Contacts of the helix formed by residues 20 - 33 (chain B) in PDB entry 2E52
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 PHE 20 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLN 3.4 4.3 + - - -
19B GLU* 1.3 73.7 + - - +
21B LYS* 1.3 58.7 + - - +
23B ALA* 3.1 6.9 + - + +
24B THR* 2.8 51.6 + - + +
58B THR* 4.1 9.4 - - + -
61B LYS* 3.7 30.1 - - + -
62B LEU* 3.5 38.1 - - + -
65B LYS* 3.8 6.7 - - + -
88B ARG* 3.8 23.6 - - - -
11E G 3.4 54.5 - - - +
12E C 3.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.3 3.2 - - + +
20B PHE* 1.3 80.7 - - - +
22B GLN* 1.3 61.0 + - - +
24B THR* 2.8 21.9 + - - +
25B ASN* 3.2 25.4 + - - +
86B GLU* 6.0 6.3 - - - -
12E C 4.4 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 5.9 2.3 - - + +
18B GLN* 3.4 28.0 + - + +
19B GLU* 3.1 21.8 + - + +
21B LYS* 1.3 76.7 - - - +
23B ALA* 1.3 65.1 + - - +
25B ASN* 3.2 13.0 + - + +
26B SER* 3.1 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 3.5 42.2 - - + +
18B GLN* 4.9 2.8 - - + +
19B GLU 2.9 12.7 + - - +
20B PHE* 3.1 11.9 + - - +
22B GLN* 1.3 77.2 - - - +
24B THR* 1.3 57.0 + - - +
26B SER 3.3 1.6 + - - -
27B LEU* 3.0 31.0 + - - +
62B LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 2.8 41.1 + - + +
21B LYS* 2.8 27.0 + - - +
23B ALA* 1.3 74.4 - - - +
25B ASN* 1.3 61.5 + - - +
27B LEU* 3.2 9.5 + - + +
28B ILE* 2.9 35.3 + - - +
62B LEU* 4.3 4.5 - - + -
65B LYS* 3.5 35.9 - - + -
69B ILE* 3.9 2.3 - - - +
12E C 5.3 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.2 25.9 + - - +
22B GLN* 3.2 12.4 + - + +
24B THR* 1.3 76.9 + - - +
26B SER* 1.3 61.3 + - - +
28B ILE* 3.3 19.9 + - - +
29B SER* 3.1 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.0 10.6 - - - +
15B LEU* 3.8 25.2 - - - +
22B GLN* 3.1 16.9 + - - +
23B ALA 3.5 8.1 - - - -
25B ASN* 1.3 72.8 - - - +
27B LEU* 1.3 65.4 + - - +
29B SER* 3.5 7.1 + - - -
30B PHE* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.8 27.1 - - + -
11B LEU* 3.9 16.4 - - + -
12B ILE* 4.2 7.9 - - + -
15B LEU* 4.0 10.8 - - + -
23B ALA 3.0 16.5 + - - +
24B THR* 3.5 11.7 - - - +
26B SER* 1.3 76.6 - - - +
28B ILE* 1.3 56.9 + - - +
30B PHE* 3.3 3.6 + - + +
31B ILE* 2.9 37.4 + - + +
62B LEU* 3.4 46.0 - - + +
65B LYS* 4.7 3.1 - - + -
66B ALA* 4.1 12.8 - - + +
69B ILE* 3.7 13.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
24B THR* 2.9 21.4 + - - +
25B ASN* 3.6 22.7 - - - +
26B SER 3.3 0.2 - - - -
27B LEU* 1.3 71.2 - - - +
29B SER* 1.3 69.1 + - - +
32B TYR* 2.9 55.4 + - + +
69B ILE* 3.7 28.2 - - + +
84B PRO* 4.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN 3.1 14.2 + - - -
26B SER* 3.7 7.6 - - - -
28B ILE* 1.3 81.9 - - - +
30B PHE* 1.3 63.1 + - - +
32B TYR* 4.2 1.9 - - - +
33B LYS* 3.2 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA 3.9 5.8 - - - -
7B LYS* 3.7 29.2 - - + -
8B LEU* 3.6 45.1 - - + -
11B LEU* 3.4 33.0 - - + -
26B SER 3.0 10.9 + - - +
27B LEU 3.6 2.9 - - - +
29B SER* 1.3 77.7 - - - +
31B ILE* 1.3 77.2 + - + +
33B LYS* 3.7 4.6 + - - +
34B LEU* 3.5 47.7 + - + +
42B LEU* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 5.0 1.6 - - + -
27B LEU* 2.9 23.1 + - + +
30B PHE* 1.3 86.7 - - + +
32B TYR* 1.3 62.9 + - - +
34B LEU* 3.3 27.8 + - + +
39B VAL* 4.3 9.8 - - + +
42B LEU* 4.1 11.2 - - + -
66B ALA* 3.7 35.0 - - + +
69B ILE* 3.6 32.3 - - + -
70B VAL* 3.9 26.5 - - + -
73B LYS* 4.2 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 2.9 35.4 + - + +
29B SER* 4.3 2.9 - - - +
31B ILE* 1.3 78.6 - - - +
33B LYS* 1.3 61.5 + - + +
34B LEU 4.2 1.0 - - - +
69B ILE* 3.6 32.5 - - + -
72B ALA* 3.6 16.5 - - - +
73B LYS* 3.6 37.4 + - + +
76B GLN* 2.9 39.7 + - - -
82B SER 4.3 1.4 + - - -
83B LYS* 4.6 0.3 - - - -
84B PRO* 4.1 10.1 - - + +
----------------------------------------------------------
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 SER* 3.2 42.2 + - - +
30B PHE* 4.1 4.9 - - - +
31B ILE 3.2 0.8 - - - -
32B TYR* 1.3 79.4 - - + +
34B LEU* 1.3 65.9 + - - +
35B ASN* 3.5 1.4 + - - -
----------------------------------------------------------
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