Contacts of the helix formed by residues 57 - 71 (chain H) in PDB entry 1ZWS
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 57 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G ASP* 3.9 4.7 - - - +
221G THR* 4.0 3.6 - - - +
47H ARG* 3.0 37.1 - - - +
55H GLY 4.2 0.4 + - - -
56H VAL* 1.3 72.0 - - - +
58H ARG* 1.3 63.8 + - - +
59H GLU* 2.9 18.5 + - - +
60H GLU* 3.0 33.1 + - - +
61H ILE* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H PRO* 6.3 0.8 - - - +
4H PHE* 3.4 25.1 - - - -
46H LYS* 5.9 6.0 - - - +
56H VAL 3.6 1.2 + - - -
57H SER* 1.3 72.4 + - - +
59H GLU* 1.3 63.5 + - - +
61H ILE* 3.0 14.1 - - - +
62H GLU* 2.9 90.1 + - - +
84H GLU* 3.4 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G ASP* 5.9 1.7 - - - +
221G THR* 4.3 14.1 + - + +
223G GLN* 3.9 5.7 + - - +
224G GLU* 5.7 0.7 - - - +
57H SER* 2.9 9.2 + - - +
58H ARG* 1.3 74.0 - - - +
60H GLU* 1.3 60.9 + - - +
61H ILE 2.7 2.5 + - - -
62H GLU* 3.0 9.1 + - - -
63H ARG* 2.6 73.8 + - + +
166H HIS* 4.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G ASP 3.8 2.9 - - - +
221G THR* 3.4 22.5 - - + +
222G LYS 4.8 1.6 + - - -
47H ARG* 4.1 1.9 + - - -
55H GLY 5.2 0.2 - - - +
56H VAL* 3.2 21.2 - - + +
57H SER* 3.0 37.7 + - - +
59H GLU* 1.3 80.0 - - - +
61H ILE* 1.3 63.9 + - - +
63H ARG* 3.0 33.6 + - - +
64H GLU* 3.2 20.6 + - - +
163H GLY 5.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H PHE* 4.4 14.8 - - + -
44H ILE* 3.2 43.5 - - + +
46H LYS* 5.3 2.0 - - - -
56H VAL* 3.7 16.4 - - + +
57H SER 2.8 24.4 + - - +
58H ARG* 3.0 18.4 - - - +
59H GLU 2.7 1.0 + - - -
60H GLU* 1.3 73.3 - - - +
62H GLU* 1.3 61.3 + - + +
64H GLU* 2.6 31.5 + - - +
65H VAL* 3.0 22.6 + - + +
89H VAL* 4.2 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H PHE* 4.5 7.0 - - + -
58H ARG* 2.9 60.6 + - - +
59H GLU* 3.8 5.7 + - - +
61H ILE* 1.3 79.5 - - - +
63H ARG* 1.3 56.6 + - - +
64H GLU 3.1 0.3 + - - -
65H VAL* 3.1 8.0 + - - -
66H SER* 2.6 39.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G THR* 4.6 3.6 - - - +
223G GLN* 2.6 33.9 - - - +
59H GLU* 2.6 44.0 + - + +
60H GLU* 3.0 40.8 + - - +
62H GLU* 1.3 72.6 - - - +
64H GLU* 1.3 50.9 + - - +
66H SER* 4.1 4.2 - - - -
67H ILE* 2.6 41.6 + - + +
163H GLY 5.5 2.6 + - - -
165H ALA 4.2 14.5 + - - +
166H HIS* 3.2 40.1 + - + -
167H GLU* 5.1 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H LYS* 2.7 31.4 + - - +
44H ILE* 3.9 16.3 - - + +
60H GLU 3.2 12.9 + - - +
61H ILE* 2.6 17.8 + - - +
63H ARG* 1.3 70.3 - - - +
65H VAL* 1.3 61.7 + - + +
67H ILE* 3.1 6.7 + - - +
