Contacts of the strand formed by residues 117 - 122 (chain A) in PDB entry 1LA5
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 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG 3.5 0.2 - - - +
95A GLU* 3.4 1.9 - - - -
96A LEU* 2.9 40.3 + - + +
104A SER* 4.1 6.7 - - - +
105A GLY 4.4 0.9 - - - +
106A TRP* 2.8 33.7 - - + +
116A ALA* 1.3 85.6 - - - +
118A PRO* 1.3 69.7 - - + +
119A VAL* 3.7 15.5 - - + -
163A LEU* 4.7 7.9 - - + -
167A ASN* 2.9 46.9 - - + +
171A LEU* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A CYS* 5.3 7.0 - - + -
94A ARG 3.4 9.4 - - - +
95A GLU* 4.3 18.2 - - + +
116A ALA* 3.8 7.0 - - + +
117A LEU* 1.3 90.4 - - + +
119A VAL* 1.3 63.9 - - - +
157A GLN* 4.5 18.9 - - - +
163A LEU* 4.7 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN 3.7 0.3 - - - +
93A CYS* 3.2 5.6 - - - +
94A ARG* 2.9 31.7 + - - +
96A LEU* 3.4 28.0 - - + -
117A LEU* 3.7 19.5 - - + -
118A PRO* 1.3 82.6 - - - +
120A PHE* 1.3 81.4 + - - +
121A CYS* 3.7 4.9 + - - -
131A LEU* 2.9 34.1 - - + -
132A VAL 3.7 13.2 - - - +
157A GLN* 4.8 5.2 - - - -
161A PHE* 5.9 0.2 - - + -
163A LEU* 4.8 11.7 - - + -
171A LEU* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 4.0 26.9 - - + -
92A ASN* 3.5 35.0 - - - -
93A CYS* 4.3 2.2 - - + +
119A VAL* 1.3 80.5 - - - +
121A CYS* 1.4 75.1 + - - +
122A ASP* 4.3 10.3 - - + -
130A TRP 3.9 0.3 - - - +
131A LEU* 3.9 0.5 - - - -
132A VAL* 2.7 61.4 + - + +
135A ARG* 2.9 38.8 - - - +
157A GLN* 3.7 20.4 - - + +
158A GLU* 5.6 3.1 - - - -
161A PHE* 5.5 0.4 - - - -
295A ARG* 6.2 0.4 - - - -
297A MET* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 3.1 39.7 - - + -
83A LEU* 4.1 18.4 - - + -
90A PRO 5.3 0.2 - - - +
91A ARG* 3.1 26.4 - - - +
92A ASN 2.9 19.4 + - - +
94A ARG* 4.3 7.9 - - - -
96A LEU* 6.0 0.9 - - - -
119A VAL* 4.2 9.4 - - - -
120A PHE* 1.4 81.7 - - - +
122A ASP* 1.3 59.7 + - - +
123A MET* 4.0 17.9 - - + -
130A TRP 3.3 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 4.2 6.0 - - - +
120A PHE* 4.1 14.8 + - + -
121A CYS* 1.3 68.6 - - - +
123A MET* 1.3 56.6 + - - +
124A ASP* 3.0 21.8 + - - +
125A THR* 2.8 30.1 + - - -
128A GLY* 3.4 5.2 - - - -
129A GLY 3.3 3.2 + - - -
130A TRP* 2.9 33.1 + - + +
132A VAL* 4.6 2.4 - - + +
295A ARG* 4.3 4.9 + - - -
297A MET* 3.3 39.8 - - + +
----------------------------------------------------------
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