Contacts of the helix formed by residues 9 - 26 (chain z) 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 z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53y THR* 4.2 4.7 - - - -
8z ARG* 1.3 76.2 - - - +
10z TYR* 1.3 64.8 + - - +
11z SER* 2.7 28.2 + - - -
12z GLN* 2.8 24.3 + - - +
13z ARG* 3.0 20.8 + - - +
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Residues in contact with TYR 10 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45y PHE* 5.1 0.4 - + - -
46y GLN* 5.2 14.9 + - + +
49y VAL* 4.6 6.5 - - + -
50y PRO* 3.7 41.1 - - + -
53y THR* 3.1 38.8 - - + +
9z SER* 1.3 75.8 - - - +
11z SER* 1.3 77.8 + - - +
13z ARG* 3.5 6.1 - - - +
14z TYR* 2.8 49.4 + + + +
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Residues in contact with SER 11 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9z SER* 2.7 21.5 + - - -
10z TYR* 1.3 102.2 - - - +
12z GLN* 1.3 59.7 + - - +
14z TYR* 3.9 4.1 - - - +
15z ALA* 2.9 30.0 + - - +
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Residues in contact with GLN 12 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401 VAL* 5.0 1.7 - - - +
431 GLN* 5.3 7.6 - - + +
441 ASN* 2.9 32.1 + - - +
471 THR* 4.9 15.4 + - - +
481 ASN* 5.5 3.6 - - - +
3138 A 4.1 3.5 + - - -
7z SER 4.7 1.5 + - - +
8z ARG* 3.6 27.0 - - - +
9z SER* 2.8 38.6 + - - +
10z TYR 3.1 0.4 - - - -
11z SER* 1.3 83.2 + - - +
13z ARG* 1.3 65.6 + - - +
15z ALA* 3.7 5.8 - - - +
16z LYS* 3.1 25.6 + - - +
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Residues in contact with ARG 13 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377 A 3.9 14.6 + - - -
387 T 4.8 5.3 + - - -
3128 T 3.8 32.0 + - + +
3138 A 3.6 57.1 + - - +
45y PHE* 4.5 9.5 - - + -
49y VAL* 3.8 20.7 + - + +
52y PHE* 4.5 4.6 - - - +
53y THR* 2.7 48.8 + - - +
56y ASN* 4.0 11.8 - - - +
8z ARG* 4.3 8.3 - - + -
9z SER 3.0 20.2 + - - +
10z TYR* 3.5 6.7 - - - +
12z GLN* 1.3 76.8 - - - +
14z TYR* 1.3 57.7 + - - +
17z TRP* 3.0 28.6 + - - +
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Residues in contact with TYR 14 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42y GLN* 3.9 10.9 + - - +
45y PHE* 3.5 34.0 - + + -
46y GLN* 3.4 40.7 + - + -
10z TYR* 2.8 35.0 + + + +
11z SER* 3.9 4.5 - - - +
13z ARG* 1.3 75.7 - - - +
15z ALA* 1.3 71.4 + - - +
17z TRP* 3.0 15.1 + + - +
18z GLN* 2.7 58.3 + - + +
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Residues in contact with ALA 15 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401 VAL* 4.1 22.7 - - + +
11z SER 2.9 20.5 + - - +
12z GLN* 3.3 8.0 + - - +
14z TYR* 1.3 84.1 - - + +
16z LYS* 1.3 61.4 + - - +
18z GLN* 3.3 5.7 + - - +
19z ALA* 3.1 19.2 + - - +
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Residues in contact with LYS 16 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 VAL* 4.7 7.6 - - + -
401 VAL* 3.9 18.8 - - + +
441 ASN* 5.5 2.9 - - - +
287 T 3.7 33.6 + - - +
297 A 2.8 31.7 + - - -
3128 T 3.3 33.0 + - - +
3138 A 3.9 21.9 + - - +
12z GLN 3.1 13.4 + - - +
15z ALA* 1.3 76.4 - - - +
17z TRP* 1.3 67.7 + - - +
19z ALA* 3.1 5.3 + - - +
20z LYS* 3.0 25.3 + - + +
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Residues in contact with TRP 17 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397 A 3.8 33.4 + - + -
3118 A 3.8 26.7 + - + -
3128 T 3.8 19.4 - - - +
41y ALA* 4.1 20.6 - - + -
42y GLN* 4.2 7.0 - - + -
45y PHE* 3.5 54.6 - + + -
13z ARG 3.0 19.7 + - - +
14z TYR* 3.4 14.8 - + - +
16z LYS* 1.3 76.8 - - - +
18z GLN* 1.3 92.6 + - - +
20z LYS* 3.4 2.3 + - - +
21z PHE* 2.9 52.5 + + + +
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Residues in contact with GLN 18 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42y GLN* 3.2 39.0 - - - +
