Contacts of the helix formed by residues 107 - 117 (chain E) in PDB entry 3K75
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 GLY 107 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LYS* 4.8 13.3 - - - +
101E THR* 4.9 1.6 - - - -
105E GLY 3.8 4.6 + - - -
106E ILE* 1.3 77.1 - - - +
108E PRO* 1.3 71.6 - - - +
109E SER* 3.3 2.2 - - - -
110E ALA* 3.2 10.6 + - - +
111E ALA* 2.8 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ILE* 4.7 6.2 - - + +
101E THR* 4.5 12.9 - - + +
107E GLY* 1.3 82.6 - - - +
109E SER* 1.3 69.0 + - - +
111E ALA* 3.0 18.0 + - + +
112E ARG* 3.1 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D SER* 4.9 10.5 + - - -
107E GLY* 3.3 0.4 - - - -
108E PRO* 1.3 81.8 - - - +
110E ALA* 1.3 62.6 + - - +
112E ARG* 3.3 12.3 + - - +
113E LYS* 3.3 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ILE* 4.2 6.5 - - + -
107E GLY* 3.2 23.3 + - - +
109E SER* 1.3 79.2 - - - +
111E ALA* 1.3 63.0 + - - +
113E LYS* 3.5 12.8 + - - +
114E LEU* 3.1 28.8 + - + +
136E GLN* 4.1 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ILE* 3.7 28.5 - - + +
100E LEU* 3.7 11.3 - - + +
101E THR* 3.9 12.8 - - - +
106E ILE* 3.8 14.6 - - + +
107E GLY 2.8 13.4 + - - +
108E PRO 3.0 9.6 + - - +
110E ALA* 1.3 73.6 - - - +
112E ARG* 1.3 68.6 + - - +
114E LEU* 3.3 5.0 + - - +
115E VAL* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E THR* 5.7 1.8 - - + -
97E ILE* 3.4 27.8 - - + +
108E PRO* 3.1 15.7 + - - +
109E SER* 3.6 11.4 - - - +
110E ALA 3.3 0.2 - - - -
111E ALA* 1.3 76.3 - - - +
113E LYS* 1.3 56.4 + - + +
115E VAL* 2.5 34.6 + - - +
116E ASP* 3.2 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D GLY 5.0 9.9 + - - -
107D GLY* 5.4 7.9 - - - +
133D ASN* 6.2 1.8 - - - +
135D HIS* 6.1 6.5 - - + -
229D SER* 5.0 0.2 + - - -
109E SER* 3.3 30.7 + - - +
110E ALA* 3.7 10.9 - - - +
112E ARG* 1.3 78.8 - - + +
114E LEU* 1.3 62.4 + - + +
116E ASP* 3.6 9.3 + - - +
117E GLU* 3.2 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E LEU* 3.4 28.9 - - + -
106E ILE* 3.8 30.1 - - + -
110E ALA* 3.1 18.8 + - + +
111E ALA 3.5 2.5 - - - +
112E ARG 3.1 0.6 - - - -
113E LYS* 1.3 75.9 - - - +
115E VAL* 1.3 62.5 + - - +
117E GLU* 3.3 14.4 + - - +
119E ILE* 3.0 53.6 + - + +
125E LEU* 4.0 11.4 - - + -
131E LYS* 4.7 10.5 - - + +
132E LEU* 4.1 20.4 - - + -
136E GLN* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D GLU* 4.3 1.8 - - - +
93E THR* 3.4 26.9 - - + +
96E SER* 4.6 13.5 - - - +
97E ILE* 3.3 29.6 - - + -
100E LEU* 4.3 6.7 - - + -
111E ALA 3.1 6.2 + - - +
112E ARG 2.5 15.1 + - - +
114E LEU* 1.3 67.9 - - - +
116E ASP* 1.3 73.7 + - - +
118E GLY* 2.8 15.9 + - - -
119E ILE 3.3 16.8 + - - +
120E LYS* 4.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 5.6 1.6 - - - +
231D GLY* 3.3 11.6 - - - -
232D GLU* 3.2 40.6 + - - +
233D THR* 5.2 8.8 + - - +
112E ARG* 3.2 14.3 + - - +
113E LYS* 3.9 10.1 - - - +
115E VAL* 1.3 83.3 - - - +
117E GLU* 1.3 59.2 + - + +
118E GLY 2.9 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D HIS* 5.8 3.7 - - - +
228D LEU 4.0 3.7 - - - +
229D SER* 3.2 41.1 + - - +
230D LYS* 3.5 24.6 + - + +
113E LYS* 3.2 28.1 + - - +
114E LEU* 3.7 15.2 + - - +
115E VAL 3.0 1.8 + - - -
116E ASP* 1.3 74.2 - - + +
118E GLY* 1.3 59.1 + - - +
119E ILE* 3.3 14.7 + - + +
128E ASN* 5.1 2.3 - - - +
131E LYS* 3.6 34.4 + - + +
----------------------------------------------------------
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