Contacts of the strand formed by residues 113 - 119 (chain H) 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 ILE 113 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G LYS* 2.7 34.3 + - - +
107H LEU* 3.5 39.3 - - + +
110H TYR* 3.0 24.8 + - + +
111H PRO 4.2 0.4 - - - +
112H GLU* 1.3 73.7 - - + +
114H VAL* 1.3 55.8 - - - +
115H GLU 3.8 3.4 - - - +
116H VAL* 3.5 31.2 - - + -
127H VAL* 3.6 27.6 - - + -
128H LYS 3.4 3.8 - - - +
129H ILE* 4.1 17.0 - - + +
140H PHE* 5.2 3.1 - - + -
144H ILE* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G LYS* 3.7 4.8 - - - +
164G GLU* 3.7 1.7 - - - -
165G THR* 2.9 52.7 + - + +
166G THR 5.5 0.4 - - - -
167G GLU 3.9 22.2 - - - +
168G LEU* 4.7 15.7 - - + -
169G PRO* 5.3 0.9 - - + -
111H PRO 4.1 7.2 - - - +
112H GLU* 3.9 12.1 - - - +
113H ILE* 1.3 73.7 - - - +
115H GLU* 1.3 62.6 + - + +
128H LYS* 2.9 45.8 + - + +
129H ILE 4.7 0.4 - - - +
130H ARG* 4.8 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G PHE* 4.5 1.9 - - - -
115G GLU* 3.9 1.9 - - - +
128G LYS* 2.8 30.9 + - - -
163G LYS* 3.2 6.3 - - - +
164G GLU* 4.2 10.7 - - + +
165G THR 4.4 8.3 - - - +
113H ILE* 3.6 2.3 - - - +
114H VAL* 1.3 89.0 - - + +
116H VAL* 1.3 65.8 + - - +
117H TYR* 3.3 26.7 + - + +
126H VAL 4.5 0.7 - - - -
127H VAL* 3.3 6.2 - - - -
128H LYS* 2.9 70.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G THR 3.7 0.3 - - - -
162G HIS* 2.8 39.4 + - + -
163G LYS* 2.9 18.0 + - + +
104H ALA* 3.8 35.4 - - + +
107H LEU* 4.1 4.5 - - + -
108H ALA* 4.0 23.1 - - - +
113H ILE* 3.5 29.4 - - + -
115H GLU* 1.3 71.8 - - - +
117H TYR* 1.3 71.0 + - - +
125H MET* 4.9 2.5 - - - -
126H VAL 3.7 2.7 - - - -
127H VAL* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 3.4 16.8 - - + -
90G PHE* 3.5 27.4 - + + -
128G LYS* 3.2 19.4 + - - -
158G VAL* 3.8 22.7 - - + -
160G LYS 3.5 2.9 - - - -
161G THR* 3.4 28.0 - - + -
163G LYS 4.4 0.7 - - - -
164G GLU* 2.5 36.3 + - + +
115H GLU* 3.3 33.5 + - + -
116H VAL* 1.3 81.1 - - - +
118H GLU* 1.3 61.7 + - - +
119H THR* 4.3 5.4 - - + -
125H MET* 3.0 7.5 - - - +
126H VAL* 2.9 44.1 + - + +
128H LYS 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G VAL* 3.4 6.4 - - - +
159G LEU* 2.7 36.0 + - + -
160G LYS* 2.8 36.4 + - - +
162G HIS* 2.6 35.0 + - + +
100H TYR* 3.2 31.4 - - - +
101H SER* 3.8 9.2 + - - -
104H ALA* 4.6 0.7 - - + -
117H TYR* 1.3 73.6 - - - +
119H THR* 1.3 55.7 + - - +
124H ASP 3.5 8.2 - - - +
125H MET* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G PHE* 4.6 2.5 - - + -
156G MET* 4.2 15.3 - - + +
157G ILE 3.4 11.7 - - - +
158G VAL* 4.2 17.3 - - + -
159G LEU* 3.9 9.5 - - - +
92H LEU* 5.8 0.3 - - - +
117H TYR* 4.0 7.0 - - + +
118H GLU* 1.3 79.9 - - - +
120H THR* 1.3 69.6 + - - +
121H GLY 3.9 0.3 + - - -
123H TYR* 3.7 9.4 + - - +
124H ASP* 3.1 15.1 + - - +
125H MET* 3.6 19.9 + - - -
126H VAL* 3.8 25.8 - - + +
----------------------------------------------------------
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