Contacts of the helix formed by residues 106 - 116 (chain H) in PDB entry 6O81
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 106 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H ARG* 3.3 18.1 + - + +
103H ARG* 3.5 33.7 - - - +
104H ILE 3.2 0.8 - - - -
105H SER* 1.3 76.6 - - - +
107H SER* 1.3 64.7 + - - +
108H ARG 3.4 2.7 - - - -
109H ASN* 3.5 23.0 + - + +
110H LYS* 3.4 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ARG 3.8 7.0 + - - -
104H ILE* 3.1 24.8 + - - +
105H SER 3.4 0.2 - - - -
106H LEU* 1.3 78.0 - - - +
108H ARG* 1.3 61.6 + - - +
110H LYS* 3.1 8.7 + - - +
111H ILE* 2.9 29.7 + - - +
231H GLU* 3.6 25.2 - - - +
232H SER 5.2 0.2 + - - -
233H PHE* 5.7 0.4 - - - -
287H ASP* 3.4 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ASP 4.9 8.2 + - - -
20H MET* 5.0 0.8 - - - +
21H ALA* 3.4 36.2 - - - +
24H VAL* 5.7 1.6 - - - +
104H ILE 5.5 2.2 - - - +
105H SER 4.7 7.2 + - - +
106H LEU 3.4 0.8 - - - -
107H SER* 1.3 74.0 - - - +
109H ASN* 1.3 61.4 + - - +
111H ILE* 3.4 9.2 + - - +
112H ALA* 2.9 28.1 + - - +
132H ARG* 3.4 33.0 - - - +
133H VAL* 3.4 29.7 - - - +
136H ARG* 3.4 42.0 - - + +
231H GLU* 3.7 20.5 + - + +
233H PHE* 5.0 3.6 - - - -
234H LYS* 6.0 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H SER 5.0 2.4 + - - +
106H LEU* 3.7 25.6 + - - +
107H SER 3.3 0.6 - - - -
108H ARG* 1.3 75.3 - - - +
110H LYS* 1.3 59.0 + - - +
112H ALA* 3.6 6.9 - - - +
113H ASP* 2.9 38.4 + - - +
136H ARG* 3.2 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU* 3.4 12.0 + - + +
107H SER* 3.1 14.0 + - - +
109H ASN* 1.3 76.3 - - - +
111H ILE* 1.3 55.9 + - - +
113H ASP* 3.5 9.8 - - - +
114H LEU* 2.8 43.1 + - + +
287H ASP* 4.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H SER* 2.9 19.6 + - - +
108H ARG* 3.7 9.6 - - - +
109H ASN 3.4 0.2 - - - -
110H LYS* 1.3 75.3 - - - +
112H ALA* 1.3 58.1 + - - +
114H LEU* 4.5 2.9 - - + -
115H CYS* 2.9 38.9 + - + +
133H VAL* 3.7 28.3 - - + +
136H ARG* 6.1 1.1 - - + -
137H VAL* 4.0 8.0 - - + +
229H VAL* 4.2 18.2 - - + -
230H ALA 4.6 3.6 - - - +
231H GLU* 4.5 10.8 - - + -
285H PHE* 3.4 27.1 - - + +
286H THR* 3.6 25.4 - - - +
287H ASP 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H ARG 2.9 17.7 + - - +
109H ASN* 3.6 8.1 - - - +
110H LYS 3.2 0.2 - - - -
111H ILE* 1.3 78.4 - - - +
113H ASP* 1.3 59.1 + - + +
116H HIS* 2.7 30.8 + - - +
136H ARG* 3.7 22.9 - - + +
137H VAL* 4.5 8.1 - - - +
140H ALA* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H ASN* 2.9 26.3 + - - +
110H LYS* 3.5 10.0 - - - +
112H ALA* 1.3 76.6 - - + +
114H LEU* 1.3 64.2 + - - +
116H HIS* 3.5 22.7 + - + -
117H THR* 4.4 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D PHE* 5.5 7.0 - - + -
110H LYS* 2.8 24.6 + - + +
111H ILE* 4.2 3.4 - - + +
113H ASP* 1.3 83.7 - - - +
115H CYS* 1.3 61.2 + - + +
116H HIS* 3.7 0.9 - - - -
117H THR* 4.0 13.5 + - - +
118H PHE* 4.5 2.4 - - - -
285H PHE* 5.6 2.5 - - + -
286H THR 3.4 26.7 - - - +
287H ASP* 4.9 4.7 - - - +
289H GLY* 3.7 21.8 - - - +
290H VAL* 3.9 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H ILE* 2.9 20.4 + - + +
114H LEU* 1.3 74.8 - - + +
116H HIS* 1.3 58.7 + - - +
117H THR 3.1 10.5 + - - -
118H PHE* 3.2 20.5 + - - +
119H ILE* 4.0 6.3 - - - +
137H VAL* 3.7 18.8 - - + -
194H ILE* 5.6 7.4 - - - -
229H VAL* 3.7 18.8 - - - -
285H PHE* 3.7 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H ALA 2.7 27.1 + - - +
113H ASP* 3.5 27.6 - - + -
115H CYS* 1.3 75.6 - - - +
117H THR* 1.3 65.1 + - + +
118H PHE 3.2 1.4 + - - -
119H ILE* 3.6 19.2 + - - +
137H VAL* 3.7 10.8 - - + +
140H ALA* 3.6 20.4 + - + -
141H ALA* 4.0 20.5 - - - +
144H ALA* 4.1 19.0 - - + +
146H LYS* 2.6 33.4 + - - +
----------------------------------------------------------
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