Contacts of the strand formed by residues 118 - 123 (chain B) in PDB entry 1F9N
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 MET 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 5.5 4.5 + - - -
110B MET* 3.0 54.1 - - - +
111B ASP* 5.4 0.9 - - - +
113B LEU* 3.7 22.2 - - + -
114B ASP 5.0 0.2 - - - +
115B TRP* 2.8 42.2 + - + +
116B ASP* 3.8 5.2 - - - +
117B GLU* 1.3 78.9 - - - +
119B MET* 1.3 62.1 + - - +
120B GLY* 4.5 5.6 - - - +
121B THR* 4.9 5.2 - - - -
130B ILE* 4.2 20.4 - - + -
131B ILE 3.8 4.3 - - - +
132B CYS* 4.7 0.9 - - - +
133B ARG* 4.4 2.9 + - - -
141B VAL* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 5.4 5.1 + - - +
88A ASP* 3.2 45.6 - - + +
89A SER* 3.4 19.5 - - - +
90A ALA* 4.0 12.1 - - + -
93A MET* 5.1 2.9 - - + +
94A ILE* 5.3 0.2 - - - -
95A VAL* 3.7 28.3 - - + +
97A LYS* 3.2 21.2 + - - -
118B MET* 1.3 74.1 - - - +
120B GLY* 1.3 58.7 + - - +
131B ILE* 2.8 24.8 + - + +
132B CYS 3.7 17.7 - - - +
133B ARG* 3.7 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.5 7.0 - - - -
97A LYS* 3.2 17.0 - - - -
111B ASP* 4.6 3.1 - - - -
118B MET* 3.5 3.9 - - - +
119B MET* 1.3 82.6 + - - +
121B THR* 1.3 72.8 + - - +
130B ILE* 4.2 1.4 - - - +
131B ILE* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 4.3 2.8 - - - +
126A ASP* 5.3 1.6 - - - +
127A THR* 3.8 14.7 + - - +
107B GLY 3.7 7.5 + - - +
110B MET* 4.8 13.9 - - + -
111B ASP* 2.8 33.5 + - - +
118B MET* 4.9 4.5 - - - -
120B GLY* 1.3 85.2 - - - +
122B ILE* 1.3 70.6 + - - +
123B CYS* 4.1 9.0 + - - -
128B ILE* 4.3 13.0 - - + -
129B LEU 3.2 11.0 - - - +
130B ILE* 4.2 23.3 - - + -
131B ILE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.2 16.8 - - + +
123A CYS 4.8 1.6 - - - +
124A GLY* 4.1 19.3 - - - +
127A THR* 3.6 47.1 - - + +
129A LEU* 4.9 5.8 - - + -
121B THR* 1.3 72.3 - - - +
123B CYS* 1.3 67.8 + - - +
127B THR 4.1 0.5 - - - +
128B ILE* 3.6 1.2 - - - -
129B LEU* 2.8 55.6 + - + +
131B ILE* 4.7 9.0 - - + -
122C ILE* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLY* 5.7 4.7 - - - -
103B ALA 3.9 13.5 - - - +
104B GLN* 4.3 11.0 - - + -
107B GLY* 3.5 32.5 - - - -
121B THR* 4.2 10.2 + - - -
122B ILE* 1.3 84.3 - - - +
124B GLY* 1.3 65.0 + - - +
127B THR 3.7 4.9 - - - +
128B ILE* 4.0 14.1 - - - -
----------------------------------------------------------
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