Contacts of the helix formed by residues 51 - 63 (chain B) in PDB entry 3ZWH
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 ASP 51 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 2.8 50.9 + - - +
50B THR* 1.3 90.1 + - - +
52B GLU* 1.3 65.8 + - - +
53B ALA* 3.6 9.3 - - + +
54B ALA* 3.1 17.5 + - - +
55B PHE* 3.0 20.3 + - - +
1928Q PHE* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 3.8 25.8 + - - -
35B LYS* 4.3 18.3 + - - +
50B THR 3.9 0.4 + - - -
51B ASP* 1.3 70.7 - - - +
53B ALA* 1.3 56.1 + - - +
55B PHE* 3.3 16.3 + - - +
56B GLN* 2.8 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 4.7 4.7 - - - +
51B ASP* 3.3 12.0 + - + +
52B GLU* 1.3 79.1 - - - +
54B ALA* 1.3 62.4 + - - +
56B GLN* 3.5 7.1 + - - +
57B LYS* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 3.7 37.7 - - + +
51B ASP* 3.1 30.4 + - - +
53B ALA* 1.3 75.4 - - - +
55B PHE* 1.3 64.6 + - - +
57B LYS* 3.2 9.8 + - - +
58B LEU 3.2 16.3 + - - -
1926Q LEU* 6.0 1.4 - - - -
1927Q PRO* 5.1 5.0 - - + +
1928Q PHE* 3.8 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 3.2 52.0 - - + -
34B LEU* 4.0 23.1 - - + -
35B LYS* 3.5 39.7 - - + -
38B LEU* 4.1 9.9 - - + -
51B ASP 3.0 9.6 + - - +
52B GLU* 3.3 22.9 + - - +
54B ALA* 1.3 74.2 - - - +
56B GLN* 1.3 62.4 - - - +
58B LEU* 3.2 6.4 + - + +
59B MET* 2.9 27.2 + - + +
1928Q PHE* 3.6 43.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 2.8 46.9 + - - +
52B GLU* 2.8 28.4 + - + +
53B ALA* 3.6 8.7 - - - +
55B PHE* 1.3 74.3 - - - +
57B LYS* 1.3 58.3 + - - +
59B MET* 3.4 6.2 + - - +
60B SER* 2.9 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA 3.1 13.9 + - - +
54B ALA* 3.5 12.1 - - - +
55B PHE 3.2 0.4 - - - -
56B GLN* 1.3 77.9 - - - +
58B LEU* 1.3 59.8 + - - +
60B SER* 3.5 5.1 + - - -
61B ASN* 2.8 42.3 + - - +
1925Q ASP* 2.9 41.7 + - - +
1926Q LEU* 3.9 9.2 - - + -
1927Q PRO* 5.3 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 5.3 0.7 - - + -
38B LEU* 3.6 31.0 - - + -
54B ALA 3.2 11.8 + - - +
55B PHE* 3.2 11.9 + - + +
57B LYS* 1.3 74.1 - - - +
59B MET* 1.3 67.3 + - - +
61B ASN* 3.1 2.8 + - - -
62B LEU* 2.9 52.5 + - + +
78B PHE* 4.4 7.9 - - + -
1917Q LEU* 5.4 0.2 - - + -
1921Q LEU* 5.3 0.2 - - + -
1926Q LEU* 4.0 32.2 - - + +
1928Q PHE* 3.7 15.9 - - + -
1929Q VAL* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU 4.0 7.2 - - - +
31B LYS* 3.8 45.3 - - + +
34B LEU* 3.5 33.4 - - + +
55B PHE* 2.9 18.6 + - + +
56B GLN* 3.6 8.3 - - - +
58B LEU* 1.3 76.0 - - - +
60B SER* 1.3 57.0 + - - +
62B LEU* 3.2 3.5 + - - +
63B ASP* 2.9 34.6 + - + +
68B ASN* 3.4 35.7 - - - +
69B GLU* 3.7 17.0 - - - +
70B VAL* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 2.9 24.0 + - - -
57B LYS* 3.7 7.4 - - - -
59B MET* 1.3 77.5 - - - +
61B ASN* 1.3 65.8 + - - +
63B ASP* 3.3 24.3 + - - +
64B SER* 5.2 0.3 - - - -
66B ARG* 5.0 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 2.8 40.4 + - - +
58B LEU 3.1 4.7 + - - +
60B SER* 1.3 80.7 + - - +
62B LEU* 1.3 65.5 + - - +
63B ASP* 4.6 0.4 - - - -
64B SER* 4.1 10.4 + - - -
1917Q LEU* 4.7 7.4 - - + +
1920Q LYS* 2.8 44.0 + - + +
1926Q LEU* 3.7 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.1 25.4 - - + -
38B LEU* 5.6 0.2 - - + -
58B LEU* 2.9 42.0 + - + +
59B MET 3.7 3.4 - - - +
61B ASN* 1.3 76.3 - - - +
63B ASP* 1.3 58.6 + - - +
64B SER* 2.9 12.2 + - - -
70B VAL* 4.1 17.0 - - + -
74B GLU* 3.4 27.1 - - - +
75B TYR* 6.3 0.2 - - - -
78B PHE* 3.7 36.6 - - + -
1917Q LEU* 3.6 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B MET* 2.9 22.6 + - + +
60B SER* 3.3 17.7 + - - +
61B ASN 3.4 0.8 - - - -
62B LEU* 1.3 72.0 - - - +
64B SER* 1.3 60.3 + - - +
66B ARG* 2.9 28.4 + - - +
67B ASP 3.1 4.2 + - - -
68B ASN* 2.7 34.0 + - - +
69B GLU 3.6 14.8 - - - +
70B VAL* 4.6 1.1 - - + +
74B GLU* 3.7 5.8 - - - -
502B CA 2.7 22.1 - - - -
----------------------------------------------------------
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