Contacts of the strand formed by residues 145 - 153 (chain A) in PDB entry 1U1L
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 LYS 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS 5.5 1.1 - - - +
114A GLU* 3.4 60.3 + - + +
116A THR 4.9 5.4 - - - -
136A ILE* 4.4 20.2 - - + -
137A MET 4.6 2.5 - - - +
138A THR* 3.6 25.5 - - + +
143A GLY 3.7 4.1 + - - +
144A LYS* 1.3 77.0 - - - +
146A ARG* 1.3 61.8 + - - +
147A GLY 3.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 5.0 0.4 - - - -
137A MET* 3.1 15.1 + - - +
138A THR* 3.7 22.3 + - - +
139A ASP* 3.6 29.0 + - + +
144A LYS* 3.9 1.3 - - + +
145A LYS* 1.3 73.4 - - - +
147A GLY* 1.3 61.7 + - - +
148A PHE* 3.5 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY* 2.9 27.6 + - - -
112A ILE* 3.2 28.7 + - - -
113A LYS 5.5 0.2 - - - -
114A GLU* 4.4 8.1 + - - -
137A MET 4.5 1.2 + - - -
145A LYS* 3.4 7.6 - - - +
146A ARG* 1.3 77.9 - - - +
148A PHE* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.6 29.2 - + + -
109A VAL 3.0 13.7 - - - +
110A GLY* 3.8 8.3 - - - -
112A ILE* 3.5 10.3 - - - +
136A ILE* 4.0 0.9 - - - +
137A MET* 3.1 55.0 + - + +
146A ARG* 3.5 61.9 - - + -
147A GLY* 1.3 79.4 - - - +
149A ALA* 1.3 63.6 + - - +
150A PHE* 3.7 18.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.6 3.5 - - - -
109A VAL* 2.7 40.7 + - + +
112A ILE* 3.7 15.2 - - + +
121A LEU* 4.0 20.4 - - + -
135A GLU 3.1 16.4 - - - +
136A ILE* 3.9 6.7 - - - -
137A MET* 4.4 0.4 - - - -
148A PHE* 1.3 78.9 - - - +
150A PHE* 1.3 69.5 + - - +
151A VAL* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 3.6 28.9 - - + -
107A ILE 3.3 10.1 - - - -
108A PHE* 4.0 24.2 - + + -
133A VAL 4.0 0.3 - - - +
134A ILE* 3.5 2.3 - - - +
135A GLU* 2.8 55.6 + - + +
137A MET* 3.8 29.2 - - + -
148A PHE* 3.7 27.6 - + - -
149A ALA* 1.3 74.7 - - - +
151A VAL* 1.3 64.7 + - - +
152A THR 4.2 0.4 - - - -
180A ALA* 4.3 10.5 - - + -
181A LEU 5.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS 3.8 1.2 - - - +
106A LYS* 3.3 1.5 - - - -
107A ILE* 2.9 41.8 + - + +
109A VAL* 4.2 19.3 - - + -
121A LEU* 4.5 18.6 - - + -
125A PHE* 4.2 15.5 - - + -
131A ILE* 3.9 29.4 - - + -
133A VAL 3.3 3.8 - - - +
134A ILE* 4.3 6.5 - - + -
149A ALA* 5.2 0.2 - - + -
150A PHE* 1.3 79.4 - - - +
152A THR* 1.3 62.3 + - - +
153A PHE* 3.8 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 3.4 18.4 - - + +
106A LYS* 3.5 28.7 - - + +
131A ILE* 3.7 4.0 - - - +
132A GLU* 2.7 38.3 + - + -
133A VAL* 2.8 36.5 + - + +
135A GLU* 4.7 3.3 + - - -
150A PHE 4.2 0.4 - - - -
151A VAL* 1.3 71.1 - - - +
153A PHE* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 2.6 40.3 + - - +
107A ILE* 3.8 12.1 - - + -
125A PHE* 3.7 35.9 - + + -
128A TYR* 4.4 0.2 - - + -
129A GLY 3.9 11.7 - - - -
130A LYS 3.3 17.9 - - - +
131A ILE* 3.8 13.0 - - + -
132A GLU* 3.9 7.8 - - - +
151A VAL* 3.8 18.6 - - + -
152A THR* 1.3 82.5 - - - +
154A ASP* 1.3 63.0 + - - +
155A ASP 3.4 16.2 - - - +
158A SER* 3.7 18.6 - - - -
159A VAL* 3.8 11.0 - - + -
162A ILE* 3.5 30.3 - - + -
----------------------------------------------------------
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