Contacts of the helix formed by residues 83 - 95 (chain A) in PDB entry 1YOH
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 GLU 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 4.5 1.9 - - - +
81A HIS* 3.3 33.0 + - - +
82A HIS* 1.3 81.9 + - - +
84A ALA* 1.3 69.5 + - + +
86A LEU* 4.1 2.4 - - - +
87A LYS* 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A HIS 3.3 0.4 - - - -
83A GLU* 1.3 84.3 - - + +
85A GLU* 1.3 69.3 + - - +
87A LYS* 4.6 2.0 - - - +
88A PRO* 3.2 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 4.7 19.5 - - + +
75A ILE* 3.9 21.2 - - + +
78A LYS* 2.6 42.7 + - - +
81A HIS 4.1 2.3 - - - +
82A HIS* 3.2 23.1 - - + +
83A GLU 4.0 0.2 + - - -
84A ALA* 1.3 84.0 + - - +
86A LEU* 1.3 67.7 + - - +
88A PRO* 3.2 11.7 - - - +
89A LEU* 3.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 4.5 8.0 - - + +
82A HIS* 2.8 44.3 + - + +
83A GLU* 4.1 3.6 - - - +
85A GLU* 1.3 77.9 - - - +
87A LYS* 1.3 63.4 + - - +
89A LEU* 3.1 8.8 + - + +
90A ALA* 3.0 22.1 + - - +
138A PHE* 3.7 35.4 - - + +
141A ASP* 3.6 30.3 - - + +
142A ILE* 3.6 27.6 - - + -
145A LYS* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU 3.2 16.4 + - - +
84A ALA* 4.6 2.2 - - - +
86A LEU* 1.3 77.8 - - - +
88A PRO* 1.3 70.0 - - + +
90A ALA* 3.5 5.8 + - - +
91A GLN* 3.1 60.5 + - + +
145A LYS* 5.0 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 3.2 23.3 - - - +
85A GLU 3.2 11.4 - - - +
87A LYS* 1.3 96.1 - - + +
89A LEU* 1.3 56.2 + - - +
91A GLN* 3.5 12.4 + - - +
92A SER* 3.0 31.6 + - - -
154A COH 4.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 5.3 4.0 - - + -
75A ILE* 3.8 28.9 - - + -
85A GLU 4.0 7.9 - - - +
86A LEU* 3.1 10.0 + - - +
88A PRO* 1.3 79.1 - - - +
90A ALA* 1.3 59.4 + - - +
92A SER* 3.2 5.1 + - - -
93A HIS* 2.9 52.9 + - + +
104A LEU* 5.7 2.9 - - + -
138A PHE* 3.9 16.6 - - + -
142A ILE* 3.4 21.1 - - + -
154A COH 3.9 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.0 14.1 + - + +
87A LYS 4.0 3.4 - - - +
89A LEU* 1.3 76.7 - - - +
91A GLN* 1.3 58.3 + - + +
94A ALA* 2.9 35.2 + - - +
142A ILE* 3.6 24.9 - - + +
145A LYS* 3.6 33.0 - - + -
146A TYR* 3.7 11.1 - - + -
149A LEU* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.1 53.0 + - + +
88A PRO* 3.8 10.0 - - - +
90A ALA* 1.3 77.6 - - + +
92A SER* 1.3 56.9 + - - +
95A THR* 2.9 39.5 + - + +
145A LYS* 6.1 2.0 - - + -
149A LEU* 4.2 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO 3.0 13.4 + - - -
89A LEU 3.2 3.8 + - - -
91A GLN* 1.3 77.1 - - - +
93A HIS* 1.3 70.3 + - - +
95A THR* 4.7 0.4 - - - -
96A LYS* 2.9 39.8 + - - +
97A HIS* 2.9 21.3 + - - -
154A COH 2.8 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 2.9 28.4 + - + +
90A ALA 4.4 0.4 - - - +
92A SER* 1.3 98.6 + - - +
94A ALA* 1.3 58.3 + - - +
97A HIS* 3.7 8.7 - + - -
98A LYS 3.1 5.9 + - - -
99A ILE* 2.8 38.3 + - + -
104A LEU* 5.1 3.8 - - + -
146A TYR* 3.5 16.9 + - + +
154A COH 2.1 106.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA 2.9 19.6 + - - +
91A GLN 4.2 1.1 - - - +
93A HIS* 1.3 80.9 - - - +
95A THR* 1.3 56.1 + - + +
98A LYS* 2.5 31.2 + - - -
99A ILE 4.8 0.7 - - - +
146A TYR* 3.6 32.4 + - + -
149A LEU* 4.7 6.1 - - + -
151A TYR* 3.1 31.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 2.9 21.5 + - + +
92A SER* 4.7 0.3 - - - -
94A ALA* 1.3 78.4 - - - +
96A LYS* 1.3 64.2 + - - +
98A LYS* 3.3 19.9 - - - +
149A LEU* 4.1 22.9 - - + -
151A TYR* 3.6 31.5 + - + +
----------------------------------------------------------
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