Contacts of the helix formed by residues 83 - 98 (chain E) in PDB entry 1YFL
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 SER 83 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E LYS 3.4 20.6 - - - -
79E LEU* 3.0 13.7 - - - +
80E SER* 2.6 40.1 + - - -
82E THR* 1.3 72.3 + - - +
84E LYS* 1.3 52.4 + - - +
86E GLU* 3.2 24.2 - - - -
87E PHE* 2.6 34.8 + - - +
109E HIS* 5.2 0.3 - - - -
127E PHE* 3.8 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E THR 2.4 24.5 + - - +
83E SER 1.3 66.2 - - - -
85E GLU* 1.3 63.2 + - + +
86E GLU* 3.7 0.4 + - - -
87E PHE* 2.9 9.0 - - - +
88E LEU* 2.7 52.2 + - + +
127E PHE* 3.7 33.6 - - + -
508H A 3.2 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E LYS* 1.3 83.8 - - + +
86E GLU* 1.3 76.3 + - - +
88E LEU* 2.9 28.4 + - - +
89E LYS* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E TYR* 3.3 25.5 - - - +
78E LYS* 3.5 16.7 - - + +
79E LEU* 3.7 5.5 - - + +
83E SER* 3.2 31.6 - - - -
84E LYS 3.7 0.2 + - - -
85E GLU* 1.3 90.6 + - + +
87E PHE* 1.3 62.3 + - - +
89E LYS* 3.1 9.2 + - - +
90E LEU* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E LEU* 3.7 9.8 - - + +
83E SER 2.6 20.3 + - - +
84E LYS 2.9 9.9 - - - +
86E GLU* 1.3 74.5 - - - +
88E LEU* 1.3 72.3 + - + +
90E LEU* 3.2 5.7 + - + +
91E ARG* 3.1 40.2 + - - +
106E LEU* 4.1 20.9 - - + -
109E HIS* 3.6 32.8 - + + -
110E GLY* 4.1 4.3 - - - -
123E PHE* 4.3 7.0 - + - -
125E THR 3.8 12.6 - - - -
126E PRO* 3.5 18.4 - - + -
127E PHE* 3.1 49.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E LYS* 2.7 35.8 + - + +
85E GLU* 3.3 32.3 - - - +
87E PHE* 1.3 82.8 - - + +
89E LYS* 1.3 60.2 + - - +
91E ARG* 3.3 45.6 + - - +
92E GLU* 3.1 22.3 + - - +
127E PHE* 6.1 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E TYR* 4.2 14.8 - - + -
85E GLU 2.9 12.1 + - - +
86E GLU* 3.1 11.4 + - - +
88E LEU* 1.3 74.1 - - - +
90E LEU* 1.3 66.5 + - - +
92E GLU* 3.0 16.0 + - + +
93E ASP* 2.8 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E VAL* 4.6 0.7 - - + -
77E TYR* 3.5 32.9 - - + +
79E LEU* 3.5 29.4 - - + -
86E GLU 3.0 9.9 + - - +
87E PHE* 3.4 9.9 - - + +
89E LYS* 1.3 77.8 - - - +
91E ARG* 1.3 65.3 + - - +
93E ASP* 3.1 3.7 + - - +
94E TYR* 2.8 23.9 + - - +
102E LEU* 3.5 36.1 - - + -
105E VAL* 3.9 17.0 - - + -
106E LEU* 3.5 29.2 - - + +
109E HIS* 4.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E PHE* 3.1 18.7 + - + +
88E LEU* 3.3 38.1 + - - +
90E LEU* 1.3 81.0 - - - +
92E GLU* 1.3 59.7 + - - +
94E TYR* 3.0 4.0 + - - +
95E ASN* 2.4 36.6 + - - +
106E LEU* 3.6 13.8 - - + +
123E PHE* 3.6 42.3 + - + +
124E THR* 4.1 3.9 + - - +
125E THR 3.0 29.9 + - - -
126E PRO* 4.1 5.3 - - - +
506H G 5.5 0.4 - - - -
507H G 3.1 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D PRO* 3.5 31.5 - - + +
88E LEU 3.1 10.1 + - - +
89E LYS* 3.0 18.1 + - + +
91E ARG* 1.3 79.4 - - - +
93E ASP* 1.3 63.8 + - - +
95E ASN* 3.0 21.6 + - + +
96E LYS* 3.1 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E TYR* 2.7 41.1 + - - +
89E LYS* 2.8 37.1 + - - +
90E LEU 3.4 7.0 - - - +
92E GLU* 1.3 72.0 - - - +
94E TYR* 1.3 65.7 + - - +
96E LYS* 3.0 30.1 + - - +
97E THR* 3.1 24.2 + - + +
102E LEU* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PRO* 4.0 15.1 + - - +
90E LEU 2.8 16.2 + - - +
91E ARG 3.4 7.0 - - - +
93E ASP* 1.3 73.2 - - - +
95E ASN* 1.3 61.6 + - - +
97E THR* 4.0 5.2 - - - -
98E ARG* 2.6 62.9 + - - +
99E ASP 3.2 31.2 - - - -
100E PRO* 4.4 1.4 - - + +
102E LEU* 4.1 12.1 - - + +
103E LEU* 3.4 39.4 - - + +
106E LEU* 3.8 24.7 - - + -
117E ILE* 5.3 2.6 - - + +
121E GLY 4.7 6.3 + - - -
123E PHE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 4.9 2.1 - - - +
91E ARG* 2.4 53.1 + - - +
92E GLU* 3.0 14.7 + - + +
94E TYR* 1.3 80.6 - - - +
96E LYS* 1.3 57.8 + - + +
98E ARG* 2.8 25.9 + - - +
122E ASN* 2.7 32.8 + - - +
123E PHE* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D PRO* 3.9 27.8 - - + +
17D GLU* 4.1 20.6 - - - +
20D SER* 4.7 14.6 - - - +
92E GLU* 3.4 38.6 + - + +
93E ASP* 3.0 25.4 + - - +
95E ASN* 1.3 80.1 - - + +
97E THR* 1.3 68.7 + - + +
98E ARG* 3.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ASP* 3.1 20.9 + - + +
94E TYR* 3.8 4.5 + - - -
96E LYS* 1.3 80.6 - - + +
98E ARG* 1.3 74.0 + - - +
99E ASP* 3.1 22.3 + - - +
102E LEU* 4.3 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PRO* 6.3 0.6 - - - +
94E TYR* 2.6 54.1 + - + +
95E ASN* 2.8 21.2 + - - +
96E LYS 4.2 5.8 - - - +
97E THR* 1.3 75.0 + - - +
99E ASP* 1.3 64.1 + - - +
100E PRO* 3.1 11.8 - - - +
120E LYS 2.7 29.5 + - - -
121E GLY* 3.2 28.5 + - - -
122E ASN* 3.6 12.3 + - - +
----------------------------------------------------------
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