Contacts of the helix formed by residues 13 - 31 (chain A) in PDB entry 3EJW
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 VAL 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.9 30.7 - - + -
11A VAL 3.3 1.0 - - - +
12A GLY* 1.3 82.3 - - - +
14A GLY* 1.3 69.1 + - - +
15A PHE* 4.0 8.7 - - + +
16A PHE* 2.8 35.4 + - + +
17A THR* 3.1 11.4 + - - -
169A ASN 4.8 0.9 - - - +
196A ALA* 4.1 19.5 - - + +
197A ASN* 3.6 36.1 - - - +
225A VAL* 6.4 0.4 - - + -
400A PAV 6.0 0.2 - - - -
70B ASP* 4.1 0.4 + - - -
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Residues in contact with GLY 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 1.3 73.7 - - - +
15A PHE* 1.3 61.9 + - - +
17A THR* 3.3 8.7 + - - -
18A SER* 2.9 29.0 + - - -
222A THR* 4.1 13.7 - - - -
225A VAL* 5.0 11.5 - - - +
315A PHE* 4.6 4.9 - - - -
70B ASP* 4.2 5.8 + - - -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.0 5.8 + - + +
14A GLY* 1.3 74.4 - - - +
16A PHE* 1.3 81.7 + + - +
18A SER* 3.5 2.1 + - - -
19A GLY* 3.1 21.3 + - - -
89A TRP* 3.8 11.9 - + - -
90A ASP* 3.6 38.4 - - - -
196A ALA* 4.2 18.4 - - + +
222A THR* 3.5 19.3 + - + +
240A LEU* 3.9 17.5 - - + -
241A TRP* 3.6 29.8 - + - -
243A VAL* 3.5 34.5 - - + +
246A GLN* 4.2 0.4 - - - -
400A PAV 3.6 21.8 - - + -
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO* 3.3 18.6 - - + -
9A LYS* 3.5 27.1 - - + -
10A LEU* 3.5 39.7 - - + +
11A VAL* 5.2 0.4 - - - -
13A VAL* 2.8 19.3 + - + +
15A PHE* 1.3 87.0 - + - +
17A THR* 1.3 66.1 + - - +
19A GLY* 3.4 0.6 + - - +
20A GLY 2.9 19.4 + - - -
36A TYR* 3.2 24.3 + - - +
65A SER* 3.8 5.8 - - - -
89A TRP* 3.6 18.1 - + - -
90A ASP* 3.5 15.0 - - - -
169A ASN* 5.3 0.9 - - - -
400A PAV 3.3 34.3 - - - -
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 4.5 3.8 + - - -
13A VAL 3.1 10.2 + - - -
14A GLY* 3.6 9.2 - - - -
16A PHE* 1.3 77.6 - - - +
18A SER* 1.3 58.3 + - - +
20A GLY* 3.4 1.2 + - - -
21A ALA* 3.0 28.6 + - + +
36A TYR* 3.5 15.0 + - + -
70B ASP* 2.5 44.2 + - + +
94B ASN* 5.3 4.3 - - - +
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLY 2.9 14.8 + - - -
15A PHE 3.8 3.4 - - - -
17A THR* 1.3 75.1 - - - +
19A GLY* 1.3 66.6 + - - +
21A ALA* 3.3 7.6 + - - +
22A GLY 3.2 17.5 + - - -
243A VAL* 3.9 16.6 - - - -
244A THR* 3.8 15.8 + - - -
315A PHE* 2.9 40.5 + - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.5 17.4 - - - -
15A PHE 3.1 15.6 + - - -
16A PHE 3.8 2.5 - - - -
18A SER* 1.3 77.7 - - - +
20A GLY* 1.3 61.7 + - - +
22A GLY* 3.2 1.9 + - - -
23A ALA 3.0 17.8 + - - -
89A TRP* 4.4 4.0 - - - -
243A VAL* 3.6 26.8 - - - +
247A GLY* 3.6 6.2 - - - -
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Residues in contact with GLY 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.5 10.3 - - - -
16A PHE 2.9 12.9 + - - -
17A THR 3.8 1.6 - - - -
19A GLY* 1.3 75.7 - - - +
21A ALA* 1.3 57.0 + - - +
23A ALA* 3.2 1.9 + - - +
24A VAL* 2.8 37.0 + - - +
36A TYR* 3.6 32.3 - - - -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 3.0 18.8 + - + +
