Contacts of the helix formed by residues 15 - 33 (chain O) in PDB entry 5X22
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 15 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216N SER* 3.7 6.3 - - - -
1217N ILE* 3.0 31.8 + - - -
1480N PHE* 4.9 1.1 - - - -
1481N VAL* 3.5 21.8 - - - +
13O VAL* 3.3 8.8 - - - +
14O ASP* 1.3 89.5 + - - +
16O LYS* 1.3 60.8 + - - +
17O TYR* 3.5 14.2 + - - -
18O ARG* 2.9 26.2 + - - +
19O LEU 3.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710N ARG* 5.3 7.1 - - - +
761N ILE* 4.8 1.4 - - + +
762N GLN* 4.6 28.0 + - + +
768N ASN* 5.3 3.0 + - - -
1208N ASP* 4.5 5.4 + - - +
1210N SER* 5.2 2.4 + - - -
1211N MET* 3.3 37.1 - - + +
1216N SER* 3.4 29.4 + - - +
1219N GLU* 5.2 0.2 + - - -
10O PHE* 3.7 31.8 - - + -
13O VAL* 4.2 8.7 - - - +
15O SER* 1.3 72.1 - - - +
17O TYR* 1.3 83.1 + - + +
19O LEU* 3.1 8.9 + - - +
20O THR* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042M ALA 4.6 0.5 + - - -
1043M TYR 3.4 16.0 + - - -
1044M GLY* 3.7 5.2 - - - -
710N ARG* 5.1 1.9 + - - -
762N GLN* 3.3 37.7 - - + -
1216N SER* 4.0 6.5 - - - -
1217N ILE 3.7 7.9 - - - -
1218N GLY 3.9 0.2 - - - -
1219N GLU* 3.2 55.6 + - + +
1475N GLY* 3.4 37.0 - - - +
1476N THR* 3.8 1.8 - - - +
1481N VAL* 3.7 7.2 - - + -
15O SER* 3.1 15.1 - - - +
16O LYS* 1.3 95.3 + - + +
18O ARG* 1.3 60.3 + - - +
20O THR* 3.3 7.6 + - - -
21O VAL* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1480N PHE* 2.9 46.7 + - - -
1481N VAL* 3.6 25.7 - - + +
1484N THR* 2.8 34.6 + - + +
13O VAL* 4.3 6.7 - - + -
14O ASP* 2.6 48.3 + - - -
15O SER* 2.9 12.2 + - - +
17O TYR* 1.3 77.3 - - - +
19O LEU* 1.3 60.9 + - - +
21O VAL* 3.3 1.6 + - - +
22O VAL* 2.9 33.2 + - + +
75O PHE* 4.3 13.9 - - - -
76O GLY* 5.8 1.7 - - - -
77O GLU* 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761N ILE* 4.1 16.4 - - + -
6O ILE* 4.6 2.7 - - + -
9O LEU* 3.8 36.3 - - + +
10O PHE* 3.5 35.4 - - + -
12O MET* 6.0 0.7 - - + -
13O VAL* 3.6 25.7 - - + +
15O SER 3.3 2.4 + - - -
16O LYS 3.1 8.8 + - - +
18O ARG* 1.3 79.7 - - - +
20O THR* 1.3 57.3 + - - +
22O VAL* 3.3 4.1 + - - +
23O VAL* 2.9 39.5 + - + +
68O LEU* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754N PHE* 4.6 2.2 - - + +
757N ALA* 3.8 8.4 - - + +
758N GLU* 3.5 39.5 - - + +
761N ILE* 3.7 17.7 - - - +
762N GLN* 2.9 34.1 + - - +
1476N THR* 3.7 5.6 - - + -
16O LYS 2.9 12.4 + - - -
17O TYR 3.5 7.2 - - - -
18O ARG 3.2 0.2 - - - -
19O LEU* 1.3 76.0 - - - +
21O VAL* 1.3 57.1 + - - +
23O VAL* 3.3 3.1 + - - +
24O ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754N PHE* 4.0 23.3 - - + -
1476N THR* 4.0 26.0 - - - +
1481N VAL* 3.6 23.3 - - + +
1482N ARG* 4.0 9.4 - - - +
1484N THR* 4.2 8.1 - - - +
17O TYR 2.9 21.6 + - - +
18O ARG 3.7 3.8 - - - +
20O THR* 1.3 75.7 - - - +
22O VAL* 1.3 58.5 + - - +
24O ALA* 3.4 1.2 + - - +
25O LYS* 2.9 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484N THR* 3.7 26.7 - - + -
1486N VAL* 3.5 25.8 - - + +
13O VAL* 5.4 0.4 - - + -
18O ARG* 2.9 19.9 + - + +
19O LEU* 3.5 10.3 - - - +
21O VAL* 1.3 76.6 - - - +
23O VAL* 1.3 64.6 + - - +
25O LYS* 5.5 0.2 - - - -
26O ARG* 2.9 25.8 + - + +
68O LEU* 3.6 33.7 - - + -
75O PHE* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757N ALA* 4.4 5.6 - - + -
761N ILE* 3.9 14.1 - - + -
9O LEU* 5.8 0.2 - - + -
19O LEU* 2.9 38.9 + - + +
20O THR 3.7 4.5 - - - +
22O VAL* 1.3 76.8 - - - +
24O ALA* 1.3 57.5 + - - +
26O ARG* 3.4 0.8 + - - -
27O ALA* 2.9 28.9 + - - +
61O VAL* 3.6 31.4 - - + -
64O ALA* 3.5 13.7 - - + +
65O MET* 3.7 24.0 - - + -
