Contacts of the helix formed by residues 98 - 112 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLN* 3.1 18.3 + - + +
97D ASP* 1.3 79.0 + - - +
99D PRO* 1.3 81.0 - - + +
100D LYS* 3.9 11.9 - - - -
101D ALA* 3.1 15.0 + - - +
102D ARG* 2.8 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D CYS* 1.3 91.8 - - + +
100D LYS* 1.3 63.4 + - + +
102D ARG* 3.5 8.4 + - + +
103D ARG* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D CYS* 3.2 11.1 - - - -
99D PRO* 1.3 83.0 - - + +
101D ALA* 1.3 61.0 + - - +
103D ARG* 3.0 47.7 + - + +
104D GLU* 2.8 28.3 + - - +
209D GLY 5.6 1.1 - - - +
212D LYS* 5.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 3.9 23.3 - - + +
96D GLN 3.5 24.0 - - - +
98D CYS* 3.1 10.1 + - - +
100D LYS* 1.3 75.0 - - - +
102D ARG* 1.3 66.8 + - - +
104D GLU* 2.9 9.6 + - - +
105D VAL* 2.9 27.5 + - - +
134D LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 5.7 0.2 - - - +
54D ILE* 3.1 32.3 - - - +
97D ASP* 2.4 43.9 + - - +
98D CYS 2.8 22.6 + - - +
99D PRO* 3.6 8.3 - - + +
101D ALA* 1.3 75.7 - - - +
103D ARG* 1.3 63.1 + - - +
105D VAL* 3.5 4.4 + - - +
106D GLU* 3.1 25.9 + - - +
125D GLU* 2.5 35.2 + - - +
132D LYS* 3.8 2.6 - - - +
134D LEU* 3.8 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D PRO 2.8 15.7 + - - +
100D LYS* 3.2 51.5 + - + +
102D ARG* 1.3 76.7 - - - +
104D GLU* 1.3 56.9 + - - +
106D GLU* 3.2 4.8 + - - +
107D LEU* 2.9 47.6 + - + +
185D ARG* 4.1 4.2 - - - +
208D PHE 5.6 0.6 + - - -
209D GLY 3.2 26.2 + - - -
210D PHE* 4.5 3.0 - - - +
211D ALA 3.3 24.0 + - - -
212D LYS* 3.4 32.3 - - - +
213D GLU 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LYS* 3.4 26.4 + - - +
95D LEU* 3.1 29.0 - - + +
100D LYS 2.8 16.0 + - - +
101D ALA* 2.9 10.0 + - - +
103D ARG* 1.3 72.6 - - - +
105D VAL* 1.3 68.4 + - - +
107D LEU* 5.0 1.3 - - - -
108D HIS* 2.9 32.6 + - + +
136D ILE* 5.1 4.0 - - + +
207D ASP* 4.8 0.2 - - - -
208D PHE* 3.5 33.4 + - + +
209D GLY* 3.4 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.4 36.6 - - + -
54D ILE* 5.0 3.4 - - + -
95D LEU* 5.2 0.7 - - + -
101D ALA 2.9 20.1 + - - +
102D ARG* 4.1 5.2 - - - +
104D GLU* 1.3 74.8 - - - +
106D GLU* 1.3 53.7 + - - +
108D HIS* 3.9 3.5 - - - +
109D TRP* 2.8 32.7 + - + +
120D ILE* 4.6 3.3 - - + +
123D VAL* 3.8 22.4 - - + -
134D LEU* 4.4 14.4 - - + -
136D ILE* 3.3 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.7 31.5 + - + +
102D ARG 3.1 20.8 + - - +
103D ARG* 3.5 6.5 - - - +
104D GLU 3.1 0.6 - - - -
105D VAL* 1.3 79.5 - - - +
107D LEU* 1.3 63.2 + - + +
109D TRP* 3.4 5.9 + - - +
110D ARG* 3.2 43.2 + - - +
127K LEU* 6.1 0.3 - - - +
132K LYS* 3.3 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ARG* 2.9 31.5 + - + +
104D GLU* 4.3 2.0 - - - +
106D GLU* 1.3 75.6 - - + +
108D HIS* 1.3 64.7 + - - +
110D ARG* 3.5 13.8 + - - +
111D ALA* 3.1 23.0 + - - +
182D ILE* 3.5 33.4 - - + +
208D PHE* 4.2 3.3 - - + +
211D ALA* 3.5 48.5 - - + +
212D LYS* 3.6 12.1 - - - +
213D GLU* 3.6 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LYS* 6.2 2.0 - - + +
104D GLU* 2.9 25.1 + - + +
105D VAL* 3.9 2.5 - - - +
107D LEU* 1.3 74.0 - - - +
109D TRP* 1.3 58.1 + - - +
111D ALA* 3.2 1.4 + - - +
112D SER* 2.7 31.6 + - - -
117D ILE* 4.2 2.7 - - + +
118D VAL* 3.1 48.3 + - + +
120D ILE* 3.4 26.5 - - + +
136D ILE* 5.2 5.3 - - - +
138D MET* 3.9 12.9 - - - -
207D ASP 5.1 3.8 - - - -
208D PHE* 3.7 45.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS* 3.7 24.6 - - - +
50D SER* 3.0 42.2 + - - -
51D GLY 3.9 5.4 - - - -
52D LEU* 3.4 46.4 - - + +
53D GLN 5.6 0.4 - - - -
105D VAL 2.8 20.1 + - - +
106D GLU* 3.6 7.4 - - - +
108D HIS* 1.3 77.6 - - - +
110D ARG* 1.3 64.8 + - + +
112D SER* 3.1 26.8 + - - -
120D ILE* 3.6 45.5 - - + +
121D VAL 5.0 5.8 - - - -
122D ASP* 5.7 1.8 - - - -
123D VAL* 5.7 0.2 - - + -
127K LEU* 3.6 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLU* 3.2 32.0 + - - +
107D LEU* 3.6 17.8 - - - +
108D HIS 3.3 0.2 - - - -
109D TRP* 1.3 80.8 - - + +
111D ALA* 1.3 58.1 + - - +
113D GLN* 3.0 35.6 - - - +
176D TYR* 3.9 3.8 - - - -
180D ILE* 4.0 18.0 + - + +
182D ILE* 4.0 25.0 - - + +
213D GLU* 2.9 44.4 + - - +
127K LEU* 3.8 23.8 - - + -
130K GLY* 3.3 27.6 + - - +
131K ARG* 5.5 2.0 - - - +
132K LYS* 5.1 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU 3.1 11.9 + - - +
108D HIS 3.5 4.3 - - - +
109D TRP 3.2 0.2 - - - -
110D ARG* 1.3 77.1 - - - +
112D SER* 1.3 57.2 + - - +
114D CYS* 3.0 21.1 + - - +
117D ILE* 3.3 19.4 - - + +
176D TYR* 4.1 4.6 - - - -
177D LEU* 3.5 22.0 - - + -
180D ILE* 4.6 2.4 - - - +
182D ILE* 5.1 0.4 - - + -
208D PHE* 3.4 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS* 4.6 9.4 - - - -
108D HIS* 2.7 23.8 + - - -
109D TRP* 3.1 24.9 + - - -
111D ALA* 1.3 74.4 - - - +
113D GLN* 1.3 65.5 + - - +
114D CYS 3.1 9.6 + - - +
115D PRO* 4.9 1.2 - - - +
117D ILE* 4.6 9.1 - - - +
118D VAL 4.2 3.7 + - - -
119D ARG* 4.9 11.0 - - - +
120D ILE* 3.9 28.0 + - - +
----------------------------------------------------------
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