Contacts of the helix formed by residues 9 - 26 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U ARG* 1.3 75.0 - - - +
10U TYR* 1.3 61.8 + - - +
11U SER* 3.6 9.6 + - - -
12U GLN* 2.8 35.8 + - - +
13U ARG* 2.8 27.8 + - - +
53V THR* 4.3 3.4 - - - -
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Residues in contact with TYR 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U SER* 1.3 74.0 - - - +
11U SER* 1.3 72.4 + - - +
13U ARG* 3.0 5.4 + - + -
14U TYR* 2.9 46.4 + + + +
45V PHE* 4.1 0.9 - + - -
46V GLN* 3.3 35.7 + - - +
49V VAL* 3.8 15.0 - - + -
50V PRO* 3.5 48.5 - - + -
53V THR* 3.5 32.4 - - + +
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Residues in contact with SER 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U SER* 3.2 9.6 + - - -
10U TYR* 1.3 88.1 - - - +
12U GLN* 1.3 59.2 + - - +
14U TYR* 4.1 3.2 - - - +
15U ALA* 3.0 30.6 + - - +
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Residues in contact with GLN 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2247 T 4.5 2.8 + - - -
40T VAL* 5.2 1.3 - - - +
43T GLN* 5.3 8.4 - - + +
44T ASN* 2.9 34.2 + - - +
47T THR* 4.6 19.4 + - - +
48T ASN* 5.2 1.6 - - - +
7U SER 4.2 5.5 + - - +
8U ARG* 3.6 29.3 - - - +
9U SER* 2.8 39.4 + - - +
11U SER* 1.3 77.4 - - - +
13U ARG* 1.3 67.0 + - - +
15U ALA* 3.7 5.6 - - - +
16U LYS* 3.2 24.4 + - - +
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Residues in contact with ARG 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2237 A 3.4 53.8 + - + +
2247 T 3.6 40.6 + - - -
1268 T 4.1 7.9 + - - -
1278 A 5.3 5.3 + - - -
8U ARG* 4.1 6.7 - - + +
9U SER 2.8 22.9 + - - +
10U TYR* 3.0 10.3 + - + +
12U GLN* 1.3 73.0 - - - +
14U TYR* 1.3 63.6 + - - +
17U TRP* 3.1 23.3 + - - +
45V PHE* 4.6 7.8 - - + -
49V VAL* 3.7 21.4 + - - +
52V PHE* 4.6 4.6 - - - +
53V THR* 2.8 43.4 + - - +
56V ASN* 4.3 10.7 - - - +
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Residues in contact with TYR 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U TYR* 2.9 36.2 + + + +
11U SER* 4.1 3.1 - - - +
13U ARG* 1.3 77.2 - - - +
15U ALA* 1.3 70.0 + - - +
17U TRP* 3.1 16.2 + + - -
18U GLN* 2.7 56.5 + - + +
42V GLN* 3.7 8.9 + - - +
45V PHE* 3.4 36.1 - + + -
46V GLN* 2.9 37.0 + - + -
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Residues in contact with ALA 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40T VAL* 4.0 21.8 - - + +
11U SER 3.0 20.9 + - - +
12U GLN* 3.7 7.9 - - - +
14U TYR* 1.3 82.4 - - - +
16U LYS* 1.3 63.3 + - - +
18U GLN* 3.3 6.3 + - - +
19U ALA* 3.2 19.2 + - - +
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Residues in contact with LYS 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2237 A 3.3 41.4 + - - +
2247 T 4.3 13.9 + - - +
1178 A 3.8 38.5 + - - +
1188 T 2.8 34.7 + - - +
37T VAL* 4.9 7.4 - - + -
40T VAL* 3.9 19.0 - - + +
44T ASN* 5.0 2.9 - - - +
8U ARG* 6.0 0.2 - - - +
12U GLN 3.2 13.2 + - - +
15U ALA* 1.3 75.3 - - - +
17U TRP* 1.3 66.5 + - - +
19U ALA* 3.1 4.5 + - - +
20U LYS* 3.0 25.8 + - + +
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Residues in contact with TRP 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2217 A 5.3 0.2 - - - -
2227 T 3.6 19.4 + - + +
2237 A 3.5 29.5 - - - +
1278 A 5.0 0.2 - + - -
1288 T 2.9 36.1 + - + -
1298 A 5.4 0.2 - - - -
13U ARG 3.1 18.4 + - - +
14U TYR* 3.1 21.6 + + - +
16U LYS* 1.3 75.9 - - - +
18U GLN* 1.3 95.3 + - - +
20U LYS* 3.4 1.6 + - - +
21U PHE* 2.9 52.6 + + + +
41V ALA* 4.1 21.5 - - + -
42V GLN* 4.3 5.2 - - + -
45V PHE* 3.5 45.4 - + + -
