Contacts of the helix formed by residues 80 - 103 (chain F) in PDB entry 5LF4
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 80 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TRP* 4.0 25.1 - - + -
19E ILE* 4.4 13.2 - - + -
22E ILE* 5.0 12.3 - - + -
120E THR* 5.9 0.7 - - - +
150E SER* 5.7 11.0 - - - +
29F ALA* 4.9 7.7 + - + +
79F GLY* 1.3 70.7 - - - -
81F LEU* 1.3 68.5 + - - +
82F ALA* 4.6 6.7 - - + +
83F ASP* 3.1 40.1 + - + +
84F ALA* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E ASN* 3.6 23.6 - - - +
63F ASN* 3.8 26.5 - - + +
64F LYS 4.0 14.8 - - - +
65F ARG* 4.3 9.6 - - + -
67F PHE* 4.5 1.6 - - + -
77F VAL* 4.1 24.0 - - + -
79F GLY 3.2 7.8 + - - +
80F LEU* 1.3 77.1 - - - +
82F ALA* 1.3 56.7 + - - +
84F ALA* 3.1 3.3 + - + -
85F ARG* 2.9 73.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E GLY 5.3 0.9 - - - +
117E GLN* 3.6 20.4 - - + +
150E SER 3.4 25.8 - - - +
151E ALA* 3.6 25.1 - - + +
152E ASN* 4.2 4.2 - - + +
80F LEU* 3.4 6.4 - - + +
81F LEU* 1.3 77.6 - - - +
83F ASP* 1.3 63.5 + - - +
85F ARG* 3.5 12.9 + - - +
86F SER* 3.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TRP* 4.2 14.2 - - - -
117E GLN* 3.0 27.9 + - - +
120E THR* 4.5 5.0 + - - -
121E GLN* 4.3 15.3 + - - +
80F LEU* 3.1 38.1 + - + +
82F ALA* 1.3 78.2 - - - +
84F ALA* 1.3 63.8 + - - +
86F SER* 3.3 3.9 + - - -
87F LEU* 3.1 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 5.0 1.1 - - + -
75F MET* 3.6 6.3 - - - +
77F VAL* 3.6 41.5 - - + +
78F ALA 5.4 5.2 - - - +
79F GLY 5.9 0.2 - - - -
80F LEU 3.0 13.2 + - - +
81F LEU* 3.1 11.4 + - + +
83F ASP* 1.3 75.5 - - - +
85F ARG* 1.3 58.2 + - - +
87F LEU* 3.1 13.0 + - - +
88F ALA* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E GLY* 6.2 2.9 - - - -
151E ALA 4.4 2.2 + - - -
152E ASN* 2.9 35.2 + - - +
153E TYR* 3.5 56.9 + - - -
63F ASN* 3.9 13.7 - - - +
64F LYS 5.0 2.4 + - - +
67F PHE* 3.9 26.8 - - + -
81F LEU* 2.9 51.4 + - + +
82F ALA* 3.8 7.3 - - - +
83F ASP 3.3 0.2 - - - -
84F ALA* 1.3 72.6 - - - +
86F SER* 1.3 64.5 + - - +
88F ALA* 3.3 10.2 + - - +
89F ASP* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E SER* 6.2 4.7 - - - +
117E GLN* 3.9 26.7 + - - -
121E GLN* 4.9 2.8 + - - -
82F ALA 3.2 12.0 + - - -
83F ASP 3.5 8.6 + - - -
85F ARG* 1.3 78.6 - - - +
87F LEU* 1.3 61.3 + - - +
89F ASP* 3.2 11.1 + - - +
90F ILE* 3.0 34.1 + - - +
118F TYR* 5.5 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F MET* 3.9 13.4 - - + +
83F ASP* 3.1 19.2 + - + +
84F ALA* 3.1 12.6 + - - +
86F SER* 1.3 78.8 + - - +
88F ALA* 1.3 58.4 + - - +
90F ILE* 3.3 4.5 + - + +
91F ALA* 2.9 29.3 + - - +
115F VAL* 4.6 12.9 - - + +
118F TYR* 4.2 25.6 - - + -
119F VAL* 4.0 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 4.1 25.4 - - + -
69F VAL* 4.0 7.0 - - + +
75F MET* 3.5 22.1 - - + +
84F ALA 2.9 13.5 + - - +
85F ARG* 3.5 12.3 - - - +
87F LEU* 1.3 74.0 - - - +
89F ASP* 1.3 60.6 + - - +
91F ALA* 3.4 2.8 + - - +
92F ARG* 2.9 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E SER* 4.3 19.6 + - - -
85F ARG* 3.0 16.7 + - - +
86F SER* 3.5 11.2 - - - +
87F LEU 3.2 0.2 - - - -
88F ALA* 1.3 73.1 - - - +
90F ILE* 1.3 61.5 + - + +
92F ARG* 3.5 30.4 + - - +
93F GLU* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F SER* 3.0 23.4 + - - +
87F LEU* 3.3 11.2 + - + +
89F ASP* 1.3 72.1 - - + +
91F ALA* 1.3 60.8 + - - +
