Contacts of the helix formed by residues 101 - 117 (chain D) in PDB entry 2NPP
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 GLU 101 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASP* 3.5 28.7 + - + +
99D VAL* 3.5 4.0 - - + +
100D GLU* 1.3 76.5 - - - +
102D THR* 1.3 72.4 + - - +
103D VAL* 2.7 32.2 + - + +
104D VAL* 3.1 17.8 + - + +
105D ARG* 3.5 3.5 + - - +
203E TYR* 4.1 3.7 - - - -
246E LYS* 3.0 39.0 + - - +
302F ARG* 3.1 22.5 + - - -
305F PRO* 4.4 9.3 - - + +
307F TYR* 3.5 12.8 - - - +
308F PHE* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLU 2.7 2.0 + - - -
101D GLU* 1.3 73.2 + - - +
103D VAL* 1.3 66.4 + - - +
104D VAL 2.8 1.6 + - - -
105D ARG* 2.9 43.0 + - - +
106D ASP* 2.5 49.2 + - - -
203E TYR* 3.3 40.8 + - + +
302F ARG* 3.4 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 3.7 34.3 - - + +
101D GLU* 2.7 20.4 + - + +
102D THR* 1.3 78.2 + - - +
104D VAL* 1.3 67.5 + - + +
106D ASP* 3.2 9.9 - - - +
107D LYS* 3.0 15.6 + - - +
302F ARG* 3.7 28.7 - - + +
304F THR* 5.7 5.4 - - + -
305F PRO* 4.8 14.1 - - + -
308F PHE* 5.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASP* 3.5 40.8 - - + +
66D LEU* 3.8 20.9 - - + +
67D LEU* 3.8 14.8 - - + +
70D ALA* 4.3 1.3 - - + +
96D LEU* 3.9 10.3 - - + +
99D VAL* 3.2 33.4 - - + -
101D GLU* 3.1 12.9 + - + +
102D THR 2.8 3.4 + - - -
103D VAL* 1.3 76.6 - - + +
105D ARG* 1.3 66.0 + - - +
106D ASP 2.8 1.9 + - - -
107D LYS* 2.9 16.1 + - - +
108D ALA* 2.9 9.2 + - - +
308F PHE* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU 3.1 17.7 - - - +
97D ALA 3.2 25.6 - - - +
99D VAL 2.9 18.4 - - - +
100D GLU 2.4 29.7 + - - -
101D GLU 3.5 0.6 + - - +
102D THR* 2.9 53.7 + - - +
104D VAL* 1.3 77.8 - - - +
106D ASP* 1.3 64.2 + - - +
108D ALA* 3.1 3.8 - - - +
109D VAL* 3.0 27.1 + - - +
141D PHE* 4.3 12.5 - - - -
142D THR* 2.9 33.2 - - - +
145D THR* 4.3 22.0 + - - +
146D SER* 4.1 7.6 + - - +
203E TYR* 4.4 7.5 + - - +
204E GLU* 6.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D THR* 2.5 36.1 + - - +
103D VAL* 3.2 13.8 + - - +
104D VAL 2.8 1.0 + - - -
105D ARG* 1.3 71.9 + - - +
107D LYS* 1.3 67.2 + - - +
109D VAL* 3.0 16.9 + - - +
110D GLU* 3.0 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 3.5 25.1 - - + +
70D ALA* 3.8 13.5 - - + -
71D GLU* 3.3 48.2 - - + -
103D VAL 3.0 5.6 + - - +
104D VAL 2.9 12.4 + - - +
106D ASP* 1.3 70.6 - - - +
108D ALA* 1.3 66.5 + - - +
110D GLU* 2.9 51.5 + - - +
111D SER* 3.0 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA* 3.9 3.9 - - - +
93D LEU* 3.9 16.8 - - + +
96D LEU* 3.5 42.0 - - + +
97D ALA* 3.5 7.4 - - - +
104D VAL 2.9 5.4 + - - +
105D ARG* 3.1 13.5 - - - +
107D LYS* 1.3 77.4 - - - +
109D VAL* 1.3 56.1 + - - +
111D SER* 3.5 3.0 + - - -
112D LEU* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ALA* 4.7 5.8 - - + -
105D ARG 3.0 14.1 + - - +
