 73.1 - - - +
21g PHE* 1.3 66.2 + - - +
23g ALA* 3.3 4.2 + - + +
24g PHE* 3.0 24.3 + - - +
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Residues in contact with PHE 21 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 A 6.1 4.3 - + - -
1507 T 5.6 3.1 - - + +
2008 T 5.8 0.4 - - - -
2018 A 4.5 23.3 - - - -
17g TRP* 2.9 47.1 + + + +
18g GLN* 3.2 11.4 + - - +
20g LYS* 1.3 78.2 - - - +
22g ASN* 1.3 72.6 + - - +
24g PHE* 3.3 12.3 + + - +
25g SER* 3.1 22.4 + - - -
34h LEU* 4.1 30.3 - - + -
37h VAL* 4.6 4.9 - - + -
38h SER* 3.6 36.8 - - - -
41h ALA* 4.3 12.6 - - + -
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Residues in contact with ASN 22 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36f ASN* 4.0 11.7 - - - +
18g GLN* 2.9 53.4 + - - +
19g ALA* 3.6 7.7 - - - +
21g PHE* 1.3 81.1 - - - +
23g ALA* 1.3 63.0 + - - +
25g SER* 2.6 25.8 + - - -
26g ASN* 3.6 3.8 + - - +
38h SER* 5.5 2.4 + - - -
42h GLN* 4.7 2.8 + - - -
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Residues in contact with ALA 23 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32f THR* 3.6 15.3 - - + +
33f ILE* 3.8 28.0 - - + -
36f ASN* 3.4 17.2 - - - +
19g ALA 3.1 10.9 + - - +
20g LYS* 3.5 12.3 - - + +
22g ASN* 1.3 79.3 - - - +
24g PHE* 1.3 62.9 + - - +
26g ASN* 3.1 22.2 + - - +
29g VAL* 3.5 9.5 - - - +
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Residues in contact with PHE 24 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 A 3.7 53.2 - - + -
1507 T 4.6 8.1 - - - +
20g LYS 3.0 16.6 + - - +
21g PHE* 3.7 11.7 - + - +
23g ALA* 1.3 75.5 - - - +
25g SER* 1.3 63.3 + - - +
26g ASN 3.0 1.9 + - - -
29g VAL* 4.0 6.1 - - - -
30g ALA* 3.3 45.0 + - + +
33g ILE* 4.3 14.4 - - + -
34g LEU* 4.0 23.1 - - + -
24h PHE* 4.4 8.1 - + - -
34h LEU* 3.4 31.6 - - + -
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Residues in contact with SER 25 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21g PHE* 3.1 14.8 + - - -
22g ASN* 2.6 23.8 + - - -
24g PHE* 1.3 76.1 - - - +
26g ASN* 1.3 62.6 + - - +
27g PRO* 3.2 4.5 - - - +
30g ALA* 5.0 0.4 - - - +
31h SER* 3.5 21.7 - - - +
34h LEU* 3.9 37.2 - - - -
35h SER* 4.6 6.3 + - - -
38h SER* 4.6 7.5 + - - -
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Residues in contact with ASN 26 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28f THR* 4.9 3.2 - - - +
32f THR* 4.0 19.6 + - + +
22g ASN 3.6 2.2 + - - +
23g ALA 3.1 15.8 + - - +
24g PHE 3.0 1.4 + - - +
25g SER* 1.3 78.8 + - - +
27g PRO* 1.4 67.0 - - - +
28g THR* 2.7 33.5 + - - +
29g VAL* 2.7 33.8 + - + -
30g ALA* 2.9 11.7 + - - -
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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
------------------------------------------------------------
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