68H LEU* 2.9 39.7 + - + +
91H LEU* 4.1 10.8 - - + +
93H LEU* 5.7 0.5 - - - +
162H PHE* 2.9 41.7 + - + +
163H GLY* 3.4 13.4 - - - +
165H ALA 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H PHE* 3.9 26.0 - - + -
44H ILE* 6.0 0.9 - - + -
61H ILE* 3.0 20.8 + - + +
62H GLU* 3.6 6.7 - - - +
64H GLU* 1.3 73.8 - - + +
66H SER* 1.3 68.2 + - - +
67H ILE 3.1 0.3 + - - -
68H LEU* 3.2 7.8 + - - +
69H ARG* 2.9 58.5 + - + +
79H LEU* 4.4 2.9 - - + -
82H VAL* 4.3 9.9 - - + -
91H LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H GLU* 2.6 24.6 + - - -
63H ARG* 4.1 5.6 - - - -
65H VAL* 1.3 76.4 - - - +
67H ILE* 1.3 66.8 + - - +
69H ARG* 3.3 11.1 + - - +
70H GLN* 3.3 33.6 + - - +
167H GLU* 5.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ARG* 2.6 26.2 - - + +
64H GLU* 3.1 9.6 + - - +
65H VAL 3.1 0.2 - - - -
66H SER* 1.3 78.3 - - - +
68H LEU* 1.3 70.4 + - - +
70H GLN* 2.7 27.1 + - - +
71H VAL* 3.2 11.5 + - + +
135H ILE* 4.0 32.8 - - + -
162H PHE* 3.8 28.7 - - + -
165H ALA* 4.2 11.4 - - + +
166H HIS* 4.2 4.7 - - - +
167H GLU* 3.9 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H GLU* 2.9 41.1 + - + +
65H VAL* 3.7 4.7 - - - +
67H ILE* 1.3 73.6 - - - +
69H ARG* 1.3 59.4 + - - +
71H VAL* 2.8 32.3 - - + +
77H ILE* 4.3 13.9 - - + +
78H THR* 5.6 0.2 - - - -
79H LEU* 4.1 27.2 + - + +
91H LEU* 4.5 9.2 - - + -
93H LEU* 4.0 30.5 - - + -
162H PHE* 3.4 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H GLU* 3.2 43.7 + - - +
3H PRO 3.9 8.3 + - - -
4H PHE* 4.0 15.5 - - - -
65H VAL* 2.9 35.1 + - - +
66H SER* 3.5 13.2 - - - +
67H ILE 2.8 4.0 + - - -
68H LEU* 1.3 75.8 - - - +
70H GLN* 1.3 60.8 + - + +
71H VAL 3.4 5.5 + - - +
72H LEU* 5.3 1.7 - - - +
79H LEU* 3.8 18.4 - - + +
82H VAL* 4.3 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H SER* 3.5 26.6 + - - +
67H ILE* 2.7 18.9 + - - +
69H ARG* 1.3 73.6 - - + +
71H VAL* 1.3 59.5 + - - +
72H LEU* 3.6 1.7 + - - +
129H TYR* 3.4 14.6 + - - -
133H LYS* 3.6 41.5 + - + +
135H ILE* 4.3 17.5 - - + +
167H GLU* 3.4 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H ILE* 4.1 6.1 - - + +
68H LEU* 2.8 52.3 - - + +
69H ARG 3.6 3.8 - - - +
70H GLN* 1.3 79.6 - - - +
72H LEU* 1.3 65.4 + - - +
73H HIS 4.1 0.2 - - - -
76H VAL* 4.3 22.4 - - + -
77H ILE 4.6 4.0 - - - +
78H THR* 5.0 4.9 - - - +
129H TYR* 3.5 13.5 - - + -
130H LEU* 3.3 32.8 - - + -
133H LYS* 5.6 0.7 - - + -
135H ILE* 4.5 13.7 - - + -
162H PHE* 4.8 5.4 - - + -
----------------------------------------------------------
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