Contacts of the strand formed by residues 107 - 114 (chain A) in PDB entry 2LFG
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 107 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 4.5 18.2 - - + +
105A PRO* 2.9 23.1 + - + +
106A PRO* 1.3 72.2 - - - +
108A GLU* 1.3 86.7 + - + +
109A LEU* 3.3 2.0 - - - +
128A SER* 2.9 43.2 + - - +
129A PRO 5.0 4.9 - - - +
130A PRO* 5.8 1.6 - - + -
131A THR* 5.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 1.3 92.6 - - + +
109A LEU* 1.3 60.4 + - - +
110A ALA* 2.9 15.0 + - - +
126A LYS 3.7 5.0 - - - +
127A TRP* 3.9 3.8 - - - -
128A SER* 2.7 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO 4.7 5.8 - - - +
107A LEU* 3.3 3.0 - - - -
108A GLU* 1.3 71.7 - - - +
110A ALA* 1.3 61.5 + - - +
111A VAL* 3.8 16.2 + - + +
125A ILE* 3.4 32.8 - - + -
126A LYS 3.9 5.4 - - - +
127A TRP* 4.5 3.1 - - + +
180A VAL* 4.1 8.7 - - + +
181A GLN* 4.2 1.1 - - - -
182A VAL* 3.6 40.4 - - + +
196A PRO* 4.1 15.7 - - + +
198A THR* 3.3 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLU 2.9 8.9 + - - +
109A LEU* 1.3 71.9 - - - +
111A VAL* 1.3 61.6 + - - +
124A TRP 3.8 0.5 - - - +
125A ILE* 3.7 1.0 - - - -
126A LYS* 2.7 73.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.8 19.9 + - + +
110A ALA* 1.3 77.4 - - - +
112A GLU* 1.3 66.0 + - - +
123A LEU* 3.6 35.4 - - + -
124A TRP 3.7 1.3 - - - -
125A ILE* 4.1 11.0 - - + -
180A VAL* 3.7 24.9 - - + -
198A THR* 4.1 10.8 - - + -
200A ILE* 3.7 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA* 4.1 0.4 - - + -
111A VAL* 1.3 78.2 - - - +
113A VAL* 1.3 83.1 + - - +
114A LYS* 3.6 27.5 + - + +
123A LEU* 3.5 5.3 - - - +
124A TRP* 2.6 60.7 + - + +
126A LYS* 5.2 7.9 - - - +
200A ILE* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 1.3 85.6 + - - +
114A LYS* 1.3 66.6 + - - +
115A GLN* 4.0 16.9 + - + +
122A TYR 3.8 4.3 - - - +
123A LEU* 4.1 12.1 - - + +
200A ILE* 5.8 3.9 - - + +
201A GLN 5.4 2.0 - - - +
202A ILE* 5.1 2.2 - - + -
203A PRO* 3.9 29.6 - - + -
206A PHE* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 3.6 26.3 + - + +
113A VAL* 1.3 74.9 - - - +
115A GLN* 1.3 62.3 + - - +
116A PRO* 3.3 4.0 - - + +
121A PRO* 3.3 2.4 - - - +
122A TYR* 2.8 70.0 + - + +
124A TRP* 3.7 42.2 - - + -
----------------------------------------------------------
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