Contacts of the strand formed by residues 113 - 122 (chain F) in PDB entry 3F5O
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 113 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F VAL* 4.6 1.6 - - + -
109F GLN* 3.7 0.5 - - - -
110F GLY* 2.8 32.6 + - - +
111F LYS 3.8 0.2 - - - -
112F THR* 1.3 93.2 - - - +
114F ALA* 1.3 57.2 + - - +
115F PHE* 4.0 18.6 - - + -
135F THR* 4.2 12.3 - - + -
136F LYS 3.3 15.5 - - - +
137F HIS* 4.0 13.5 - - + +
138F LEU* 4.5 3.4 - - - -
84H VAL* 3.8 36.1 - - + -
113H LEU* 4.4 17.7 - - + -
137H HIS* 4.3 9.4 - - - +
150H COA 3.0 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LEU* 3.6 37.2 - - + -
108F LYS 3.5 5.4 - - - +
109F GLN* 3.6 14.1 - - + -
113F LEU* 1.3 74.1 - - - +
115F PHE* 1.3 64.3 - - - +
116F THR* 5.0 1.1 - - - -
134F HIS 3.9 0.9 - - - +
135F THR* 3.4 4.7 - - - +
136F LYS* 2.9 35.0 + - + +
138F LEU* 4.3 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F VAL* 3.7 1.9 - - - +
107F LEU* 2.8 32.7 + - + -
108F LYS* 2.8 31.4 + - + +
110F GLY 5.3 0.2 - - - -
113F LEU* 4.0 29.2 - - + -
114F ALA* 1.3 74.4 - - - +
116F THR* 1.3 61.4 + - - +
133F ARG* 6.0 0.7 - - + -
134F HIS 3.7 3.4 - - - -
135F THR* 3.5 15.3 - - + -
89G THR* 3.2 33.7 - - + -
90G TYR 3.9 9.6 - - - -
91G MET* 3.5 31.9 - - + -
84H VAL* 3.7 24.9 - - + -
150H COA 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F SER* 3.2 35.5 - - - +
71F ALA* 5.3 0.2 - - + -
72F LEU* 4.0 32.5 - - + -
105F HIS 3.2 13.2 - - - +
106F VAL* 4.2 8.7 - - + -
107F LEU* 4.2 3.3 - - - +
114F ALA 5.0 0.4 - - - -
115F PHE* 1.3 81.0 - - - +
117F SER* 1.3 60.1 + - - +
118F VAL* 5.2 0.2 - - - -
133F ARG* 3.1 10.2 - - - +
134F HIS* 2.9 47.4 + - - +
136F LYS* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F THR 3.9 0.2 - - - +
104F ALA* 3.3 2.9 - - - +
105F HIS* 2.8 56.7 + - - -
107F LEU* 4.0 17.0 - - - +
116F THR* 1.3 74.5 - - - +
118F VAL* 1.3 65.6 + - - +
119F ASP* 4.7 1.7 + - - -
131F GLN* 4.4 13.0 + - - +
132F GLY 3.4 11.2 + - - -
133F ARG* 4.4 0.6 - - - +
131G GLN* 3.9 13.5 + - - -
133G ARG* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU 5.0 0.2 - - - +
64F VAL* 3.7 45.3 - - + +
67F ILE* 5.1 0.2 - - + -
68F SER* 3.7 16.8 - - - +
102F ILE* 3.5 32.1 - - + -
103F THR 3.3 9.2 - - - +
104F ALA* 3.8 9.9 - - + -
116F THR* 5.0 0.9 - - - +
117F SER* 1.3 82.1 + - - +
119F ASP* 1.3 68.3 + - - +
120F LEU* 4.1 10.6 - - + +
130F ALA 4.2 0.2 - - - +
131F GLN* 3.3 4.9 - - - +
132F GLY 2.8 32.2 + - - +
134F HIS* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F VAL 3.6 1.4 - - - +
102F ILE* 3.5 2.6 - - - -
103F THR* 2.9 43.0 + - - +
105F HIS* 6.5 0.9 - - - -
117F SER* 4.7 2.8 + - - -
118F VAL* 1.3 73.8 - - - +
120F LEU* 1.3 63.2 + - - +
121F THR* 4.8 5.9 - - - +
128F LEU* 3.9 19.3 - - + +
130F ALA 3.6 3.6 - - - -
131F GLN* 2.9 34.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F LEU* 4.1 9.6 - - + -
60F THR* 4.0 24.7 - - + +
63F LEU* 4.1 14.4 - - + -
64F VAL* 4.0 26.7 - - + -
100F ILE* 4.0 24.7 - - + -
101F VAL 3.2 4.9 - - - +
102F ILE* 3.9 14.1 - - + -
118F VAL* 4.1 9.2 - - + +
119F ASP* 1.3 75.3 - - - +
121F THR* 1.3 58.7 + - - +
128F LEU* 3.5 4.7 - - - +
129F ILE* 2.7 44.5 + - + -
130F ALA* 2.9 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ILE* 3.3 5.7 - - - +
101F VAL* 2.8 59.9 + - + +
103F THR* 5.4 2.5 - - - +
119F ASP* 4.8 6.7 - - - +
120F LEU* 1.3 77.5 + - - +
122F ASN* 1.3 64.3 + - - +
123F LYS* 5.3 0.2 - - - -
126F GLY* 3.5 20.1 + - - +
127F LYS 3.3 7.2 + - - -
128F LEU* 4.1 12.3 - - - +
129F ILE* 3.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F GLU* 3.5 37.6 + - - +
99F ASP 3.8 6.4 + - - +
100F ILE* 6.1 0.2 - - - +
121F THR* 1.3 73.6 - - - +
123F LYS* 1.3 58.2 + - - +
124F ALA* 2.7 35.5 + - - +
125F THR* 3.0 31.5 + - - +
126F GLY* 2.8 31.0 + - - -
127F LYS* 2.8 15.6 + - + +
129F ILE* 3.7 13.3 - - + +
----------------------------------------------------------
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