Contacts of the helix formed by residues 98 - 113 (chain E) in PDB entry 3A2C
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 CYS 98 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLN* 3.2 15.8 + - + +
97E ASP* 1.3 82.5 + - - +
99E PRO* 1.3 80.6 - - + +
100E LYS* 3.0 10.5 - - - -
101E ALA* 2.8 17.5 + - - +
102E ARG* 2.7 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E CYS* 1.3 88.9 - - + +
100E LYS* 1.3 58.8 + - + +
102E ARG* 3.3 10.7 + - + +
103E ARG* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E CYS* 3.0 10.0 - - - -
99E PRO* 1.3 80.7 - - + +
101E ALA* 1.3 66.9 + - - +
103E ARG* 3.1 52.0 + - - +
104E GLU* 3.1 23.0 + - - +
209E GLY 4.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E LEU* 3.9 28.2 - - + +
96E GLN 3.4 24.5 - - - +
98E CYS* 2.8 17.3 + - - +
100E LYS* 1.3 78.1 - - - +
102E ARG* 1.3 61.6 + - - +
104E GLU* 3.5 3.9 + - - +
105E VAL* 3.2 27.9 + - - +
134E LEU* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ILE* 3.5 27.4 - - - +
97E ASP* 2.3 41.2 + - - +
98E CYS 2.7 16.0 + - - +
99E PRO* 3.4 12.8 - - + +
101E ALA* 1.3 75.2 - - - +
103E ARG* 1.3 65.4 + - - +
105E VAL* 3.6 4.6 + - - +
106E GLU* 3.2 22.9 + - - +
125E GLU* 2.5 26.9 + - - +
132E LYS* 5.1 0.8 - - - +
134E LEU* 3.4 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E PRO 2.9 14.4 + - - +
100E LYS* 3.1 47.6 + - - +
102E ARG* 1.3 75.4 - - - +
104E GLU* 1.3 65.2 + - - +
106E GLU* 3.0 7.5 + - - +
107E LEU* 2.9 41.8 + - + +
185E ARG* 5.1 3.0 - - - +
209E GLY 4.0 15.2 + - - -
210E PHE* 4.4 6.9 - - - +
211E ALA 3.4 21.1 + - - -
212E LYS* 3.1 33.3 - - - +
213E GLU* 5.8 0.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
93E LYS* 3.2 30.0 + - - +
95E LEU* 3.6 21.6 - - + +
100E LYS 3.1 8.3 + - - +
101E ALA* 3.7 8.8 - - - +
103E ARG* 1.3 81.6 - - - +
105E VAL* 1.3 61.9 + - + +
107E LEU* 3.8 4.4 - - - +
108E HIS* 2.8 34.8 + - + +
136E ILE* 4.4 4.9 - - + +
207E ASP* 5.1 0.3 - - - -
208E PHE* 3.2 38.1 + - + +
209E GLY* 3.1 20.6 + - - +
211E ALA 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E LEU* 3.4 27.1 - - + -
54E ILE* 5.0 2.2 - - + -
95E LEU* 4.9 1.8 - - + -
101E ALA 3.2 16.7 + - - +
102E ARG* 4.1 6.5 - - - +
103E ARG 3.2 0.4 - - - -
104E GLU* 1.3 79.8 - - + +
106E GLU* 1.3 57.3 + - - +
108E HIS* 3.9 3.8 - - - +
109E TRP* 2.9 28.9 + - - +
120E ILE* 4.3 4.1 - - + +
123E VAL* 3.7 28.5 - - + -
134E LEU* 4.4 15.3 - - + -
136E ILE* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 5.4 0.7 - - - +
132B LYS* 3.0 43.5 + - - +
52E LEU* 4.0 23.2 + - + +
102E ARG 3.2 16.4 + - - +
103E ARG* 3.0 6.9 + - - +
105E VAL* 1.3 82.8 - - - +
107E LEU* 1.3 65.3 + - + +
109E TRP* 3.6 9.5 + - - +
