Contacts of the helix formed by residues 23 - 37 (chain g) in PDB entry 5W97
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 LEU 23 (chain g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 4.8 13.0 - - + -
303c PEK 4.0 22.3 - - + +
5g LYS* 3.9 32.8 - - - +
18g PHE 4.2 0.2 + - - -
19g LEU* 3.1 27.6 + - + +
22g GLY* 1.3 80.3 - - - +
24g ALA* 1.3 60.6 + - - +
25g LEU 3.6 1.6 - - - -
26g PRO* 3.6 4.0 - - - +
27g SER* 2.6 38.9 + - - +
103g CDL 4.6 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139c ALA* 3.7 30.8 - - + +
142c VAL* 4.1 15.9 - - + -
19g LEU 2.9 15.1 + - - +
20g THR* 3.7 14.8 - - + +
23g LEU* 1.3 73.9 - - + +
25g LEU* 1.3 64.2 + - + +
27g SER* 3.1 17.2 + - - -
28g VAL* 3.2 15.6 + - - +
103g CDL 4.4 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139c ALA* 4.8 3.6 - - + -
165c ILE* 4.3 13.7 - - + -
169c LEU* 4.2 34.1 - - + -
303c PEK 4.4 42.6 - - + +
20g THR* 2.9 27.0 + - + +
21g PHE* 3.7 34.3 - - + +
24g ALA* 1.3 71.2 - - + +
26g PRO* 1.4 68.0 - - + +
28g VAL* 3.0 9.7 + - + +
29g ALA* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 26 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B CHD 4.5 11.7 - - + -
303c PEK 4.5 42.8 - - + -
21g PHE 3.1 29.2 - - - +
22g GLY 3.7 15.9 - - - +
23g LEU* 3.6 11.7 - - - +
25g LEU* 1.4 91.2 - - + +
27g SER* 1.3 56.6 + - - +
29g ALA* 3.3 8.1 + - + +
30g LEU* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135c SER* 4.5 4.0 - - - -
23g LEU* 2.6 24.8 + - - +
24g ALA 3.1 8.0 + - - -
26g PRO* 1.3 76.0 - - - +
28g VAL* 1.3 58.2 + - - +
30g LEU* 3.7 6.4 - - - +
31g CYS* 2.8 33.7 + - - +
103g CDL 3.6 60.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132c LEU* 3.7 1.4 - - + +
135c SER* 3.6 24.5 - - - +
136c VAL* 4.1 12.1 - - + -
139c ALA* 3.5 23.3 - - + -
169c LEU* 4.6 9.9 - - + -
172c TYR* 3.9 22.0 - - + -
303c PEK 6.2 3.6 - - + -
24g ALA 3.5 12.1 - - - +
25g LEU* 3.0 14.4 + - + +
27g SER* 1.3 77.0 - - - +
29g ALA* 1.3 50.2 + - - +
32g THR* 2.5 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303c PEK 4.4 21.1 - - + -
25g LEU 2.9 11.7 + - - +
26g PRO* 3.4 12.8 - - + +
28g VAL* 1.3 73.4 - - - +
30g LEU* 1.3 64.1 + - + +
32g THR* 3.3 6.2 + - - -
33g LEU* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 4.7 25.6 - - + -
314A ILE* 6.2 1.1 - - + -
303c PEK 4.0 35.7 - - + -
26g PRO 2.9 20.8 + - - +
27g SER* 3.7 4.9 - - - +
29g ALA* 1.3 78.5 - - + +
31g CYS* 1.3 58.2 + - - +
33g LEU* 3.1 19.0 - - + +
34g ASN* 2.8 28.6 + - - +
103g CDL 4.1 56.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 31 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128c GLU 5.5 0.5 - - - +
131c LEU* 4.2 13.2 - - - -
132c LEU* 3.8 17.2 + - + +
135c SER* 3.6 26.2 - - - +
27g SER 2.8 19.8 + - - +
30g LEU* 1.3 69.3 - - - +
32g THR* 1.3 67.7 + - - +
34g ASN* 3.5 7.9 + - - +
35g SER* 3.2 21.1 + - - -
103g CDL 3.4 46.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132c LEU* 3.4 16.9 - - + +
172c TYR* 3.2 27.3 + - - +
28g VAL* 2.5 35.0 + - - +
29g ALA* 3.5 7.7 - - - -
31g CYS* 1.3 70.7 - - - +
33g LEU* 1.3 56.8 + - - +
35g SER* 2.9 21.9 + - - -
36g TRP* 2.9 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.5 20.0 - - + -
29g ALA 2.8 17.5 + - - +
30g LEU* 3.1 21.5 - - + +
32g THR* 1.3 71.5 - - - +
34g ASN* 1.3 62.8 + - - +
36g TRP* 3.3 20.7 + - + +
37g LEU* 3.2 42.0 + - + +
103g CDL 4.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127c LEU 3.2 23.4 - - - +
128c GLU* 5.1 0.2 - - - -
30g LEU 2.8 15.5 + - - +
31g CYS 3.8 8.5 - - - +
32g THR 3.3 0.2 + - - -
33g LEU* 1.3 73.7 - - - +
35g SER* 1.3 62.0 + - - +
37g LEU* 3.4 10.0 + - - +
38g HIS* 3.2 38.9 + - - +
103g CDL 3.5 69.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128c GLU* 3.7 30.1 + - - +
129c VAL* 4.0 13.0 + - - +
132c LEU* 4.1 14.3 - - - +
31g CYS 3.2 11.9 + - - -
32g THR* 2.9 10.9 + - - -
34g ASN* 1.3 75.4 + - - +
36g TRP* 1.3 64.1 + - - -
37g LEU 3.2 0.9 + - - -
38g HIS* 3.3 19.1 + - - +
39g SER* 3.6 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32g THR* 2.9 17.6 + - + +
33g LEU* 3.3 20.1 + - + +
35g SER* 1.3 75.0 - - - +
37g LEU* 1.3 85.4 + - + +
38g HIS 3.5 2.9 + - - -
39g SER* 5.1 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 5.1 13.7 - - + -
78B LEU* 5.3 12.6 - - + -
33g LEU* 3.2 38.1 + - + +
34g ASN* 3.5 5.6 + - - +
35g SER 3.2 0.6 - - - -
36g TRP* 1.3 106.5 - - + +
38g HIS* 1.3 69.3 + - - +
103g CDL 3.8 56.8 - - + +
----------------------------------------------------------
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