18A SER* 3.6 8.7 - - - +
19A GLY 3.2 0.2 - - - -
20A GLY* 1.3 76.8 - - - +
22A GLY* 1.3 57.2 + - - +
24A VAL* 3.9 5.8 - - - +
25A LYS* 3.0 30.7 + - - +
244A THR* 5.1 2.0 - - + -
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER 3.2 10.3 + - - -
19A GLY 3.7 0.7 - - - -
21A ALA* 1.3 77.3 - - - +
23A ALA* 1.3 55.9 + - - +
25A LYS* 3.5 6.7 + - - +
26A ALA* 3.0 29.8 + - - +
244A THR* 3.4 34.9 - - - +
248A LYS* 3.8 12.0 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.5 38.1 - - + -
19A GLY 3.0 10.0 + - - +
20A GLY 3.5 7.9 - - - +
22A GLY* 1.3 75.8 - - - +
24A VAL* 1.3 62.4 + - - +
26A ALA 3.3 1.0 + - - -
27A GLY 3.0 17.8 + - - -
34A VAL* 3.6 7.1 - - + +
247A GLY 3.5 13.9 - - - +
251A VAL* 3.4 23.9 - - + +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLY 2.8 23.2 + - - +
21A ALA* 3.9 6.1 - - - +
23A ALA* 1.3 72.3 - - - +
25A LYS* 1.3 64.6 + - - +
27A GLY* 3.1 11.3 + - - -
28A GLU* 3.3 27.2 + - + +
34A VAL* 4.0 29.4 - - + +
36A TYR* 4.1 20.9 - - + +
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 3.0 18.6 + - - +
22A GLY* 3.7 7.9 - - - +
24A VAL* 1.3 77.3 - - - +
26A ALA* 1.3 62.1 + - - +
28A GLU* 3.0 29.1 + - - +
29A GLU* 3.0 40.0 + - + +
244A THR* 6.0 4.3 - - + -
248A LYS* 6.2 2.5 - - + -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY 3.0 18.1 + - - +
23A ALA 3.3 4.9 + - - +
25A LYS* 1.3 76.9 - - - +
27A GLY* 1.3 57.4 + - - +
29A GLU* 3.1 7.7 + - - +
30A VAL* 2.8 33.6 + - - +
248A LYS* 3.7 24.6 - - + +
251A VAL* 3.7 15.0 - - + -
252A PHE* 3.7 20.4 - - + -
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 3.0 10.5 + - - -
24A VAL 3.1 6.6 + - - -
26A ALA* 1.3 77.9 - - - +
28A GLU* 1.3 56.4 + - - +
30A VAL* 4.3 0.7 - - - -
31A GLY* 2.8 12.1 + - - -
32A ALA 2.8 43.7 + - - +
34A VAL* 3.6 17.7 - - - -
251A VAL* 3.8 5.3 - - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.3 24.6 + - + +
25A LYS* 3.0 21.2 + - - +
27A GLY* 1.3 77.0 - - - +
29A GLU* 1.3 62.8 + - + +
31A GLY* 3.7 7.2 + - - -
32A ALA 4.9 1.1 - - - +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.0 44.4 + - + +
26A ALA* 3.1 10.3 + - - +
28A GLU* 1.3 80.1 - - + +
30A VAL* 1.3 60.4 + - - +
248A LYS* 2.9 39.7 + - - +
252A PHE* 3.7 12.6 - - + -
272A PRO* 4.7 1.0 - - - +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 2.8 21.1 + - - +
27A GLY 3.9 0.4 - - - +
29A GLU* 1.3 73.0 - - - +
31A GLY* 1.3 60.4 + - - +
32A ALA* 3.8 23.6 - - + -
251A VAL* 4.2 10.3 - - + -
252A PHE* 3.6 35.9 - - + +
255A ASP* 3.6 30.3 - - + +
259A LYS* 3.6 15.7 + - - +
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLU* 3.0 38.7 - - - +
2A ASN 4.6 1.2 + - - -
27A GLY 2.8 8.6 + - - -
28A GLU* 3.7 5.1 + - - -
29A GLU 3.4 3.8 + - - -
30A VAL* 1.3 81.2 - - - +
32A ALA* 1.3 57.0 + - - +
255A ASP* 4.8 0.7 - - - +
259A LYS* 4.7 6.9 + - - -
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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
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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