Contacts of the helix formed by residues 21 - 32 (chain I) in PDB entry 3SWD
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 ALA 21 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLY* 1.3 68.6 - - - -
22I LYS* 1.3 66.4 + - - +
23I ASN 4.4 1.8 - - - +
24I ALA* 3.6 20.9 - - + +
25I ALA* 2.9 24.9 + - - +
45I PRO* 4.5 0.7 - - - -
190I GLU* 4.6 9.9 - - + +
228I VAL* 3.6 2.8 - - - +
229I LEU* 2.7 28.9 + - + +
230I PRO 3.9 9.4 - - - +
231I ASP* 3.6 14.7 - - - +
232I ARG 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLY 3.2 3.6 + - - -
21I ALA* 1.3 70.8 - - - +
23I ASN* 1.3 84.0 + - - +
25I ALA* 3.4 1.5 + - - +
26I LEU* 3.1 40.2 + - + +
45I PRO* 4.1 9.4 - - + -
47I LEU* 4.1 26.2 - - + -
49I ASP* 3.1 27.1 + - - -
231I ASP* 3.1 10.0 + - - +
370I LEU* 3.5 17.5 - - - -
371I ARG* 3.8 20.4 - - - +
397I ARG 3.8 5.8 - - - +
398I GLY* 3.7 20.6 - - - -
501I EPZ 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 23 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ALA* 3.2 2.2 - - - +
22I LYS* 1.3 106.1 + - - +
24I ALA* 1.3 56.4 + - - +
26I LEU* 4.7 2.5 - - - +
27I PRO* 3.1 22.8 - - - +
95I TRP* 5.0 0.2 - - - -
190I GLU* 3.3 27.9 - - + +
231I ASP* 4.8 0.2 + - - -
233I ILE* 6.0 0.8 - - - +
305I ASP* 4.1 7.1 + - - -
371I ARG* 4.4 11.2 - - - +
501I EPZ 3.2 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ALA* 3.0 18.9 + - + +
23I ASN* 1.3 75.7 - - - +
25I ALA* 1.3 71.2 + - - +
26I LEU 3.2 1.1 - - - -
27I PRO* 3.0 12.2 - - - +
28I ILE* 3.2 23.9 + - + +
190I GLU* 3.8 13.6 - - + +
193I ASP* 4.1 11.2 - - + +
228I VAL* 3.6 17.3 - - + -
229I LEU* 3.7 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ALA 2.9 16.3 + - - +
22I LYS* 3.7 5.2 - - - +
24I ALA* 1.3 78.9 - - - +
26I LEU* 1.3 56.4 + - - +
28I ILE* 3.3 1.8 + - - +
29I LEU* 2.9 39.4 + - + +
44I VAL* 4.2 30.7 - - + -
45I PRO* 4.3 7.9 - - + -
50I VAL* 4.5 10.1 - - + -
228I VAL* 4.1 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LYS* 3.1 26.4 + - + +
23I ASN* 5.0 2.0 - - - +
25I ALA* 1.3 79.2 - - - +
27I PRO* 1.3 66.7 - - + +
29I LEU* 3.4 5.1 + - + +
30I PHE* 3.0 33.2 + - + -
49I ASP* 4.0 31.2 - - + +
50I VAL* 4.2 15.3 - - + +
53I SER* 3.5 20.6 - - - +
90I MET* 3.8 26.0 - - + -
92I ALA* 4.1 16.6 - - + -
95I TRP* 4.1 10.1 - - + -
501I EPZ 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ASN 3.1 26.5 - - - +
24I ALA 3.0 17.5 - - - +
26I LEU* 1.3 85.1 - - + +
28I ILE* 1.3 59.4 + - - +
30I PHE* 3.2 4.5 + - + +
31I ALA* 2.9 29.0 + - - +
95I TRP* 3.5 30.5 - - + -
163I VAL* 6.5 0.4 - - + -
167I VAL* 4.1 23.6 - - + +
171I CYS* 5.3 1.7 - - - -
190I GLU* 5.3 2.0 - - + +
194I THR* 3.4 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ALA* 3.2 22.2 + - + +
25I ALA* 3.6 3.6 - - - +
27I PRO* 1.3 76.5 - - - +
29I LEU* 1.3 63.2 + - - +
31I ALA* 2.9 18.7 + - - +
32I ALA* 3.0 11.3 + - - +
41I ILE* 3.5 33.4 - - + -
193I ASP* 4.1 22.4 - - - +
194I THR* 4.1 14.6 - - - +
197I PHE* 3.8 35.6 - - + -
226I TYR* 4.2 9.6 - - + -
228I VAL* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ALA* 2.9 35.0 + - + +
26I LEU* 3.9 5.2 - - + +
27I PRO 3.4 0.4 - - - -
28I ILE* 1.3 76.1 - - + +
30I PHE* 1.3 61.1 + - + +
32I ALA* 3.3 16.5 - - - +
33I LEU 4.3 0.3 + - - -
41I ILE* 4.5 24.7 - - + -
44I VAL* 5.0 4.5 - - + -
50I VAL* 4.1 25.8 - - + +
53I SER* 3.9 27.4 - - - +
54I MET* 4.6 9.2 - - + -
57I LEU* 3.6 25.3 - - + +
70I VAL* 4.8 8.1 - - + -
72I ILE* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 3.0 29.0 + - + -
27I PRO 3.2 5.7 + - - +
28I ILE 3.1 1.0 - - - -
29I LEU* 1.3 73.8 - - - +
31I ALA* 1.3 65.0 + - - +
32I ALA 3.1 2.5 - - - -
33I LEU* 3.3 17.9 + - + +
53I SER* 3.8 29.4 - - - -
56I LEU* 3.5 34.3 - - + -
57I LEU* 4.3 17.9 - - + -
90I MET* 4.2 10.8 - - + -
92I ALA* 4.2 10.3 - - + -
93I SER* 4.1 14.6 - - - -
95I TRP* 3.8 34.3 - + + +
96I ALA* 4.0 17.5 - - + -
99I PRO* 3.4 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PRO 2.9 16.8 + - - +
28I ILE* 2.9 6.4 + - - +
30I PHE* 1.3 72.0 - - - +
32I ALA* 1.3 65.7 + - - +
33I LEU 3.0 2.7 - - - -
34I LEU* 2.9 26.5 + - - +
35I ALA 4.1 0.9 + - - -
99I PRO* 4.4 8.5 - - - -
171I CYS* 4.1 14.6 - - - -
194I THR* 4.6 2.7 - - + -
197I PHE* 3.9 13.4 - - + -
198I LEU* 3.9 25.9 - - + +
201I LEU* 5.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ILE 3.0 9.0 + - - +
29I LEU 3.3 15.3 - - - +
30I PHE 3.1 0.4 - - - -
31I ALA* 1.3 72.8 - - - +
33I LEU* 1.3 56.7 + - + +
34I LEU 2.8 12.0 + - - -
35I ALA* 2.8 21.9 + - - +
39I VAL* 4.2 11.7 - - + -
41I ILE* 5.4 0.2 - - + -
57I LEU* 5.5 0.4 - - + -
72I ILE* 3.7 34.5 - - + -
74I ALA* 3.6 9.5 - - - +
197I PHE* 4.1 11.2 - - + -
----------------------------------------------------------
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