Contacts of the helix formed by residues 23 - 34 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 1.3 86.0 - - - +
24B GLU* 1.3 75.3 + - - +
25B LEU* 3.0 15.9 + - - +
26B GLU* 2.6 32.1 + - - +
27B ALA* 3.3 7.8 + - - +
102B ARG 3.8 5.2 - - - -
103B ALA* 3.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 6.1 1.3 - - + -
23B THR* 1.3 81.5 - - - +
25B LEU* 1.3 52.8 + - - +
27B ALA* 3.1 6.4 + - - +
28B ILE* 2.7 42.2 + - + +
49B GLU* 3.9 22.7 - - + -
54B PHE* 3.6 24.2 - - + -
102B ARG* 2.9 50.1 + - - +
103B ALA* 3.9 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 4.7 7.4 - - + -
190A LEU* 3.4 52.3 - - + +
194A TRP* 3.7 24.9 - - + -
23B THR* 3.0 13.0 + - - +
24B GLU* 1.3 80.8 - - - +
26B GLU* 1.3 80.5 + - - +
27B ALA 2.9 0.5 + - - -
28B ILE* 2.9 3.8 + - - +
29B MET* 2.8 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 4.3 13.5 - - - +
21B ALA 5.2 1.3 - - - +
22B TYR* 3.9 21.8 - - + -
23B THR* 2.6 46.2 + - - +
25B LEU* 1.3 94.3 - - - +
27B ALA* 1.3 62.3 + - - +
29B MET* 3.5 19.0 + - + +
30B TYR* 3.1 22.0 + - - +
60B PHE* 3.8 8.3 - - + -
191B SER* 4.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 5.0 5.2 - - + -
23B THR 3.3 9.0 + - - +
24B GLU* 3.1 14.3 + - - +
25B LEU 3.0 0.6 - - - -
26B GLU* 1.3 77.3 - - - +
28B ILE* 1.3 65.6 + - - +
30B TYR* 3.0 7.8 + - - +
31B ALA* 3.0 21.6 + - - +
46B PHE 5.0 0.7 - - - -
54B PHE* 4.4 11.2 - - + -
56B CYS* 4.1 27.1 - - + -
57B LEU 5.8 1.3 + - - +
60B PHE* 4.3 11.2 - - - -
102B ARG 5.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA 4.9 1.1 - - - +
189A ARG* 4.6 0.7 - - - +
190A LEU* 4.0 16.6 - - + -
194A TRP* 4.4 11.9 - - + -
24B GLU 2.7 28.4 + - - +
25B LEU 3.6 3.1 - - - +
27B ALA* 1.3 71.8 - - - +
29B MET* 1.3 57.0 + - - +
31B ALA* 3.1 2.1 + - - +
32B LEU* 2.9 36.1 + - + +
46B PHE 3.8 9.4 - - - +
47B ILE* 3.2 44.4 - - + +
49B GLU* 3.5 31.2 - - + +
54B PHE* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.8 5.8 - - + -
29A MET* 3.4 31.2 - - + +
190A LEU* 3.8 20.8 - - + +
25B LEU* 2.8 29.7 + - + +
26B GLU* 3.6 29.2 - - + +
28B ILE* 1.3 77.5 - - - +
30B TYR* 1.3 63.1 + - - +
32B LEU* 3.5 3.9 + - - +
33B GLY* 3.0 19.8 + - - -
187B LEU* 4.8 15.6 - - + +
188B TYR* 5.9 0.2 - - - -
190B LEU* 4.0 35.0 - - + +
191B SER* 4.3 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU 3.1 13.2 + - - +
27B ALA 3.0 10.8 + - - +
29B MET* 1.3 76.8 - - - +
31B ALA* 1.3 68.6 + - - +
33B GLY* 3.1 3.4 + - - -
34B VAL* 2.8 42.5 + - + +
57B LEU* 4.4 11.7 - - + -
59B THR* 2.8 42.4 + - - -
60B PHE* 3.7 31.9 - + + -
62B VAL* 5.3 1.8 - - + +
63B ILE* 3.2 30.1 - - + -
188B TYR* 3.4 33.6 + + - -
191B SER* 3.7 9.8 + - - +
217B LEU 4.3 4.9 + - - -
220B PHE* 5.1 0.9 - - - -
221B GLY* 3.7 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA 3.0 10.3 + - - +
28B ILE 3.1 8.0 + - - +
30B TYR* 1.3 76.2 - - - +
32B LEU* 1.3 63.3 + - - +
34B VAL* 3.1 9.5 + - - +
35B GLY 3.2 0.5 + - - -
36B ALA* 3.1 28.5 + - + -
46B PHE* 3.6 29.8 - - + +
47B ILE* 5.1 1.3 - - + -
57B LEU* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 4.3 15.9 - - + +
186A ALA* 3.7 27.1 - - + +
187A LEU* 3.9 25.6 - - + +
190A LEU* 4.3 8.3 - - + -
28B ILE* 2.9 25.2 + - + +
29B MET* 3.9 3.8 - - - +
31B ALA* 1.3 75.3 - - - +
33B GLY* 1.3 60.8 + - - +
34B VAL 2.9 5.7 + - - -
35B GLY* 3.0 13.9 + - - -
36B ALA 3.7 19.8 - - - +
47B ILE* 4.1 22.9 - - + -
184B GLN* 3.8 5.9 + - - -
187B LEU* 3.9 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET 3.0 13.3 + - - -
30B TYR 3.5 4.5 - - - -
32B LEU* 1.3 76.3 - - - +
34B VAL* 1.3 56.0 + - - +
184B GLN* 3.0 18.1 + - - -
187B LEU* 3.6 24.1 - - - +
188B TYR* 3.7 18.8 - - - +
218B CYS* 3.2 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 2.8 34.4 + - + +
31B ALA 3.1 11.0 + - - +
32B LEU 2.9 0.4 - - - -
33B GLY* 1.3 78.2 - - - +
35B GLY* 1.3 49.0 + - - +
57B LEU* 3.7 25.8 - - + -
188B TYR* 4.4 5.4 - - + -
218B CYS 3.5 12.3 - - - +
221B GLY* 3.1 37.2 - - - +
222B PHE* 3.1 20.4 - - - -
225B ARG* 2.4 33.4 + - - +
----------------------------------------------------------
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