106D ASP* 3.0 10.3 + - - +
108D ALA* 1.3 73.9 - - - +
110D GLU* 1.3 67.6 + - - +
112D LEU* 4.2 6.1 - - + -
113D ARG* 2.8 43.1 + - + +
146D SER* 3.5 37.5 - - - +
149D GLY* 4.5 7.2 - - - -
150D LEU* 3.3 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLU* 5.3 0.2 - - - +
106D ASP 3.0 10.6 + - - +
107D LYS* 2.9 50.5 + - - +
109D VAL* 1.3 76.7 - - - +
111D SER* 1.3 59.7 + - - +
113D ARG* 3.4 9.8 - - - +
114D ALA* 3.0 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA 3.1 23.9 + - - -
71D GLU* 4.4 4.3 + - - -
74D GLY* 3.6 24.7 - - - -
93D LEU* 4.1 10.3 - - - -
107D LYS* 3.0 12.2 + - - +
108D ALA 3.6 7.4 - - - -
110D GLU* 1.3 74.2 + - - +
112D LEU* 1.3 69.1 + - - +
113D ARG 3.0 1.1 - - - -
114D ALA* 2.6 20.0 + - - +
115D ILE* 2.8 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LEU* 3.4 32.3 - - + -
93D LEU* 3.8 24.8 - - + +
97D ALA* 4.3 20.6 - - + -
108D ALA 3.0 24.2 + - - +
109D VAL* 3.7 4.7 - - + +
111D SER* 1.3 73.5 - - - +
113D ARG* 1.3 63.7 + - - +
115D ILE* 3.7 5.2 - - - +
116D SER* 3.0 25.3 + - - -
128D PHE* 3.6 17.0 - - + -
131D LEU* 4.1 15.5 - - + -
150D LEU* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D VAL* 2.8 41.4 + - + +
110D GLU* 3.4 8.3 - - - +
112D LEU* 1.3 74.6 - - - +
114D ALA* 1.3 63.1 + - - +
116D SER* 2.7 26.9 + - - -
117D HIS* 3.2 10.6 + - - -
149D GLY* 3.6 16.2 + - - +
150D LEU* 4.0 9.0 - - + -
152D SER* 3.6 9.9 + - - -
153D VAL* 3.9 20.2 - - + +
188D LYS* 3.7 16.4 - - - +
191D GLU* 3.1 40.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D GLY* 4.7 7.0 - - - +
110D GLU* 3.0 15.5 + - + +
111D SER* 2.6 18.9 + - - +
113D ARG* 1.3 71.6 - - - +
115D ILE* 1.3 64.8 + - + +
116D SER 3.2 1.6 + - - -
117D HIS* 3.6 17.5 + - - +
118D GLU* 4.5 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU 4.3 2.7 - - - +
74D GLY* 3.6 33.0 - - - +
77D THR* 3.8 12.8 - - - +
86D VAL* 3.9 19.3 - - + +
89D LEU* 3.9 24.2 - - + -
90D LEU* 3.8 26.7 - - + -
93D LEU* 4.0 10.8 - - + -
111D SER 2.8 13.4 + - - +
112D LEU* 3.7 11.0 - - - +
114D ALA* 1.3 70.4 - - - +
116D SER* 1.3 63.4 + - - +
117D HIS 3.2 0.7 - - - -
118D GLU* 3.1 17.1 + - - +
119D HIS* 2.7 25.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU 3.0 14.0 + - - -
113D ARG 2.7 20.0 + - - -
114D ALA 3.1 1.2 - - - -
115D ILE* 1.3 78.2 - - - +
117D HIS* 1.3 69.7 + - - +
119D HIS* 2.8 37.5 + - - +
124D LEU* 4.3 4.5 - - - +
128D PHE* 3.7 26.7 - - - -
153D VAL* 3.5 20.2 + - - +
157D ARG* 3.8 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ARG* 3.2 19.3 + - + -
114D ALA* 3.7 10.7 + - - +
115D ILE 3.2 0.4 - - - -
116D SER* 1.3 87.6 + - - +
118D GLU* 1.3 62.6 + - + +
119D HIS 3.0 12.5 + - - +
153D VAL* 4.0 24.0 + - + +
157D ARG* 4.0 17.2 + - - +
----------------------------------------------------------
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