Contacts of the helix formed by residues 81 - 90 (chain B) in PDB entry 4F2N
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 THR 81 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 3.4 36.5 + - + +
26B LEU 5.0 1.8 - - - -
27B PRO* 3.7 14.1 - - + +
29B LEU 3.4 8.5 - - - +
30B ARG* 3.5 32.8 - - - +
80B LYS* 1.3 76.5 - - - +
82B ILE* 1.3 64.1 + - - +
83B GLU* 3.8 6.3 - - - -
84B GLU* 3.1 39.7 + - - +
85B ILE* 3.5 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.9 35.6 + - + +
30B ARG 3.5 23.3 - - - +
31B TYR* 3.8 12.8 - - + +
33B ALA* 4.4 1.6 - - + -
70B LEU* 4.0 14.8 - - + -
81B THR* 1.3 71.8 - - - +
83B GLU* 1.3 58.5 + - - +
85B ILE* 2.9 24.4 + - + +
86B ILE* 3.1 10.8 + - + +
102B ALA* 3.4 35.7 - - + +
105B HIS* 3.7 28.7 - - + -
106B PHE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR 4.9 0.5 - - - +
24B HIS* 3.5 18.7 - - + +
25B THR* 2.8 26.7 + - - -
26B LEU* 2.7 37.1 + - - +
29B LEU 4.8 0.4 + - - -
81B THR* 3.2 8.4 - - - +
82B ILE* 1.3 78.7 - - + +
84B GLU* 1.3 57.2 + - - +
86B ILE* 3.3 10.0 + - + +
87B LEU* 2.9 39.2 + - + +
106B PHE* 3.5 30.2 - - + -
180B LEU* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 5.0 7.7 + - - +
77B TYR* 4.7 7.6 - - + -
80B LYS* 3.3 46.8 + - + +
81B THR* 3.1 28.2 + - - +
83B GLU* 1.3 78.1 - - - +
85B ILE* 1.3 62.0 + - + +
87B LEU* 3.4 7.2 + - - +
88B ALA* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 3.7 36.1 - - + -
70B LEU* 4.5 9.2 - - + -
74B GLY* 5.2 0.7 - - - -
77B TYR* 3.5 41.5 - - + -
81B THR 3.9 8.1 - - - +
82B ILE* 2.9 19.0 + - + +
84B GLU* 1.3 77.2 - - - +
86B ILE* 1.3 55.7 + - - +
88B ALA 3.2 1.6 + - - -
89B THR* 2.8 38.2 + - + +
98B MET* 3.9 28.0 - - + -
102B ALA* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 3.1 12.8 + - + +
83B GLU* 3.5 15.0 - - + +
85B ILE* 1.3 73.6 - - - +
87B LEU* 1.3 59.2 + - - +
89B THR* 3.2 6.7 + - - -
90B THR* 2.9 33.6 + - - -
99B PHE* 3.8 14.7 - - + +
102B ALA* 3.9 6.5 - - + +
103B ALA* 3.7 28.3 - - + +
106B PHE* 3.6 39.5 - - + -
178B CYS* 4.6 7.0 - - - -
180B LEU* 4.0 10.5 - - + -
181B THR* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B CYS* 6.1 5.4 - - - -
24B HIS* 6.0 4.0 - - + +
83B GLU* 2.9 25.0 + - + +
84B GLU* 4.0 6.7 - - - +
86B ILE* 1.3 77.1 - - - +
88B ALA* 1.3 59.9 + - - +
90B THR* 3.5 19.3 - - + +
180B LEU* 3.7 39.5 - - + +
181B THR* 4.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 3.5 27.4 - - + +
84B GLU* 3.0 20.2 + - + +
85B ILE 3.8 2.5 - - - +
87B LEU* 1.3 76.1 - - - +
89B THR* 1.3 61.3 + - - +
90B THR 5.2 0.4 - - - -
92B ILE* 3.6 20.5 - - - +
95B SER* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 4.8 5.4 - - - +
85B ILE* 2.8 25.2 + - + +
86B ILE* 3.4 5.2 + - - -
88B ALA* 1.3 82.7 - - - +
90B THR* 1.3 65.5 + - - +
91B GLY 3.4 0.5 + - - -
92B ILE* 3.2 23.1 + - - +
95B SER* 3.8 27.4 - - - +
98B MET* 3.8 31.6 - - + -
99B PHE* 3.4 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE 2.9 14.6 + - - +
87B LEU* 3.5 24.4 - - + +
88B ALA 5.2 0.2 - - - -
89B THR* 1.3 77.3 + - - +
91B GLY* 1.3 62.4 + - - +
92B ILE* 3.1 12.5 + - - +
99B PHE* 3.7 22.2 - - - -
181B THR* 3.5 32.5 + - + +
----------------------------------------------------------
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