14z TYR* 2.7 58.7 + - + +
15z ALA* 3.5 7.0 - - - +
17z TRP* 1.3 82.3 - - - +
19z ALA* 1.3 62.2 + - - +
21z PHE* 3.2 6.5 + - - +
22z ASN* 2.9 62.6 + - - +
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Residues in contact with ALA 19 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 ASN* 3.4 35.9 - - - +
371 VAL* 3.7 16.2 - - + -
401 VAL* 4.5 4.5 - - + -
15z ALA 3.1 9.6 + - - +
16z LYS* 3.1 10.6 + - - +
18z GLN* 1.3 79.3 - - - +
20z LYS* 1.3 58.2 + - - +
22z ASN* 3.5 10.1 + - - +
23z ALA* 3.0 26.0 + - - +
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Residues in contact with LYS 20 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331 ILE* 3.9 19.7 - - + -
371 VAL* 3.6 15.9 - - + -
297 A 2.8 31.8 + - - +
307 T 3.1 24.0 + - - -
3118 A 3.4 44.6 + - + +
3128 T 3.2 21.3 + - - +
16z LYS* 3.0 21.7 + - + +
17z TRP 3.9 3.4 - - - +
19z ALA* 1.3 73.3 - - - +
21z PHE* 1.3 65.4 + - - +
23z ALA* 3.3 4.6 + - + +
24z PHE* 3.0 24.3 + - - +
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Residues in contact with PHE 21 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397 A 5.7 2.9 - + - -
407 T 4.5 23.1 - - - -
3108 T 6.0 1.8 - - - -
3118 A 5.2 2.6 - - - -
34y LEU* 3.9 31.2 - - + -
37y VAL* 4.5 5.2 - - + -
38y SER* 3.5 38.6 - - - -
41y ALA* 4.5 9.4 - - + -
17z TRP* 2.9 49.9 + + + +
18z GLN* 3.6 11.2 - - - +
20z LYS* 1.3 77.4 - - - +
22z ASN* 1.3 72.0 + - - +
24z PHE* 3.3 11.5 + + - +
25z SER* 3.0 23.2 + - - -
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Residues in contact with ASN 22 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 ASN* 4.0 11.4 - - - +
38y SER* 5.5 2.1 + - - -
42y GLN* 4.6 3.5 + - - -
18z GLN* 2.9 52.9 + - - +
19z ALA* 3.5 8.9 - - - +
21z PHE* 1.3 80.1 - - - +
23z ALA* 1.3 62.8 + - - +
25z SER* 2.6 25.7 + - - -
26z ASN* 3.6 4.3 + - - +
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Residues in contact with ALA 23 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321 THR* 3.6 14.6 - - + -
331 ILE* 3.8 28.0 - - + -
361 ASN* 3.5 16.1 - - - +
19z ALA 3.0 13.3 + - - +
20z LYS* 3.5 9.9 - - + +
22z ASN* 1.3 80.4 - - - +
24z PHE* 1.3 62.7 + - - +
26z ASN* 3.1 21.7 + - - +
29z VAL* 3.3 11.1 - - - +
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Residues in contact with PHE 24 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417 A 6.0 0.4 - - - -
3108 T 3.7 50.7 - - + +
3118 A 5.4 3.1 - - - +
24y PHE* 4.4 9.0 - + - -
34y LEU* 3.5 31.4 - - + -
20z LYS 3.0 17.2 + - - +
21z PHE* 3.7 11.2 - + - +
23z ALA* 1.3 75.7 - - - +
25z SER* 1.3 61.9 + - - +
26z ASN 3.0 1.6 + - - -
29z VAL* 3.8 6.3 - - - +
30z ALA* 3.3 44.6 + - - +
33z ILE* 4.2 19.1 - - + -
34z LEU* 4.0 25.8 - - + -
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Residues in contact with SER 25 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31y SER* 3.4 21.7 + - - +
34y LEU* 3.8 38.6 - - - -
35y SER* 4.5 6.5 - - - -
38y SER* 4.7 6.9 + - - -
21z PHE* 3.0 14.6 + - - -
22z ASN* 2.6 23.7 + - - -
24z PHE* 1.3 75.1 - - - +
26z ASN* 1.3 61.1 + - - +
27z PRO* 3.2 4.0 - - - +
30z ALA* 4.9 0.4 - - - -
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Residues in contact with ASN 26 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321 THR* 4.0 19.2 + - + +
22z ASN 3.6 2.4 + - - +
23z ALA 3.1 15.3 + - - +
24z PHE 3.0 1.2 + - - -
25z SER* 1.3 78.8 + - - +
27z PRO* 1.4 68.3 - - - +
28z THR* 2.9 24.4 + - - -
29z VAL* 2.7 37.8 + - + -
30z ALA* 2.8 11.8 + - - -
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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