Contacts of the helix formed by residues 102 - 112 (chain E) in PDB entry 3J41
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 ALA 102 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ILE 3.7 1.0 + - - -
101E SER* 1.3 71.4 + - - +
103E ALA* 1.3 55.5 + - - +
105E LEU* 3.6 6.1 + - - +
106E ARG* 3.1 27.7 + - - +
118E ASP* 5.5 3.3 - - + +
121E VAL* 4.7 9.8 - - + +
122E ASP* 6.1 1.8 - - - +
125E ILE* 3.6 30.1 - - + +
134E GLY* 3.2 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E SER* 3.1 14.0 + - - +
102E ALA* 1.3 79.4 - - - +
104E GLU* 1.3 56.2 + - + +
106E ARG* 3.5 6.6 + - - +
107E HIS* 2.9 49.7 + - + +
118E ASP* 5.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E PHE 3.8 17.7 - - - +
93E ASP* 3.0 6.9 - - - +
94E LYS* 3.0 23.5 + - + +
95E ASP* 2.9 14.2 - - - +
99E TYR 3.5 0.3 - - - +
100E ILE* 4.0 6.3 - - + -
101E SER* 2.9 41.7 + - - +
103E ALA* 1.3 67.7 - - + +
105E LEU* 1.3 64.8 + - - +
107E HIS* 3.0 31.4 + - + +
108E VAL* 3.0 15.4 + - - +
135E GLN* 4.8 1.4 - - - +
203E CA 2.6 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 4.2 19.3 - - + -
92E PHE* 3.8 31.2 - - + -
100E ILE* 3.8 25.8 - - + +
101E SER 3.0 16.4 + - - +
102E ALA* 3.6 7.2 - - - +
104E GLU* 1.3 75.0 - - - +
106E ARG* 1.3 61.1 + - - +
108E VAL* 3.3 6.3 - - - +
109E MET* 3.0 34.5 + - - +
121E VAL* 4.4 13.2 - - + -
125E ILE* 3.9 28.5 - - + -
136E VAL* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ALA 3.1 17.9 + - - +
103E ALA* 3.8 6.1 - - - +
105E LEU* 1.3 75.3 - - - +
107E HIS* 1.3 58.1 + - + +
109E MET* 4.0 8.9 - - + +
110E THR* 2.8 46.0 + - - +
115E LYS* 4.2 12.7 - - - +
116E LEU* 2.8 30.9 + - + +
117E THR* 3.6 14.4 + - - +
118E ASP* 2.7 58.7 + - + +
121E VAL* 5.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E PHE 5.5 0.2 - - - +
94E LYS* 4.9 18.4 - - + +
103E ALA* 2.9 48.4 + - + +
104E GLU* 3.0 22.3 + - + +
106E ARG* 1.3 73.6 - - + +
108E VAL* 1.3 58.7 + - - +
110E THR* 3.3 3.8 + - - -
111E ASN* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 4.9 0.2 - - + -
240A SER* 6.5 0.4 - - - -
91E VAL* 4.6 9.6 - - + +
92E PHE* 3.8 60.1 - - + +
104E GLU 3.0 14.6 + - - +
105E LEU* 3.3 16.6 - - - +
107E HIS* 1.3 72.8 - - - +
109E MET* 1.3 66.1 + - + +
111E ASN* 3.1 24.0 + - + +
112E LEU* 3.5 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.8 39.7 - - + +
236A ILE* 5.2 3.4 - - + -
237A LEU* 3.8 35.7 - - + +
105E LEU* 3.0 28.2 + - - +
106E ARG* 4.0 5.8 - - + +
108E VAL* 1.3 75.2 - - + +
110E THR* 1.3 62.5 + - - +
112E LEU* 3.1 19.3 + - - +
113E GLY 3.9 0.2 + - - -
114E GLU* 3.3 46.6 - - - +
116E LEU* 5.5 0.4 - - + -
121E VAL* 4.4 19.3 - - + -
124E MET* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ARG* 2.8 37.5 + - - +
107E HIS* 3.9 4.3 - - - -
109E MET* 1.3 74.8 - - - +
111E ASN* 1.3 56.4 + - - +
113E GLY* 2.9 20.9 + - - -
114E GLU 3.6 20.1 + - - +
115E LYS* 4.5 22.5 - - + -
116E LEU 4.8 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E HIS 3.0 13.5 + - - +
108E VAL* 3.2 19.5 - - + +
110E THR* 1.3 75.5 - - - +
112E LEU* 1.3 62.3 + - + +
113E GLY 3.3 0.8 + - - -
111F ASN* 5.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 5.1 11.4 - - + -
240A SER* 3.8 24.7 - - - +
108E VAL* 3.5 23.3 - - + +
109E MET* 3.1 13.3 + - - +
111E ASN* 1.3 81.0 - - + +
113E GLY* 1.3 58.8 + - - +
114E GLU* 3.4 7.2 + - + +
----------------------------------------------------------
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