68O LEU* 3.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753N SER* 4.4 5.6 - - - -
754N PHE* 3.5 48.5 - - + +
757N ALA* 3.9 8.9 - - + +
20O THR 2.9 17.3 + - - +
21O VAL 3.7 2.2 - - - +
23O VAL* 1.3 76.7 - - - +
25O LYS* 1.3 62.8 + - - +
27O ALA* 3.2 6.8 + - - +
28O GLN* 3.0 28.9 + - - +
61O VAL* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754N PHE* 4.4 13.7 - - + -
1482N ARG 4.0 7.5 + - - -
1483N PHE* 3.7 12.9 + - - +
1484N THR 2.6 33.1 + - - +
1485N GLN* 4.4 13.7 - - + +
1486N VAL* 4.3 9.4 - - + +
21O VAL* 2.9 34.0 + - + +
22O VAL 3.9 2.7 - - - +
24O ALA* 1.3 75.5 - - - +
26O ARG* 1.3 63.9 + - - +
28O GLN* 3.1 16.5 + - - +
29O GLN* 2.9 31.1 + - + +
32O ARG* 5.3 0.2 + - - -
82O GLU* 5.4 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486N VAL* 4.2 11.6 - - + +
1488N ASP* 3.7 15.2 + - - +
22O VAL* 2.9 20.6 + - + +
23O VAL* 3.7 4.0 - - - +
25O LYS* 1.3 75.3 - - - +
27O ALA* 1.3 58.6 + - - +
29O GLN* 2.6 41.3 + - - +
30O LEU* 2.9 45.9 + - + +
37O ASN* 3.0 40.8 + - - +
38O THR* 3.9 0.8 - - - +
39O VAL* 4.1 8.7 - - - +
64O ALA* 3.9 15.0 - - + +
67O GLU* 2.6 33.5 + - - +
73O LEU* 3.7 29.7 - - + +
89O MET* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753N SER* 4.4 6.5 - - - -
23O VAL 2.9 18.3 + - - +
24O ALA 3.5 5.2 - - - +
26O ARG* 1.3 76.6 - - - +
28O GLN* 1.3 57.3 + - - +
30O LEU* 3.2 4.5 + - - +
31O LEU* 2.9 33.7 + - - +
60O ALA* 3.4 38.8 - - + +
61O VAL* 3.9 16.2 - - + +
64O ALA* 3.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075M ASP* 3.5 28.5 + - - +
752N SER* 5.7 1.6 - - - -
753N SER* 4.4 11.3 - - - +
754N PHE* 3.7 35.7 - - - +
24O ALA 3.0 18.2 + - - +
25O LYS* 3.1 16.1 + - - +
27O ALA* 1.3 72.7 - - - +
29O GLN* 1.3 60.6 + - - +
31O LEU* 3.4 8.1 + - - +
32O ARG* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486N VAL* 2.6 35.2 + - - +
1487N VAL* 4.8 0.9 - - - -
25O LYS* 2.9 22.9 + - - +
26O ARG* 2.6 46.1 + - - +
28O GLN* 1.3 77.1 - - - +
30O LEU* 1.3 62.1 + - - +
32O ARG* 3.4 18.3 + - - +
33O HIS* 3.1 35.1 + - + +
37O ASN* 3.6 11.2 + - - +
85O LEU* 4.5 13.3 - - - +
89O MET* 4.3 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O ARG* 2.9 48.9 + - - +
27O ALA* 3.5 6.7 - - - +
29O GLN* 1.3 77.0 - - - +
31O LEU* 1.3 61.6 + - - +
34O GLY* 3.1 3.1 + - - -
35O PHE* 2.9 48.4 + - + -
37O ASN* 3.7 15.7 - - - +
38O THR* 4.2 8.3 - - - +
60O ALA* 3.9 10.5 - - + +
63O TRP* 3.6 28.0 - - + -
64O ALA* 4.0 5.4 - - - +
67O GLU* 3.4 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074M GLU 6.3 0.4 - - - -
1075M ASP* 4.2 17.5 - - + +
753N SER* 3.5 24.7 - - - +
27O ALA 2.9 20.7 + - - +
28O GLN* 3.8 5.8 - - - +
30O LEU* 1.3 76.4 - - - +
32O ARG* 1.3 62.2 + - - +
34O GLY* 3.4 11.3 + - - -
35O PHE* 4.4 15.9 - - + -
58O PRO 4.8 6.5 - - - +
60O ALA* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075M ASP* 6.1 3.4 - - - +
28O GLN* 2.9 41.9 + - - +
29O GLN* 3.9 23.3 - - - +
30O LEU 3.3 0.2 - - - -
31O LEU* 1.3 78.3 - - - +
33O HIS* 1.3 81.1 + - + +
34O GLY 3.3 0.6 + - - -
86O GLN* 6.0 6.6 - - - +
90O GLU* 5.8 4.9 - - - -
95O VAL* 4.7 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O GLN* 3.1 14.2 + - - +
32O ARG* 1.3 101.4 + - + +
34O GLY* 1.3 63.9 + - - +
35O PHE 3.3 0.9 - - - -
36O LYS* 3.3 24.6 + - - +
37O ASN* 3.3 41.7 - - + +
86O GLN 5.3 0.4 - - - -
89O MET* 3.3 51.0 - - + +
90O GLU* 4.5 10.8 - - + -
93O TYR* 3.4 26.2 + + + +
94O PRO 5.2 4.1 - - - +
95O VAL* 5.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
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