Contacts of the helix formed by residues 100 - 114 (chain A) in PDB entry 2NN6
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 VAL 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 2.2 53.3 + - - +
97A ASP* 4.2 3.4 - - - +
98A LEU 2.7 0.2 + - - -
99A LEU* 1.3 68.5 - - - +
101A LYS* 1.3 83.9 - - - +
103A ASN* 3.8 0.2 - - - +
104A ARG* 2.9 25.0 + - - +
93B ARG 5.1 0.4 - - - +
96B CYS* 4.8 14.8 - - + -
97B GLU* 4.0 23.8 - - + +
100B LEU* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP 3.3 20.1 + - - +
98A LEU* 3.0 9.3 + - - +
100A VAL* 1.3 84.9 - - - +
102A LEU* 1.3 74.3 + - + +
104A ARG* 3.8 0.5 - - - +
105A LEU* 2.5 56.5 + - + +
108A ARG* 6.2 0.2 - - - +
220A LEU* 6.3 1.4 - - - +
235A GLN* 3.2 31.0 - - + +
237A SER* 5.0 9.2 + - - -
97B GLU* 4.3 14.1 - - + +
100B LEU* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.5 14.4 - - + -
82A LEU* 5.8 5.6 - - + -
98A LEU* 2.3 57.5 + - + +
101A LYS* 1.3 96.8 - - - +
103A ASN* 1.3 64.2 + - - +
105A LEU* 3.5 18.8 - - + -
106A MET* 2.7 28.6 + - - +
145A ILE* 4.7 20.4 - - + -
146A ILE* 4.2 32.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.9 9.0 - - - +
79A ASN* 3.7 10.8 + - - -
80A LEU* 2.4 61.0 + - - +
99A LEU* 2.7 34.6 + - + +
100A VAL 3.2 1.8 + - - -
102A LEU* 1.3 77.5 - - - +
104A ARG* 1.3 58.1 + - - +
106A MET* 3.4 2.9 - - - +
107A GLU* 2.9 34.9 + - - +
93B ARG* 5.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL 2.9 15.5 + - - +
103A ASN* 1.3 73.2 - - - +
105A LEU* 1.3 55.6 + - - +
107A GLU* 3.0 29.9 + - - +
108A ARG* 2.6 59.5 + - + +
111A ARG* 5.8 6.1 - - - +
112A ASN* 5.1 0.6 + - - -
93B ARG* 4.8 22.7 - - + +
94B LYS* 5.4 8.9 - - - +
97B GLU* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 2.5 52.1 + - + +
102A LEU* 3.5 18.2 - - + +
104A ARG* 1.3 72.9 - - - +
106A MET* 1.3 65.6 + - - +
108A ARG* 3.1 54.6 - - - +
109A CYS* 3.9 3.3 + - - +
146A ILE* 4.8 8.7 - - + -
222A VAL* 4.8 11.2 - - + -
233A THR* 5.8 3.0 - - + +
235A GLN* 3.3 32.5 - - + +
97B GLU* 4.3 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.7 24.7 - - + -
80A LEU* 5.7 3.6 - - + -
102A LEU 2.7 21.8 + - - +
103A ASN* 3.4 3.6 - - - +
105A LEU* 1.3 73.1 - - - +
107A GLU* 1.3 56.1 - - - +
108A ARG 2.7 14.6 + - - -
109A CYS* 3.2 16.1 + - - -
110A LEU* 3.1 37.5 - - + +
136A LEU* 5.0 0.4 - - + -
146A ILE* 3.9 20.6 - - + +
149A ALA* 3.8 14.1 - - + +
150A SER* 3.0 49.8 - - - +
153A ALA* 4.2 11.7 - - + -
154A ILE* 6.1 2.2 - - + -
191A PRO 6.0 0.2 - - - +
193A CYS* 4.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.0 36.0 - - - -
78A PHE* 3.0 28.5 + - + +
103A ASN* 2.9 17.0 + - - +
104A ARG* 3.0 31.0 + - - +
106A MET* 1.3 79.9 - - - +
108A ARG* 1.3 64.4 + - - +