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Residues in contact with GLN 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U TYR* 2.7 49.7 + - + +
15U ALA* 3.5 11.0 - - - +
17U TRP* 1.3 87.5 - - - +
19U ALA* 1.3 62.7 + - - +
21U PHE* 3.2 6.1 + - - -
22U ASN* 2.9 62.7 + - - +
42V GLN* 3.2 36.7 - - - +
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Residues in contact with ALA 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36T ASN* 3.4 33.6 - - - +
37T VAL* 3.7 18.2 - - + -
40T VAL* 4.3 7.4 - - + -
15U ALA 3.2 9.8 + - - +
16U LYS 3.1 9.0 + - - +
18U GLN* 1.3 79.8 - - - +
20U LYS* 1.3 58.4 + - - +
22U ASN* 3.5 8.4 + - - +
23U ALA* 3.1 26.7 + - - +
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Residues in contact with LYS 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2227 T 3.5 40.4 + - + +
2237 A 3.1 29.8 + - - +
1188 T 2.8 31.9 + - - +
1198 A 3.2 26.7 + - - -
33T ILE* 4.0 21.1 - - + -
37T VAL* 3.7 15.5 - - + -
16U LYS* 3.0 20.9 + - + +
17U TRP 3.9 2.7 - - - +
19U ALA* 1.3 73.7 - - - +
21U PHE* 1.3 65.0 + - - +
23U ALA* 3.3 3.9 + - + +
24U PHE* 3.0 24.9 + - - +
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Residues in contact with PHE 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2217 A 6.1 3.8 - + - -
2227 T 5.6 2.6 - - - +
1288 T 5.8 0.4 - - - -
1298 A 4.5 23.1 - - - -
17U TRP* 2.9 48.1 + + + +
18U GLN* 3.6 10.3 - - - +
20U LYS* 1.3 78.0 - - - +
22U ASN* 1.3 72.7 + - - +
24U PHE* 3.3 12.9 + + - +
25U SER* 3.1 23.1 + - - -
34V LEU* 4.1 30.5 - - + -
37V VAL* 4.6 4.5 - - + -
38V SER* 3.6 37.7 - - - -
41V ALA* 4.3 12.1 - - + -
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Residues in contact with ASN 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36T ASN* 4.0 11.9 + - - +
18U GLN* 2.9 52.4 + - - +
19U ALA* 3.6 8.3 - - - +
21U PHE* 1.3 81.0 - - - +
23U ALA* 1.3 62.3 + - - +
25U SER* 2.6 26.6 + - - -
26U ASN* 3.6 3.5 + - - +
38V SER* 5.5 2.4 + - - -
42V GLN* 4.7 3.1 + - - -
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Residues in contact with ALA 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32T THR* 3.6 14.8 - - + +
33T ILE* 3.8 28.0 - - + -
36T ASN* 3.4 17.2 - - - +
19U ALA 3.1 12.1 + - - +
20U LYS* 3.5 11.9 - - + +
21U PHE 3.2 0.2 - - - -
22U ASN* 1.3 79.0 - - - +
24U PHE* 1.3 63.9 + - - +
26U ASN* 3.1 22.0 + - - +
29U VAL* 3.5 9.3 - - - +
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Residues in contact with PHE 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2217 A 3.7 52.7 - - + -
2227 T 4.6 8.3 - - - +
1298 A 6.3 0.4 - - - -
20U LYS 3.0 15.9 + - - +
21U PHE* 3.7 11.9 - + - +
23U ALA* 1.3 76.7 - - - +
25U SER* 1.3 62.4 + - - +
26U ASN 3.0 2.0 + - - -
29U VAL* 4.0 6.1 - - - -
30U ALA* 3.3 45.8 + - + +
33U ILE* 4.3 14.1 - - + -
34U LEU* 4.0 22.2 - - + -
24V PHE* 4.4 9.2 - + - -
34V LEU* 3.4 30.3 - - + -
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Residues in contact with SER 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U PHE* 3.1 15.0 + - - -
22U ASN* 2.6 23.4 + - - -
24U PHE* 1.3 76.1 - - - +
26U ASN* 1.3 61.6 + - - +
27U PRO* 3.2 4.5 - - - +
30U ALA* 5.0 0.4 - - - -
31V SER* 3.5 21.9 - - - +
34V LEU* 3.9 36.1 - - - -
35V SER* 4.6 6.2 - - - -
38V SER* 4.6 7.9 + - - -
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Residues in contact with ASN 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T THR* 4.9 3.2 - - - +
32T THR* 4.0 19.4 + - + +
22U ASN 3.6 2.4 + - - +
23U ALA 3.1 15.3 + - - +
24U PHE 3.0 1.2 + - - +
25U SER* 1.3 78.1 + - - +
27U PRO* 1.4 68.1 - - - +
28U THR* 2.7 33.4 + - - +
29U VAL* 2.7 35.3 + - + -
30U 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