110E ARG* 3.3 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ARG* 2.9 31.6 + - + +
104E GLU* 4.0 3.1 - - - +
106E GLU* 1.3 78.0 - - + +
108E HIS* 1.3 66.6 + - - +
110E ARG* 3.3 32.6 + - - +
111E ALA* 3.1 22.5 + - - +
182E ILE* 3.9 21.2 - - + +
208E PHE* 4.3 3.2 - - + -
211E ALA* 3.3 50.3 - - + +
212E LYS* 3.7 12.6 - - - +
213E GLU* 3.9 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LYS* 6.3 0.4 - - + -
104E GLU* 2.8 26.7 + - + +
105E VAL* 3.9 1.1 - - - +
107E LEU* 1.3 77.1 - - - +
109E TRP* 1.3 63.3 + - - +
111E ALA* 3.2 2.1 + - - -
112E SER* 2.9 24.0 + - - -
117E ILE* 3.8 11.1 - - + +
118E VAL* 2.9 51.3 - - + +
120E ILE* 3.4 22.1 - - + +
136E ILE* 5.7 4.0 - - + -
138E MET* 3.3 17.5 - - + +
207E ASP* 4.8 0.4 + - - -
208E PHE* 3.7 39.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.4 16.5 - - + +
49E LYS* 4.9 12.1 - - - -
50E SER* 3.1 37.3 + - - -
51E GLY* 3.9 9.6 - - - -
52E LEU* 3.4 48.0 - - + +
53E GLN 5.8 0.7 - - - -
105E VAL 2.9 18.4 + - - +
106E GLU* 3.7 9.9 - - - +
108E HIS* 1.3 77.9 - - - +
110E ARG* 1.3 65.3 + - - +
112E SER* 3.2 22.4 + - - -
113E GLN* 4.0 4.5 + - - +
120E ILE* 3.8 39.0 - - + +
121E VAL 5.4 4.7 - - - -
122E ASP* 5.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.0 26.7 - - + -
130B GLY* 3.0 29.9 + - - -
131B ARG* 4.9 4.5 - - - +
132B LYS* 5.1 7.9 - - - +
106E GLU* 3.3 29.4 + - - +
107E LEU* 3.4 26.9 - - - +
108E HIS 3.2 0.4 - - - -
109E TRP* 1.3 81.3 - - - +
111E ALA* 1.3 56.9 + - - +
113E GLN* 2.7 40.2 - - - +
176E TYR* 3.9 1.2 + - - -
180E ILE* 3.6 23.6 + - + +
182E ILE* 3.8 16.2 - - + +
213E GLU* 2.8 42.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
107E LEU 3.1 9.8 + - - +
108E HIS 3.2 2.0 + - - +
110E ARG* 1.3 73.1 - - - +
112E SER* 1.3 56.9 + - - +
113E GLN 3.0 5.8 - - - -
114E CYS* 2.8 22.1 + - - +
117E ILE* 3.3 36.2 - - + +
176E TYR* 3.9 9.0 - - - -
177E LEU* 3.4 23.6 - - + -
180E ILE* 4.4 2.0 - - + -
208E PHE* 3.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E HIS* 2.9 28.6 + - - -
109E TRP* 3.4 15.9 + - - -
110E ARG 3.2 1.0 - - - -
111E ALA* 1.3 74.0 - - - +
113E GLN* 1.3 69.3 + - - +
114E CYS 2.9 11.5 + - - +
115E PRO* 5.0 0.9 - - - +
117E ILE* 4.4 8.5 - - - +
118E VAL 3.6 4.5 + - - -
119E ARG* 4.5 13.1 - - - +
120E ILE* 3.5 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.2 28.6 + - + +
129B ALA 6.0 0.2 - - - +
130B GLY* 3.8 21.9 - - - +
49E LYS* 4.4 22.8 - - + +
109E TRP 4.0 3.9 + - - +
110E ARG* 2.7 27.9 - - - +
112E SER* 1.3 78.6 - - - +
114E CYS* 1.3 58.0 + - - +
115E PRO* 3.7 6.9 - - - +
176E TYR* 2.5 31.3 + - + +
180E ILE* 4.2 1.0 - - - +
----------------------------------------------------------
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