110A LEU* 2.9 27.3 + - + +
111A ARG* 3.7 22.3 + - + +
93B ARG* 5.2 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 6.2 0.2 - - - +
104A ARG* 2.6 40.3 + - - +
105A LEU* 3.1 41.8 + - - +
106A MET 2.7 2.0 + - - -
107A GLU* 1.3 76.1 - - - +
109A CYS* 1.3 52.3 + - - +
110A LEU 2.7 13.5 + - - -
111A ARG* 3.0 3.3 + - - +
112A ASN* 2.6 30.7 + - - +
233A THR* 4.5 6.3 - - + -
234A ILE 5.1 0.4 - - - -
235A GLN* 4.2 1.2 - - - +
97B GLU* 3.7 23.4 + - - -
101B GLN* 5.2 8.3 + - - +
199B GLU* 2.8 31.7 + - - +
201B ASP* 2.8 49.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU 3.9 2.4 + - - +
106A MET* 3.2 15.9 + - - +
108A ARG* 1.3 77.0 - - - +
110A LEU* 1.3 79.1 + - - +
112A ASN* 3.3 14.9 + - + +
113A SER* 3.0 27.7 + - - -
191A PRO* 4.1 19.2 - - - +
193A CYS* 4.9 13.9 - - - -
224A ALA* 4.2 10.3 - - + -
232A CYS* 4.5 2.9 - - + -
233A THR* 3.0 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 5.9 6.7 - - + -
78A PHE* 3.5 28.5 - - + -
106A MET* 3.1 27.4 - - + +
107A GLU* 2.9 34.1 - - + +
108A ARG 2.7 4.8 + - - -
109A CYS* 1.3 91.0 - - - +
111A ARG* 1.3 60.6 + - + +
112A ASN 3.1 3.8 - - - -
114A LYS 3.1 19.4 + - - -
115A CYS* 3.9 10.5 - - - -
116A ILE* 3.7 15.1 - - + +
153A ALA* 5.9 2.2 - - + -
154A ILE* 6.2 3.8 - - + -
191A PRO* 5.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 4.2 12.6 - - - +
76A LEU* 3.1 34.2 + - + +
77A PHE* 3.8 21.4 - - - -
104A ARG* 5.8 6.5 - - - +
107A GLU* 4.4 20.0 + - + +
108A ARG* 3.0 7.1 + - - +
110A LEU* 1.3 80.3 - - + +
112A ASN* 1.3 64.6 + - - +
113A SER 3.4 0.2 - - - -
114A LYS* 3.2 27.5 - - - +
116A ILE* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 5.1 0.7 + - - -
108A ARG* 2.6 39.3 + - - +
109A CYS* 3.3 14.4 - - - +
111A ARG* 1.3 82.5 - - - +
113A SER* 1.3 62.3 + - - +
114A LYS* 3.4 5.7 + - - +
232A CYS* 2.9 31.8 + - + +
233A THR* 3.2 3.8 - - - +
201B ASP* 3.2 33.9 + - - +
202B ALA* 3.8 1.7 - - - +
203B ARG* 4.6 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A CYS 3.0 15.2 + - - -
112A ASN* 1.3 80.0 - - - +
114A LYS* 1.3 61.9 + - - +
115A CYS* 2.5 44.6 + - - +
189A HIS* 3.3 23.7 - - - +
191A PRO* 3.9 6.1 - - - -
226A ASN* 3.5 5.9 + - - +
232A CYS* 3.5 20.9 - - - -
203B ARG* 5.0 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 5.9 2.6 - - - +
110A LEU 3.1 8.4 + - - -
111A ARG* 3.2 20.0 - - - +
112A ASN 3.2 4.4 - - - +
113A SER* 1.3 78.3 - - - +
115A CYS* 1.3 52.8 + - - +
116A ILE* 2.6 41.9 + - + +
117A ASP* 4.3 0.3 + - - -
188A HIS* 4.6 5.0 - - - -
189A HIS* 4.3 3.6 + - - -
179B ALA 5.7 3.2 + - - -
180B GLY* 5.3 9.3 + - - -
----------------------------------------------------------
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