Contacts of the helix formed by residues 28 - 40 (chain B) in PDB entry 4PCW
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 28 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP* 4.3 13.3 + - - +
26B THR* 4.0 1.0 + - - -
27B LEU* 1.3 75.0 - - - +
29B LYS* 1.3 76.3 + - - +
30B LYS* 3.5 9.8 + - - +
31B GLU* 2.9 40.3 + - - +
32B LEU* 2.8 27.9 + - - +
57B MET* 5.3 1.6 - - - -
66B LYS 4.9 1.1 - - - -
67B LYS* 5.3 4.5 - - - +
101B CA 4.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 1.3 89.3 - - - +
30B LYS* 1.3 57.6 + - - +
32B LEU* 4.4 3.8 - - - -
33B LYS* 3.0 29.1 + - - +
53B VAL* 3.4 18.9 - - + +
57B MET* 4.4 20.2 - - + -
66B LYS* 3.0 40.1 + - + -
67B LYS* 5.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 5.5 8.1 + - - +
21B ASP* 5.8 5.5 - - - +
28B SER* 3.3 9.2 + - - +
29B LYS* 1.3 76.9 - - - +
31B GLU* 1.3 72.5 + - + +
33B LYS* 3.2 9.9 + - + +
34B GLU* 3.2 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 2.9 30.9 - - - +
20B LYS* 3.1 19.9 + - + +
21B ASP* 2.9 37.7 + - + +
26B THR 3.3 4.2 - - - +
27B LEU* 3.4 6.8 - - + -
28B SER* 2.9 34.1 + - - +
30B LYS* 1.3 84.8 - - + +
32B LEU* 1.3 63.3 + - - +
34B GLU* 3.4 10.2 + - - +
35B LEU* 3.2 20.6 + - - +
101B CA 2.3 24.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
27B LEU* 4.4 24.6 - - + +
28B SER 2.8 19.7 + - - +
29B LYS 3.8 2.9 - - - +
31B GLU* 1.3 75.3 - - - +
33B LYS* 1.3 65.3 + - - +
35B LEU* 3.1 10.5 + - + +
36B LEU* 3.0 44.9 + - + +
53B VAL* 3.9 20.0 - - + +
56B PHE* 4.7 6.7 - - + -
57B MET* 3.9 28.9 - - - +
60B LEU* 4.9 11.2 - - + -
68B ILE* 3.9 14.6 - - + -
73B PHE* 6.0 2.9 - - + -
76B MET* 5.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS 3.0 19.2 + - - +
30B LYS* 3.2 8.5 + - + +
32B LEU* 1.3 77.6 - - - +
34B GLU* 1.3 60.1 + - + +
36B LEU* 3.5 5.0 + - - +
37B GLU* 3.0 44.1 + - + +
53B VAL* 3.8 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 3.6 13.7 - - + -
20B LYS* 2.7 39.8 + - - +
30B LYS* 3.2 12.9 + - + +
31B GLU* 3.8 9.5 - - - +
32B LEU 3.2 0.2 - - - -
33B LYS* 1.3 78.3 - - + +
35B LEU* 1.3 65.2 + - - +
37B GLU* 3.4 10.4 + - - +
38B LYS* 3.0 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 5.1 0.9 - - + -
13B LEU* 3.9 23.3 - - + +
14B PHE* 4.8 1.6 - - - -
17B TYR* 3.9 34.2 - - + -
27B LEU* 4.1 20.0 - - + -
31B GLU 3.2 10.4 + - - +
32B LEU* 3.1 13.1 + - + +
34B GLU* 1.3 79.0 - - - +
36B LEU* 1.3 72.0 + - + +
38B LYS 3.3 0.5 + - - -
39B GLU* 2.8 54.4 + - + +
40B PHE* 4.7 5.4 - - + -
73B PHE* 4.1 22.4 - - + -
76B MET* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.0 41.4 + - + +
33B LYS* 3.9 4.7 - - - +
35B LEU* 1.3 81.2 - - + +
37B GLU* 1.3 57.6 + - - +
40B PHE* 2.8 64.7 + - + +
52B MET* 3.9 36.8 - - + +
53B VAL* 4.2 4.7 - - + -
56B PHE* 3.9 32.8 - - + -
76B MET* 4.1 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 3.0 37.9 + - + +
34B GLU* 3.7 9.4 - - - +
35B LEU 3.2 0.4 - - - -
36B LEU* 1.3 79.4 - - - +
38B LYS* 1.3 80.5 + - + +
40B PHE 3.6 5.8 - - - +
41B ARG* 3.5 26.6 + - - +
42B GLN 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 6.0 1.9 - - - +
17B TYR* 3.4 25.4 - - + +
34B GLU* 3.0 38.6 + - + +
35B LEU 3.9 1.1 - - - +
37B GLU* 1.3 98.4 + - + +
39B GLU* 1.3 67.5 + - - +
41B ARG* 3.1 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER 5.1 1.6 - - - +
2A THR* 3.6 16.1 - - - +
3A LEU* 2.8 36.0 + - + -
4A LEU* 3.6 17.5 - - - +
13B LEU* 3.3 25.9 - - + +
16B GLN* 5.6 0.7 - - - +
17B TYR* 4.4 13.4 + - + -
35B LEU* 2.8 40.9 + - + +
38B LYS* 1.3 77.4 - - + +
40B PHE* 1.3 81.4 + - + +
41B ARG* 3.9 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.7 19.7 - - + -
4A LEU* 4.3 22.4 - - + -
35B LEU* 4.7 1.8 - - + -
36B LEU* 2.8 58.6 + - + +
37B GLU* 3.6 4.6 - - - +
39B GLU* 1.3 90.4 - - + +
41B ARG* 1.3 62.8 + - - +
42B GLN* 3.6 21.7 + - - +
56B PHE* 5.2 6.7 - + - -
76B MET* 3.8 13.0 - - + -
80B LEU* 3.3 39.5 - - + -
----------------------------------------------------------
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