Contacts of the strand formed by residues 148 - 154 (chain A) in PDB entry 3L7Y
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 148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.5 9.0 - - - +
84A GLN* 2.9 30.2 + - - +
86A ARG* 4.7 5.2 - - + -
89A ILE* 3.9 31.1 - - + +
107A LEU* 3.8 31.0 - - + -
108A SER 3.5 4.5 - - - +
109A GLY* 3.6 17.3 - - - -
114A TYR* 3.8 20.4 - + - -
143A LEU* 4.5 12.1 - - + -
144A PRO* 3.7 38.8 - - + -
146A GLU* 3.0 27.1 - - + -
147A ARG* 1.3 73.5 - - - +
149A PHE* 1.3 60.7 + - - +
150A LYS 4.5 6.7 - - - +
151A LEU* 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.4 40.6 - - + +
70A ALA* 4.2 17.7 - - + +
71A ASN* 3.3 43.5 - - + -
81A GLU* 3.8 20.0 - - + -
82A VAL 3.3 18.9 - - - +
83A PHE* 3.3 32.5 - + - -
84A GLN* 3.6 16.5 - - - +
108A SER 2.9 6.6 + - - +
109A GLY 4.3 10.8 - - - -
110A GLU* 4.1 20.4 - - + -
148A PHE* 1.3 74.5 - - - +
150A LYS* 1.3 61.6 + - - +
189A ILE* 5.0 1.4 - - - +
190A THR* 4.7 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 3.1 23.9 + - - +
46A ASN* 4.6 0.4 - - - +
47A PRO* 4.4 9.3 - - - +
67A GLU* 2.8 33.2 + - - +
68A ASN* 4.2 6.1 - - - +
84A GLN* 3.5 7.4 - - - +
108A SER* 2.9 41.6 + - - +
130A PHE 5.6 0.2 + - - -
131A PHE* 5.0 3.6 - - - -
148A PHE* 3.5 2.2 - - - +
149A PHE* 1.3 81.0 + - + +
151A LEU* 1.3 73.2 + - - +
152A THR* 3.4 21.3 - - - -
187A ASP* 3.6 28.5 - - + +
188A ILE 3.6 9.9 - - - +
189A ILE* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 3.8 16.4 - - - +
89A ILE* 4.1 16.2 - - + -
92A ILE* 3.8 28.5 - - + -
93A ILE* 4.0 12.3 - - + -
105A ILE* 4.7 6.3 - - + -
106A ALA 3.3 9.6 - - - +
107A LEU* 3.5 30.7 - - + -
108A SER* 4.6 0.4 - - - +
148A PHE* 4.9 2.5 - - + -
150A LYS* 1.3 87.9 - - - +
152A THR* 1.3 69.5 + - - +
153A LEU* 5.5 1.1 - - + -
176A LEU* 6.3 0.4 - - + -
187A ASP* 3.4 2.9 - - - -
188A ILE* 2.8 49.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
104A VAL 3.3 2.6 - - - +
105A ILE* 3.6 1.9 - - - -
106A ALA* 2.7 46.6 + - - +
108A SER* 5.4 0.5 - - - -
127A LEU* 5.0 7.4 - - + +
130A PHE* 5.8 3.4 - - + -
131A PHE* 4.9 9.6 - - + -
150A LYS* 3.4 14.0 - - - -
151A LEU* 1.3 76.8 + - - +
153A LEU* 1.3 76.8 + - - +
154A GLN 4.1 0.6 + - - +
181A SER* 5.1 0.2 - - - +
185A TYR* 3.9 22.2 - - + -
186A ILE 3.4 6.3 - - - +
187A ASP* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 3.9 30.7 - - + -
103A ALA* 4.2 10.8 - - + -
104A VAL 3.2 3.4 - - - +
105A ILE* 3.7 32.1 - - + -
151A LEU* 5.5 1.6 - - + -
152A THR* 1.3 87.3 - - - +
154A GLN* 1.3 60.8 + - - +
155A VAL* 3.8 12.5 + - + +
163A ILE* 4.0 19.5 - - + -
167A ILE* 4.2 3.1 - - + -
185A TYR* 3.4 5.4 - - - -
186A ILE* 2.7 43.9 + - + +
188A ILE* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN 4.1 2.9 - - - +
103A ALA* 3.5 2.8 - - - -
104A VAL* 2.9 44.6 + - + +
123A ILE* 3.3 35.6 - - - +
126A MET* 2.9 38.4 - - - +
127A LEU* 4.8 6.2 - - + +
152A THR* 4.1 0.4 + - - +
153A LEU* 1.3 69.7 - - - +
155A VAL* 1.3 67.9 + - - +
184A GLY* 3.5 11.4 - - - +
185A TYR* 3.4 26.8 + - + -
----------------------------------------------------------
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