Contacts of the helix formed by residues 92 - 107 (chain B) in PDB entry 1ZHH
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 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.6 11.2 - - - -
90B ASP* 3.4 20.7 + - + +
91B ARG* 1.3 72.9 - - - +
93B THR* 1.3 65.4 + - - +
94B ASP* 3.2 21.3 + - - +
95B VAL* 3.3 35.3 + - + +
96B LEU 3.4 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 4.0 12.5 - - - -
91B ARG 3.5 5.5 + - - -
92B ASP* 1.3 73.2 + - - +
94B ASP* 1.3 60.6 + - - +
96B LEU* 3.4 2.8 + - - +
97B ASN* 3.0 49.6 + - - +
125B TRP* 4.0 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP* 3.2 10.5 + - - +
93B THR* 1.3 77.3 - - - +
95B VAL* 1.3 65.6 + - + +
97B ASN* 3.7 7.1 + - - +
98B PHE* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 4.2 19.3 - - + -
92B ASP* 3.3 29.6 + - + +
94B ASP* 1.3 77.4 - - + +
96B LEU* 1.3 62.2 + - - +
98B PHE* 3.6 6.3 + - - +
99B PHE* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 4.6 6.7 - - + -
84B ILE* 4.0 26.9 - - + -
87B PHE* 3.6 35.9 - - + -
92B ASP 3.4 10.3 + - - +
93B THR 3.8 7.0 - - - +
94B ASP 3.3 0.4 - - - -
95B VAL* 1.3 76.9 - - - +
97B ASN* 1.3 64.4 + - - +
99B PHE* 3.3 11.2 + - + +
100B PHE* 3.2 51.4 + - + -
117B LEU* 3.8 10.8 - - + -
125B TRP* 3.6 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 3.0 39.4 + - - +
94B ASP* 4.2 7.2 + - - +
96B LEU* 1.3 71.7 - - - +
98B PHE* 1.3 60.4 + - - +
100B PHE* 3.4 6.5 + - - +
101B LEU* 3.0 38.3 + - + +
125B TRP* 3.3 29.7 + - - +
127B ASP* 5.0 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP 3.3 16.6 + - - +
95B VAL* 3.9 6.7 - - - +
96B LEU 3.3 0.2 - - - -
97B ASN* 1.3 75.3 - - - +
99B PHE* 1.3 67.2 + - - +
101B LEU* 3.3 17.7 + - + +
102B SER* 3.0 41.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 4.3 5.6 - - + -
81B SER* 3.2 32.5 - - - -
83B VAL* 3.8 30.5 - - + -
84B ILE* 4.0 26.5 - - + -
95B VAL 3.2 14.6 + - - +
96B LEU* 3.3 11.2 - - + +
98B PHE* 1.3 80.4 - - - +
100B PHE* 1.3 77.2 + + - +
102B SER* 3.3 15.3 + - - -
103B ILE* 3.2 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 4.6 10.1 - - + -
84B ILE* 3.8 24.5 - - + -
96B LEU* 3.2 40.9 + - + +
97B ASN* 3.4 5.1 + - - +
99B PHE* 1.3 91.2 - + - +
101B LEU* 1.3 64.9 + - - +
103B ILE* 3.6 7.4 + - + +
104B ASP* 3.0 33.3 + - - +
115B ARG* 3.3 47.8 - - - +
117B LEU* 5.3 6.3 - - + -
125B TRP* 3.6 33.7 - + + -
127B ASP* 6.5 0.4 - - + -
186B SER* 5.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASN* 3.0 25.7 + - + +
98B PHE* 3.5 20.2 - - + +
99B PHE 3.3 0.2 - - - -
100B PHE* 1.3 78.4 - - - +
102B SER* 1.3 56.7 + - - +
104B ASP* 3.7 6.9 + - + +
105B GLN* 3.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.0 34.8 + - - -
99B PHE* 3.7 10.7 - - - -
100B PHE 3.2 0.2 - - - -
101B LEU* 1.3 75.1 - - - +
103B ILE* 1.3 66.0 + - - +
105B GLN* 3.4 22.9 + - - +
106B SER* 3.6 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 5.0 15.7 - - + +
78B ASN* 3.5 37.9 - - - +
99B PHE* 3.2 56.6 + - + +
100B PHE* 3.6 7.6 + - + +
101B LEU 3.5 0.2 - - - -
102B SER* 1.3 74.2 - - - +
104B ASP* 1.3 69.2 + - - +
106B SER* 2.7 25.6 + - - +
107B ASP* 3.5 7.3 + - - +
115B ARG* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 3.0 19.7 + - - +
101B LEU* 3.9 7.7 - - + +
103B ILE* 1.3 77.9 - - - +
105B GLN* 1.3 64.9 + - - +
108B PRO* 3.1 30.9 - - + +
111B THR* 3.1 32.1 - - + +
115B ARG* 3.1 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.2 20.9 + - - +
102B SER* 3.4 14.7 - - - +
103B ILE 3.2 0.4 - - - -
104B ASP* 1.3 78.0 - - - +
106B SER* 1.3 62.5 + - - +
108B PRO* 3.4 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 5.8 1.4 - - - -
102B SER 3.6 6.1 + - - -
103B ILE* 2.7 27.2 + - - +
105B GLN* 1.3 79.9 - - - +
107B ASP* 1.3 60.8 + - - +
108B PRO* 3.4 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 5.0 0.5 - - - +
74B HIS* 2.7 37.6 + - + +
103B ILE 3.5 5.0 + - - +
104B ASP* 3.4 3.1 - - - -
106B SER* 1.3 85.0 + - - +
108B PRO* 1.3 65.1 - - - +
109B SER* 3.9 6.2 + - - -
110B HIS* 3.0 40.4 + - - +
111B THR* 3.4 12.0 - - - +
----------------------------------------------------------
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