Contacts of the helix formed by residues 23 - 34 (chain K) in PDB entry 1S9C
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 THR 23 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K TYR* 1.3 85.2 - - - +
24K GLU* 1.3 73.0 + - - +
25K LEU* 3.0 16.8 + - - +
26K GLU* 2.7 32.0 + - - +
27K ALA* 3.3 7.8 + - - +
102K ARG 4.0 5.4 - - - -
103K ALA* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K THR* 1.3 81.1 - - - +
25K LEU* 1.3 57.9 + - - +
27K ALA* 3.1 6.8 + - - +
28K ILE* 2.8 36.5 + - + +
49K GLU* 3.8 28.9 - - + -
54K PHE* 3.6 19.5 - - + -
102K ARG* 3.2 46.0 + - - +
103K ALA* 4.0 7.1 - - - +
194L TRP* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K THR* 3.0 13.4 + - - +
24K GLU* 1.3 79.4 - - - +
26K GLU* 1.3 79.6 + - - +
28K ILE* 3.1 4.4 + - - +
29K MET* 2.8 38.3 + - + +
29L MET* 4.9 6.1 - - + -
190L LEU* 3.4 50.5 - - + +
194L TRP* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K TYR* 4.3 14.4 - - - +
21K ALA 5.1 1.3 - - - +
22K TYR* 3.6 24.4 - - + -
23K THR* 2.7 44.9 + - - +
25K LEU* 1.3 93.5 - - - +
27K ALA* 1.3 61.8 + - - +
29K MET* 3.6 18.1 + - + +
30K TYR* 3.1 22.0 + - - +
60K PHE* 3.8 6.7 - - + -
191K SER* 4.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K TYR* 5.0 4.9 - - + -
23K THR 3.3 9.0 + - - +
24K GLU* 3.3 12.8 - - - +
25K LEU 3.0 0.2 - - - -
26K GLU* 1.3 76.8 - - - +
28K ILE* 1.3 66.3 + - - +
30K TYR* 3.0 8.2 + - - +
31K ALA* 2.9 21.5 + - - +
46K PHE 5.0 0.9 - - - -
54K PHE* 4.4 12.3 - - + -
56K CYS* 4.1 28.5 - - + -
57K LEU 5.9 1.4 + - - -
60K PHE* 4.2 11.8 - - - -
102K ARG 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLU* 2.8 28.0 + - + +
25K LEU 3.6 3.1 - - - +
27K ALA* 1.3 71.8 - - - +
29K MET* 1.3 62.8 + - - +
31K ALA* 3.1 2.6 + - - +
32K LEU* 2.9 29.7 + - + +
46K PHE 3.8 9.0 - - - +
47K ILE* 3.2 45.8 - - + +
49K GLU* 3.5 28.9 - - + +
54K PHE* 3.7 18.4 - - + -
186L ALA 4.9 1.3 - - - +
189L ARG* 4.5 0.7 - - - +
190L LEU* 4.0 16.2 - - + -
194L TRP* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K LEU* 2.8 37.9 + - + +
26K GLU* 3.6 21.3 - - + +
28K ILE* 1.3 77.2 - - - +
30K TYR* 1.3 60.8 + - - +
32K LEU* 3.8 4.2 - - - +
33K GLY* 3.0 20.4 + - - -
187K LEU* 4.8 18.4 - - + +
188K TYR* 5.9 0.3 - - - -
190K LEU* 4.2 29.4 - - + +
191K SER* 4.4 7.5 + - - +
25L LEU* 4.9 5.6 - - + -
29L MET* 3.3 33.9 - - + +
190L LEU* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K GLU 3.1 13.5 + - - +
27K ALA 3.0 10.4 + - - +
29K MET* 1.3 77.6 - - - +
31K ALA* 1.3 69.4 + - - +
33K GLY* 3.1 3.7 + - - -
34K VAL* 2.8 49.9 + - + +
57K LEU* 4.3 12.1 - - + -
59K THR* 2.8 42.1 + - - -
60K PHE* 3.7 30.7 - + + -
62K VAL* 5.3 2.0 - - + +
63K ILE* 3.1 30.3 - - + -
188K TYR* 3.4 30.8 + + - -
191K SER* 3.7 10.9 + - - +
217K LEU 4.3 5.0 + - - -
220K PHE* 5.1 1.0 - - - -
221K GLY* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K ALA 2.9 10.9 + - - +
28K ILE 3.1 7.6 + - - +
30K TYR* 1.3 77.3 - - + +
32K LEU* 1.3 63.4 + - - +
34K VAL* 3.1 11.8 + - - +
35K GLY 3.2 0.9 + - - -
36K ALA* 3.1 32.1 + - + -
46K PHE* 3.6 25.4 - - + +
47K ILE* 5.1 1.8 - - + -
57K LEU* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K ILE* 2.9 23.1 + - + +
29K MET* 3.8 3.8 - - - +
31K ALA* 1.3 75.1 - - - +
33K GLY* 1.3 60.4 + - - +
34K VAL 3.0 5.4 + - - -
35K GLY* 3.0 13.9 + - - -
36K ALA 3.6 19.1 - - - +
47K ILE* 4.1 22.4 - - + -
184K GLN* 3.8 6.1 + - - -
187K LEU* 3.9 14.7 - - + +
183L ASN* 4.2 15.7 - - + +
186L ALA* 3.6 28.0 - - + +
187L LEU* 3.9 26.2 - - + -
190L LEU* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K MET 3.0 14.2 + - - -
30K TYR* 3.5 4.3 - - - -
32K LEU* 1.3 74.9 - - - +
34K VAL* 1.3 57.6 + - - +
184K GLN* 3.0 18.6 + - - -
187K LEU* 3.6 24.0 - - - +
188K TYR* 3.7 19.8 - - - +
218K CYS* 3.2 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 2.8 33.8 + - + +
31K ALA 3.1 11.4 + - - +
32K LEU 3.0 0.6 - - - -
33K GLY* 1.3 78.2 - - - +
35K GLY* 1.3 48.7 + - - +
57K LEU* 3.7 25.1 - - + -
59K THR* 5.6 0.4 - - - +
188K TYR* 4.2 11.0 - - + -
218K CYS 3.6 8.5 - - - +
221K GLY* 3.2 36.8 - - - +
222K PHE* 3.1 20.5 - - - -
225K ARG* 2.4 31.6 + - - +
----------------------------------------------------------
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