Contacts of the strand formed by residues 127 - 131 (chain E) in PDB entry 1QZW
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 VAL 127 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ASN* 6.1 4.7 - - + +
117E ALA* 4.3 20.2 - - + +
120E TYR* 4.8 6.3 - - + -
121E LYS* 4.1 24.0 - - + +
125E TYR 2.8 18.1 + - - +
126E LYS* 1.3 81.9 - - - +
128E GLY* 1.3 68.0 - - - +
129E LEU* 4.5 0.7 - - + -
152E VAL* 3.0 42.0 - - + -
179E MET* 3.6 14.8 - - - +
181E ILE* 2.6 27.9 - - + +
182E ILE* 3.7 1.9 - - - +
183E ILE* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E VAL* 1.3 87.0 - - - +
129E LEU* 1.3 65.9 + - - -
153E GLN 4.4 4.3 - - - -
174E PHE* 4.4 14.4 - - - -
179E MET* 5.9 0.4 - - - -
182E ILE* 3.1 16.2 - - - +
183E ILE* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ALA* 4.8 13.9 - - + -
114E GLY* 5.2 2.9 - - - +
117E ALA* 3.4 27.4 - - + -
127E VAL* 4.3 1.1 - - + -
128E GLY* 1.3 85.1 - - - +
130E VAL* 1.3 73.6 + - - +
143E LEU* 6.0 1.8 - - + -
150E ILE* 6.2 0.9 - - + -
152E VAL* 3.1 35.9 - - + -
153E GLN 3.2 10.0 + - - +
154E VAL* 2.9 32.8 - - + +
155E TYR* 3.1 6.8 + - - -
174E PHE* 4.1 3.1 - - - -
182E ILE* 5.1 0.2 - - - -
183E ILE* 3.2 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E LEU* 1.3 88.4 - - - +
131E ALA* 1.3 72.5 + - - +
132E ALA* 2.8 10.9 + - - -
143E LEU* 5.4 1.3 - - - -
154E VAL* 3.9 4.0 - - - -
155E TYR* 3.1 26.5 - - + +
166E ILE* 4.5 18.6 - - + +
167E ALA* 5.0 4.5 - - - +
170E GLY* 4.1 4.0 - - - -
171E VAL 4.6 1.8 - - - +
174E PHE* 3.3 31.2 - - + -
182E ILE* 5.4 0.4 - - + -
183E ILE 3.3 5.1 + - - -
184E VAL* 2.9 37.5 - - + +
185E ASP* 4.0 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E VAL* 1.3 78.0 - - - +
132E ALA* 1.3 54.9 + - - +
133E ASP 3.3 10.5 + - - +
134E VAL* 5.4 3.6 - - - +
139E ALA* 4.1 9.0 - - + -
140E TYR* 3.7 47.1 - - + +
143E LEU* 4.3 11.9 - - + -
154E VAL* 4.6 3.0 - - + +
155E TYR 3.0 9.0 + - - +
156E GLY* 4.2 1.5 - - - -
157E GLU 5.5 0.3 + - - -
166E ILE* 4.4 12.5 - - - +
----------------------------------------------------------
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