Contacts of the helix formed by residues 86 - 97 (chain F) in PDB entry 3IFS
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 TYR 86 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E THR* 4.0 16.8 - - + +
79F VAL* 5.7 0.2 - - - -
81F GLY 3.7 14.6 - - - +
82F ILE* 3.8 4.9 - - - -
83F GLY 2.9 12.0 + - - +
84F GLY 3.2 1.2 + - - -
85F SER* 1.3 80.9 - - - +
87F LEU* 1.3 92.7 + - + +
88F GLY 3.5 1.7 + - - -
89F ALA* 3.6 6.7 + - - +
90F ARG* 3.0 53.7 + - - +
116F PHE* 3.5 46.5 - + + -
119F GLN* 3.7 35.2 + - + +
280F TYR* 3.3 14.8 + + - -
----------------------------------------------------------
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
----------------------------------------------------------
309E THR* 5.8 2.0 - - + -
310E ASP* 5.9 3.1 - - - +
313E SER* 4.1 12.8 - - - +
83F GLY* 3.0 15.7 + - - +
84F GLY* 5.5 0.7 - - - -
86F TYR* 1.3 100.7 - - + +
88F GLY* 1.3 61.2 + - - +
90F ARG* 4.1 2.8 - - - +
91F ALA* 2.9 32.1 + - - +
280F TYR* 4.1 13.4 - - + +
283F GLU* 3.6 44.6 - - + +
284F TRP* 4.1 13.6 - - + +
287F GLN* 3.4 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLY* 4.4 9.4 + - - -
86F TYR 3.5 0.6 - - - -
87F LEU* 1.3 77.3 - - - +
89F ALA* 1.3 62.0 + - - +
91F ALA* 3.5 3.5 - - - +
92F ALA* 3.1 23.6 + - - +
211F VAL* 3.6 29.1 - - - +
284F TRP* 3.6 20.0 - - - -
394F PHE* 4.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F VAL* 5.7 1.3 - - + -
84F GLY 5.6 0.4 + - - -
85F SER 5.6 3.1 - - - +
86F TYR* 3.6 9.5 + - - +
87F LEU 3.4 0.4 - - - -
88F GLY* 1.3 74.2 - - - +
90F ARG* 1.3 58.2 + - - +
92F ALA* 3.3 1.9 + - - +
93F ILE* 2.9 37.1 + - + +
116F PHE* 4.4 8.5 - - + -
143F ILE* 6.1 0.2 - - + -
211F VAL* 4.2 2.0 - - - +
215F VAL* 4.5 3.5 - - + +
216F GLY* 4.3 12.6 - - - +
219F PRO* 4.0 32.1 - - + -
220F ILE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F TYR* 3.0 44.5 + - + +
87F LEU 4.1 1.8 - - - +
89F ALA* 1.3 80.7 - - - +
91F ALA* 1.3 62.7 + - - +
93F ILE* 4.5 2.2 - - + -
94F GLU* 2.8 51.7 + - + +
116F PHE* 3.7 36.8 - - + +
119F GLN* 4.6 7.3 - - - +
125F TYR* 5.2 3.4 + - - -
280F TYR* 3.5 43.8 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
87F LEU 2.9 20.0 + - - +
88F GLY* 3.5 6.1 - - - +
90F ARG* 1.3 76.7 - - - +
92F ALA* 1.3 56.5 + - - +
94F GLU* 4.1 0.7 - - - +
95F MSE 3.0 32.8 + - - +
277F ALA 4.7 1.9 - - - +
280F TYR* 3.7 16.0 - - - +
281F PHE* 3.6 35.7 + - + +
284F TRP* 4.3 7.2 - - + -
394F PHE* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLY 3.1 6.5 + - - +
89F ALA 3.7 0.2 - - - +
91F ALA* 1.3 80.2 - - - +
93F ILE* 1.3 63.5 + - - +
95F MSE 3.3 0.6 + - - -
96F LEU* 3.1 31.9 + - + +
220F ILE* 3.4 37.0 - - + -
225F LEU* 3.9 2.2 - - - +
230F MSE 4.5 5.4 - - + -
394F PHE* 3.5 32.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ALA 2.9 23.8 + - - +
90F ARG* 4.1 4.5 - - - +
92F ALA* 1.3 75.4 - - - +
94F GLU* 1.3 63.8 + - + +
97F ASN* 3.1 46.0 + - - +
101F TYR* 4.9 11.8 - - + +
114F VAL* 3.9 33.0 - - + +
116F PHE* 4.3 8.3 - - + -
219F PRO* 3.7 31.6 - - + +
220F ILE* 4.2 9.6 - - + +
223F SER* 3.7 20.2 - - - +
225F LEU* 4.4 1.3 - - + -
----------------------------------------------------------
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 ARG* 2.8 58.9 + - + +
91F ALA 4.3 1.1 - - - +
93F ILE* 1.3 80.7 - - + +
95F MSE 1.3 65.7 + - - +
96F LEU 3.5 0.3 + - - -
97F ASN* 3.7 12.4 - - - +
98F HIS 5.1 2.3 - - - +
99F SER* 5.7 1.6 - - - -
276F PRO 5.5 1.7 - - - +
277F ALA* 3.6 24.6 - - - +
279F GLN* 5.4 3.3 - - - +
280F TYR* 3.4 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ALA 3.0 16.3 + - - +
92F ALA 3.9 2.9 - - - +
94F GLU* 1.3 78.9 - - - +
96F LEU* 1.3 73.8 + - + +
97F ASN 3.7 2.0 - - - +
277F ALA* 3.5 18.4 + - - +
278F LEU* 3.1 33.2 - - + -
281F PHE* 3.5 37.2 - - + -
386F ILE* 6.2 0.2 - - - -
389F LEU* 3.9 37.4 - - + +
390F ASN 5.5 0.2 - - - +
394F PHE* 3.8 28.5 - - + -
397F LEU* 4.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ALA 3.1 18.3 + - - +
95F MSE 1.3 101.8 - - + +
97F ASN* 1.3 60.7 + - - +
225F LEU* 3.6 34.1 - - + +
230F MSE 4.0 13.7 - - + -
389F LEU 3.7 8.7 - - - +
390F ASN* 3.7 32.8 - - - +
391F GLU* 4.0 26.5 - - + +
394F PHE* 4.1 9.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
128E ASP* 4.9 0.5 - - - +
93F ILE* 3.1 24.3 + - - +
94F GLU 3.7 10.8 - - - +
95F MSE 3.7 1.6 - - - +
96F LEU* 1.3 84.1 + - - +
98F HIS* 1.3 69.4 + - - +
99F SER* 3.5 1.9 + - - -
101F TYR* 3.7 31.6 - - + -
223F SER* 3.1 42.7 + - - -
224F GLY 5.5 0.4 - - - -
225F LEU* 3.7 14.2 - - - +
277F ALA* 5.6 1.0 - - - +
----------------------------------------------------------
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