Contacts of the strand formed by residues 87 - 95 (chain E) in PDB entry 2ZNZ
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 MET 87 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E TYR 3.4 2.7 - - - +
86E SER* 1.3 79.5 + - - +
88E LEU* 1.3 70.8 + - - +
89E ALA 5.0 0.4 - - - +
129E ILE 5.5 0.4 - - - +
130E ARG* 3.3 9.9 + - - +
131E THR* 3.0 54.7 + - - +
133E ASN* 4.1 11.7 - - - +
134E SER* 3.7 34.1 - - - +
137E LEU* 4.1 11.9 - - + -
157E ILE* 3.8 43.5 - - + -
158E VAL 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E SER 4.1 1.6 + - - -
87E MET* 1.3 82.0 - - - +
89E ALA* 1.3 64.0 + - - +
90E PHE* 5.4 0.7 - - + -
128E LYS* 3.6 32.8 - - + -
129E ILE 3.5 11.0 - - - +
130E ARG* 3.7 37.7 - - + +
158E VAL* 3.0 49.1 + - + +
161E THR* 4.3 5.4 - - - +
164E GLU* 4.0 5.4 - - - +
117F TYR* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E MET* 4.6 1.3 - - + -
88E LEU* 1.3 79.0 - - - +
90E PHE* 1.3 64.2 + - - +
128E LYS* 3.5 5.5 - - - +
129E ILE* 2.9 48.0 + - + +
137E LEU* 4.2 8.3 - - + -
155E THR* 3.9 20.2 - - + -
156E MET 3.3 13.0 - - - +
157E ILE* 4.0 10.8 - - + -
158E VAL* 4.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LEU* 5.4 0.4 - - + -
89E ALA* 1.3 72.3 - - - +
91E ILE* 1.3 62.4 + - - +
92E LEU 3.9 1.4 + - - -
126E VAL* 3.6 23.1 - - + -
127E VAL 3.2 8.7 - - - +
128E LYS* 3.8 29.8 - - + -
154E HIS 3.9 0.2 - - - +
155E THR* 3.4 1.3 - - - -
156E MET* 2.7 62.0 + - + +
158E VAL* 3.9 21.1 - - + -
90F PHE* 3.7 25.1 - + - -
117F TYR* 3.6 40.2 - + + -
119F THR* 4.5 4.0 - - + -
126F VAL* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E PHE* 1.3 75.0 - - - +
92E LEU* 1.3 65.7 + - - +
93E VAL* 3.8 7.9 + - + +
125E MET 3.5 3.1 - - - +
126E VAL* 3.7 0.3 - - - -
127E VAL* 2.7 49.1 + - + +
129E ILE* 3.6 36.1 - - + -
137E LEU* 4.5 2.5 - - + -
141E LEU* 3.7 20.2 - - + +
144E ILE* 3.8 20.9 - - + -
153E THR* 3.6 37.2 - - + -
154E HIS 3.9 2.0 - - - +
155E THR* 3.9 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E PHE* 5.4 0.2 - - + -
91E ILE* 1.3 74.0 - - - +
93E VAL* 1.3 59.7 + - - +
119E THR* 5.8 0.2 - - - +
123E TYR* 3.6 40.9 - - + -
125E MET 3.3 3.1 - - - +
126E VAL* 3.9 28.9 - - + -
153E THR* 3.2 5.9 - - - -
154E HIS* 2.8 56.3 + - + +
156E MET* 4.0 35.4 - - + -
92F LEU* 5.8 3.8 - - + -
156F MET* 4.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E ILE* 3.9 22.9 - - + +
92E LEU* 1.3 77.2 - - - +
94E LYS* 1.3 72.6 + - - +
95E VAL* 3.8 9.3 + - + +
103E VAL* 4.5 6.5 - - + -
107E LEU* 4.6 6.5 - - + -
123E TYR* 3.8 3.8 - - - +
124E ASP* 2.9 24.3 + - - +
125E MET* 2.9 24.0 + - + +
127E VAL* 4.0 19.1 - - + -
144E ILE* 4.8 4.9 - - + -
150E VAL* 4.1 24.7 - - + -
152E GLY 3.7 8.3 - - - +
153E THR* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL* 1.3 72.8 - - - +
95E VAL* 1.3 74.7 + - - +
100E TYR* 4.9 4.2 + - - -
122E ASP 3.4 25.8 - - - +
123E TYR* 3.6 19.2 - - + -
124E ASP* 2.8 25.0 + - - +
150E VAL* 3.8 3.8 - - - -
151E GLU* 2.8 55.2 + - + +
152E GLY* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL* 4.4 5.2 - - + +
94E LYS* 1.3 95.1 + - - +
96E LYS* 1.3 70.0 + - - +
97E ALA 3.7 1.6 + - - -
98E GLY 4.6 0.9 + - - -
99E LYS 3.5 9.9 - - - +
100E TYR* 3.5 48.7 + - + +
103E VAL* 4.1 17.7 - - + -
124E ASP* 2.8 17.4 + - + +
125E MET* 4.0 30.1 - - + -
149E GLY 3.3 7.9 - - - +
151E GLU* 4.4 3.0 - - - +
----------------------------------------------------------
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