Contacts of the strand formed by residues 114 - 119 (chain E) in PDB entry 3ZP0
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 HIS 114 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E VAL 3.8 13.6 + - - -
78E PRO* 4.1 2.5 - - + +
79E GLU* 3.6 36.2 + - + +
80E TRP* 4.3 1.6 - + - -
112E ILE* 3.8 9.2 - - - +
113E ASN* 1.3 80.9 - - + +
115E PHE* 1.3 83.4 + - - +
116E GLU* 5.1 9.0 - - + +
261E VAL* 2.9 60.8 + - + +
262E LYS* 3.3 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E TRP* 3.8 24.5 - + + -
65E LEU* 3.8 22.7 - - + -
77E VAL* 4.3 10.7 + - + +
80E TRP* 4.0 12.8 - + + -
105E LEU* 6.0 1.3 - - + -
109E LEU* 3.6 23.6 - - + -
112E ILE* 4.0 30.5 - - + -
114E HIS* 1.3 97.1 + - - +
116E GLU* 1.3 59.6 + - - +
117E LYS 4.1 0.6 + - - -
177E LEU* 4.0 23.6 - - + -
258E TYR* 3.8 28.7 - + + -
259E LYS 3.4 15.0 - - - -
260E ILE* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E HIS* 5.1 8.0 - - + +
115E PHE* 1.3 73.0 - - - +
117E LYS* 1.3 65.5 + - - +
118E ILE* 4.3 7.1 - - - +
258E TYR* 4.3 1.3 - - - -
259E LYS* 2.7 62.2 + - + +
261E VAL* 3.6 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E TRP 5.3 0.8 + - - -
67E GLY* 5.5 1.8 - - - -
74E PHE 4.7 0.8 + - - -
75E ILE* 2.9 47.7 + - - +
76E ASN* 3.8 20.4 + - - +
115E PHE 4.1 1.2 - - - -
116E GLU* 1.3 74.7 - - - +
118E ILE* 1.3 67.2 + - - +
150E ASN* 3.2 29.9 + - - +
256E TYR* 3.6 31.4 - - + -
257E ALA 3.7 6.1 - - - +
258E TYR* 3.4 41.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E GLU* 3.5 9.1 + - - +
117E LYS* 1.3 79.7 - - - +
119E GLN* 1.3 70.0 + - - +
120E ILE* 4.3 3.3 - - + +
168E TYR* 4.0 10.3 - - - +
172E ASN* 3.5 13.7 - - - +
176E LEU* 4.3 7.9 - - + -
256E TYR* 4.0 5.2 - - - -
257E ALA* 2.9 38.2 + - - +
259E LYS* 2.4 79.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ILE* 1.3 79.0 - - - +
120E ILE* 1.3 61.8 + - - +
121E ILE 4.4 0.2 - - - +
122E PRO* 3.4 45.9 - - + +
123E LYS 4.2 1.2 - - - +
168E TYR* 5.3 2.3 - - - -
255E GLU* 3.5 37.7 + - - +
256E TYR* 3.6 26.9 + - + -
----------------------------------------------------------
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