Contacts of the strand formed by residues 146 - 154 (chain A) in PDB entry 1LNU
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 PHE 146 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 5.7 0.2 - - + -
13A VAL* 3.8 33.9 - - + -
22A GLN* 5.1 2.2 - - - -
112A ASN 2.9 10.0 + - - -
113A ILE* 2.6 47.2 + - + +
114A PHE* 4.2 13.9 - + - -
116A PRO* 4.3 15.3 - - + -
138A PHE* 3.6 39.9 - + + -
139A PHE 3.1 22.0 - - - +
140A VAL* 4.4 8.7 - - + -
141A ASN* 3.0 7.4 - - - +
144A TYR 3.5 15.7 - - - -
145A SER* 1.3 92.4 - - - +
147A HIS* 1.3 59.1 + - - +
34B VAL* 5.0 2.5 - - + -
36B GLN* 3.3 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 5.3 4.2 + - - -
109A PHE* 3.2 25.9 - + + -
110A VAL 2.8 18.6 - - - +
111A ASP* 3.3 22.5 + - - +
113A ILE* 4.1 2.7 - - - -
138A PHE* 4.7 0.4 - - - -
139A PHE* 2.8 65.8 + + + +
140A VAL 3.9 7.4 - - - -
141A ASN* 2.6 28.0 + - - -
146A PHE* 1.3 72.3 - - - +
148A LYS* 1.3 60.2 + - - +
149A LEU* 4.0 4.4 - - + +
176B ARG* 6.0 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 5.3 0.2 + - - -
108A CYS 3.9 0.9 - - - +
110A VAL* 2.9 31.3 + - - +
113A ILE* 3.6 15.2 - - + +
118A ILE* 4.4 9.2 - - + -
120A ILE* 4.0 16.4 - - + -
135A GLU* 2.5 36.5 + - - +
136A THR* 2.3 42.4 + - - +
137A SER* 4.3 8.5 - - - +
138A PHE* 4.0 35.9 - - + +
147A HIS* 1.3 74.4 - - - +
149A LEU* 1.3 85.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.8 2.7 - - + -
107A ILE* 3.7 19.7 - - + -
108A CYS 3.7 1.3 - - - -
109A PHE* 3.2 54.5 - - + -
120A ILE* 5.1 0.7 - - - -
135A GLU* 3.2 5.9 - - - +
136A THR* 2.8 51.6 + - + +
139A PHE* 4.4 7.2 - - + -
147A HIS* 4.0 8.7 - - + -
148A LYS* 1.3 88.6 - - - +
150A SER* 1.3 59.6 + - - +
151A TYR* 4.0 15.3 - - + +
176B ARG 5.7 1.3 - - - +
177B ASN 4.6 5.6 - - - +
178B GLY* 4.7 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 3.7 0.3 - - - +
107A ILE* 3.5 4.9 - - - +
108A CYS* 3.0 35.4 + - - -
120A ILE* 3.9 33.4 + - - +
122A TRP* 3.2 23.6 + - - -
133A VAL* 4.3 4.7 - - - +
134A TYR 3.2 9.8 + - - -
135A GLU* 4.2 7.9 + - - +
149A LEU* 1.3 74.7 - - - +
151A TYR* 1.3 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A MET* 3.9 4.4 - - + +
95A LYS* 6.4 1.8 - - + -
105A THR* 3.7 22.4 - - + -
106A LEU 3.5 3.6 - - - -
107A ILE* 4.0 22.0 - - + -
122A TRP* 3.2 7.5 + - - -
132A GLY 3.7 1.1 - - - +
133A VAL* 3.2 6.4 - - - -
134A TYR* 2.5 71.1 + + + +
136A THR* 3.3 30.8 - - + +
149A LEU* 4.0 8.7 - - + +
150A SER* 1.3 79.0 + - - +
152A LEU* 1.3 60.0 + - - +
153A THR* 4.0 1.1 - - - +
177B ASN 2.7 28.7 + - - -
178B GLY* 3.3 21.0 - - - -
179B ASP* 3.6 11.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 3.3 6.7 - - - +
106A LEU* 2.8 53.2 + - + +
122A TRP* 2.8 55.9 - - + +
124A ARG* 4.8 7.9 - - - +
129A VAL* 5.2 8.1 - - + -
131A ASP 5.3 2.0 - - - +
132A GLY 3.9 2.0 - - - +
133A VAL* 4.7 6.1 - - + +
151A TYR* 1.3 71.8 - - - +
153A THR* 1.3 79.4 + - - +
154A PHE* 3.4 16.1 + - + -
162A TYR* 4.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 6.1 4.5 - - + -
104A ASN 3.9 6.5 - - - +
105A THR* 4.2 11.9 + - - +
124A ARG* 4.8 3.1 + - - -
131A ASP 4.8 1.9 - - - +
132A GLY* 2.8 34.7 + - - +
151A TYR* 4.0 1.1 - - - +
152A LEU* 1.3 78.8 - - - +
154A PHE* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PRO* 5.4 2.0 - - + -
98A VAL* 5.7 1.8 - - + -
103A PRO* 3.8 5.0 - - - +
104A ASN* 2.8 81.7 + - + +
105A THR 3.7 0.2 - - - -
106A LEU* 3.6 22.4 - - + -
124A ARG* 4.3 7.6 - - - +
152A LEU* 3.5 24.5 - - + -
153A THR* 1.3 77.2 - - - +
155A ILE* 1.3 74.3 + - - +
156A PRO* 3.6 25.6 - - + -
162A TYR* 3.4 42.6 - + + +
179A TRP* 4.2 21.1 - + - -
----------------------------------------------------------
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