93F GLU* 3.2 17.6 + - - +
94F GLU* 2.8 34.2 + - + +
115F VAL* 4.6 14.4 - - + -
118F TYR* 3.5 64.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F VAL* 4.0 25.6 - - + -
75F MET* 4.7 5.2 - - - -
87F LEU 2.9 17.1 + - - +
88F ALA* 3.6 4.5 - - - +
90F ILE* 1.3 75.6 - - - +
92F ARG* 1.3 63.4 + - - +
94F GLU* 3.2 3.3 + - - +
95F ALA* 3.0 21.0 + - - +
111F LEU* 3.6 12.2 - - + +
115F VAL* 3.7 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 4.2 20.2 - - - +
68F ASN* 3.0 28.7 + - - +
69F VAL* 3.5 27.7 - - - +
88F ALA* 2.9 30.8 + - - +
89F ASP* 3.5 27.2 + - - +
90F ILE 3.3 0.4 - - - -
91F ALA* 1.3 77.1 - - - +
93F GLU* 1.3 57.7 + - - +
95F ALA* 3.2 2.6 + - - +
96F SER* 2.9 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ASP 2.9 17.3 + - - +
90F ILE* 3.6 19.3 - - - +
92F ARG* 1.3 76.6 - - - +
94F GLU* 1.3 57.5 + - - +
96F SER* 3.4 6.0 + - - -
97F ASN* 2.9 55.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ILE* 2.8 22.4 + - + +
91F ALA* 3.5 6.1 - - - +
93F GLU* 1.3 78.1 - - - +
95F ALA* 1.3 56.7 + - - +
97F ASN* 3.9 10.3 + - - +
98F PHE* 3.0 31.5 + - - +
106F ILE* 4.4 5.2 - - + +
110F HIS* 5.4 0.5 + - - -
111F LEU* 4.0 14.1 - - + -
114F ARG* 2.5 66.6 + - + +
115F VAL* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F VAL 4.1 3.4 - - - +
70F ASP* 3.3 37.9 - - + +
91F ALA 3.0 15.9 + - - +
92F ARG 3.7 3.8 - - - +
94F GLU* 1.3 75.6 - - - +
96F SER* 1.3 61.5 + - - +
98F PHE* 3.5 3.2 + - - +
99F ARG* 3.1 25.2 + - - +
106F ILE* 3.8 24.2 + - + +
111F LEU* 4.3 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ARG 2.9 16.7 + - - -
93F GLU* 3.6 8.3 - - - -
95F ALA* 1.3 77.2 - - - +
97F ASN* 1.3 65.5 + - - +
99F ARG* 3.3 15.6 + - - +
100F SER* 3.1 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F GLU* 2.9 48.9 + - - +
94F GLU* 4.0 10.4 + - - +
96F SER* 1.3 72.5 + - - +
98F PHE* 1.3 59.8 + - - +
100F SER* 3.3 7.1 + - - -
101F ASN* 2.9 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU* 3.0 20.8 + - - +
95F ALA 3.6 4.7 - - - +
97F ASN* 1.3 77.0 - - - +
99F ARG* 1.3 56.9 + - - +
101F ASN* 4.9 0.9 - - - +
102F PHE* 2.9 58.8 + + + +
104F TYR* 3.3 61.9 - + - -
106F ILE* 3.5 27.4 - - + -
107F PRO* 3.7 8.5 - - + -
110F HIS* 3.5 36.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ASP* 3.0 39.7 + - - -
71F ARG* 3.7 23.2 - - - +
95F ALA 3.1 14.0 + - - +
96F SER* 3.3 13.9 + - - +
98F PHE* 1.3 76.0 - - - +
100F SER* 1.3 58.4 + - - +
103F GLY* 2.8 31.2 + - - -
104F TYR* 3.6 21.3 - - - +
105F ASN* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F SER* 3.1 17.0 + - - -
97F ASN* 3.6 11.8 - - - -
98F PHE 3.3 0.2 - - - -
99F ARG* 1.3 78.5 - - - +
101F ASN* 1.3 65.4 + - - +
103F GLY* 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ASN* 2.9 31.7 + - - +
98F PHE* 4.9 0.6 - - - +
100F SER* 1.3 83.2 - - - +
102F PHE* 1.3 85.2 - - + +
103F GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F PHE* 2.9 49.5 + + + +
101F ASN* 1.3 93.5 - - + +
103F GLY* 1.3 61.2 + - - +
104F TYR* 3.5 26.7 + + + -
110F HIS* 5.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F PHE 3.8 0.2 + - - -
99F ARG* 2.8 24.8 + - - -
100F SER 4.5 1.1 - - - -
101F ASN 3.7 1.2 - - - -
102F PHE* 1.3 76.0 - - - +
104F TYR* 1.3 63.1 + - - +
----------------------------------------------------------
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