Contacts of the strand formed by residues 118 - 125 (chain B) in PDB entry 3FA6
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 GLU 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TRP* 4.2 2.0 - - - -
10B ILE* 3.7 18.0 - - - +
11B ARG* 3.7 16.1 + - - -
112B GLU 3.7 0.2 - - - +
113B LEU* 3.4 6.2 - - - +
114B THR* 2.9 46.9 + - + +
116B ASP* 4.2 15.0 - - + +
117B GLY* 1.3 82.4 - - - +
119B LEU* 1.3 60.6 - - - +
120B ILE* 4.8 3.9 - - + +
133B VAL* 3.5 23.2 - - + +
134B PHE 3.4 6.5 - - - +
135B VAL* 4.1 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.7 31.9 - - + -
7B TRP* 3.6 40.1 - - + -
41B VAL* 5.1 4.7 - - + -
43B ILE* 3.9 23.3 - - + -
111B LEU* 4.3 22.2 - - + -
112B GLU 3.4 13.9 - - - +
113B LEU* 4.1 6.7 - - + -
118B GLU* 1.3 71.7 - - - +
120B ILE* 1.3 62.6 + - - +
132B LYS 3.7 0.9 - - - +
133B VAL* 3.4 3.6 - - - +
134B PHE* 2.8 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B THR* 3.5 2.8 + - - +
111B LEU* 3.3 6.7 - - - -
112B GLU* 2.9 54.7 + - + +
114B THR* 3.4 31.0 - - + -
118B GLU* 4.8 4.5 - - + +
119B LEU* 1.3 75.3 - - - +
121B ASP* 1.3 60.9 + - - +
122B THR* 3.9 12.5 + - - +
131B THR* 3.7 27.8 - - + -
132B LYS 3.6 3.4 - - - +
133B VAL* 4.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TRP* 4.5 0.9 - - - +
110B THR 3.3 9.7 - - - +
111B LEU* 3.7 16.8 - - + +
119B LEU 4.0 0.6 + - - -
120B ILE* 1.3 72.1 - - - +
122B THR* 1.3 67.2 + - - +
123B MET* 3.8 10.8 - - - +
130B CYS 3.7 0.9 - - - +
131B THR* 3.4 4.3 - - - +
132B LYS* 2.8 44.8 + - + +
134B PHE* 4.0 17.5 - - + -
138B LSR 3.3 55.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TRP* 3.1 7.1 - - - +
110B THR* 2.8 52.2 + - + +
120B ILE* 3.9 15.1 - - - +
121B ASP* 1.3 76.1 + - - +
123B MET* 1.3 60.5 + - - +
124B THR* 4.5 9.4 - - + +
129B VAL* 3.5 33.0 - - + -
130B CYS 3.3 4.3 - - - +
131B THR* 4.3 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.7 1.3 - - + -
18B LEU* 3.6 24.4 - - + +
76B VAL* 4.6 14.1 - - + -
108B SER 3.5 4.5 - - - +
109B TRP* 4.0 5.4 - - + -
121B ASP* 3.8 11.0 - - - +
122B THR* 1.3 76.6 - - - +
124B THR* 1.3 62.1 + - - +
129B VAL* 3.7 1.2 - - - -
130B CYS* 2.8 48.6 + - - +
132B LYS* 3.9 14.4 - - + -
138B LSR 3.1 70.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.8 3.6 - - - +
106B LYS* 4.2 4.2 + - - +
107B THR* 3.2 21.1 - - - +
108B SER* 2.7 40.7 + - - +
110B THR* 6.1 2.2 - - + -
122B THR* 4.5 13.2 - - + -
123B MET* 1.3 80.3 - - - +
125B ALA* 1.3 62.4 + - - +
126B ASP 4.6 8.2 + - - -
128B VAL 3.3 7.9 - - - -
129B VAL* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.7 11.6 - - + +
21B VAL* 3.6 27.0 - - + +
22B LEU* 3.8 24.0 - - + -
105B PRO* 4.1 4.5 - - + -
106B LYS 3.3 5.4 - - - -
107B THR* 4.3 1.6 - - + -
124B THR* 1.3 76.1 - - - +
126B ASP* 1.3 69.8 + - - +
127B ASP 3.1 0.5 + - - -
128B VAL* 3.0 25.1 + - - +
----------------------------------------------------------
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