Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 4L2A
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 LEU 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 4.2 9.0 - - + +
95A ALA* 3.6 34.3 + - + +
96A ILE* 3.6 33.7 - - + +
99A LYS* 3.1 32.3 - - + +
100A TRP* 3.7 16.4 - - + -
125A LEU* 4.1 12.6 - - + -
126A VAL 3.4 13.9 - - - +
127A LYS* 4.4 1.6 - - - -
131A GLY 4.0 0.4 + - - -
132A SER* 1.3 76.4 + - - +
134A ASP* 1.3 61.2 + - - +
153A ILE* 4.1 15.3 - - + -
191A PHE* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 4.1 17.9 + - - -
100A TRP* 3.9 9.4 + - - -
125A LEU* 3.3 5.9 - - - +
126A VAL* 2.9 35.0 + - + +
128A LEU* 3.7 32.5 - - + +
132A SER 3.9 0.2 + - - -
133A LEU* 1.3 76.6 - - - +
135A ILE* 1.3 81.8 + - - +
136A VAL* 4.4 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TRP* 3.5 27.4 - - + +
106A PHE* 3.7 15.3 - - + -
109A ALA* 3.8 15.5 - - + +
110A LEU* 3.6 36.3 - - + +
113A LYS* 3.8 30.5 + - + -
123A THR* 3.7 24.7 - - + -
124A TRP 3.2 11.4 - - - +
125A LEU* 4.5 0.9 - - + -
134A ASP* 1.3 87.0 + - - +
136A VAL* 1.3 70.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 4.6 1.8 - - - +
123A THR* 3.6 0.7 - - - -
124A TRP* 2.8 41.3 + - + -
126A VAL* 3.9 36.8 - - + -
128A LEU* 5.6 1.6 - - + -
134A ASP* 4.4 11.2 - - + +
135A ILE* 1.3 81.1 - - - +
137A ASN* 1.3 66.7 + - - +
138A THR* 5.0 3.8 - - + -
144A PRO* 4.4 10.8 - - + -
150A VAL* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 2.8 54.1 + - - +
116A ASN 4.7 1.8 + - - -
117A ASN* 3.2 30.2 + - - +
122A TRP 3.4 3.4 - - - -
123A THR* 2.7 29.8 + - - +
136A VAL* 1.3 76.9 - - - +
138A THR* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 4.0 1.5 + - - -
121A SER* 3.3 6.1 - - - -
122A TRP* 2.8 40.3 + - - +
124A TRP* 2.8 34.2 + - + +
136A VAL* 5.0 4.3 - - + -
137A ASN* 1.3 78.7 - - - +
139A SER* 1.4 60.1 + - - +
142A ALA* 2.9 37.2 + - + +
143A THR* 4.2 8.1 - - - +
144A PRO* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 5.1 3.5 + - - -
118A PHE 5.1 5.3 + - - -
120A SER 3.8 7.4 - - - -
121A SER* 4.3 1.6 - - - +
138A THR* 1.4 74.4 - - - +
140A ASN* 1.3 76.6 + - - +
141A ALA 3.2 0.7 + - - -
142A ALA* 3.0 23.2 + - - +
140B ASN* 5.4 6.6 + - - -
----------------------------------------------------------
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