Contacts of the helix formed by residues 149 - 164 (chain A) in PDB entry 3N2E
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 GLY 149 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA 3.6 7.3 + - - -
147A ARG 3.3 4.4 + - - -
148A GLY* 1.3 79.8 - - - +
150A LEU* 1.3 65.8 + - - -
151A ASN* 3.3 2.5 - - - -
152A ASN* 3.3 4.0 + - - +
153A SER* 3.2 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 3.9 27.1 - - - +
17A LEU* 4.3 12.1 - - + +
20A GLU* 3.7 42.6 - - + +
149A GLY* 1.3 71.5 - - - -
151A ASN* 1.3 66.3 + - - +
153A SER* 3.2 8.5 + - - -
154A LEU* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 5.6 0.3 - - - +
149A GLY 3.3 0.6 - - - -
150A LEU* 1.3 84.8 - - + +
152A ASN* 1.3 52.1 + - - +
154A LEU* 3.3 10.5 + - - +
155A LYS* 2.8 34.6 + - - +
151C ASN* 4.7 6.7 + - + +
152C ASN* 2.9 48.7 + - - +
155C LYS* 4.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP* 3.9 12.7 + - - +
148A GLY* 3.7 25.8 + - - +
149A GLY 3.3 8.5 + - - +
151A ASN* 1.3 75.1 - - - +
153A SER* 1.3 65.9 + - - +
155A LYS* 3.3 15.0 + - - +
156A GLN* 3.1 47.4 + - - +
121B ASN* 5.8 2.1 - - - +
151C ASN* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.1 20.2 - - - -
97A LEU* 5.5 2.1 - - - +
144A ILE* 3.7 15.2 - - - +
145A ASP 3.7 0.5 + - - -
146A ALA* 3.4 28.7 - - - +
149A GLY 3.2 15.8 + - - -
150A LEU* 3.6 8.6 - - - -
152A ASN* 1.3 76.5 - - - +
154A LEU* 1.3 62.7 + - - +
156A GLN* 3.2 13.4 + - - +
157A VAL* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.8 13.4 - - + +
20A GLU* 3.9 30.7 - - + +
21A LEU* 3.7 42.2 - - + +
24A ALA* 4.5 6.7 - - + -
150A LEU* 2.9 19.9 + - + +
151A ASN* 3.4 13.5 - - - +
153A SER* 1.3 77.2 - - - +
155A LYS* 1.3 62.0 + - - +
157A VAL* 3.1 4.1 + - - +
158A LEU* 3.0 36.6 + - + +
155C LYS* 3.5 32.3 - - + +
159C GLN* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN 2.8 19.1 + - - +
152A ASN* 3.7 20.2 - - - +
153A SER 3.3 0.2 - - - -
154A LEU* 1.3 74.0 - - - +
156A GLN* 1.3 80.8 + - - +
158A LEU* 3.4 3.0 + - - +
159A GLN* 3.0 38.3 + - - +
120B ASN 3.7 17.2 + - - -
121B ASN* 3.8 18.1 - - - +
20C GLU* 5.0 0.2 + - - -
151C ASN* 3.3 27.5 + - - +
154C LEU* 3.7 22.1 - - + +
155C LYS* 3.8 24.4 - - + +
158C LEU* 4.1 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE 4.5 2.0 + - - -
144A ILE* 3.9 17.8 - - + +
145A ASP* 3.0 47.3 - - - +
152A ASN* 3.1 32.3 + - - +
153A SER* 3.2 5.7 + - - +
155A LYS* 1.3 89.4 - - - +
157A VAL* 1.3 69.7 + - - +
158A LEU 3.2 0.3 + - - -
159A GLN* 3.3 15.4 + - - +
160A PHE* 3.3 22.7 + - + -
117B PRO* 3.7 24.7 + - - +
120B ASN* 5.3 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 5.0 2.0 - - + -
17A LEU* 4.4 19.3 - - + -
21A LEU* 3.6 38.4 - - + -
95A PHE* 4.1 22.9 - - + -
144A ILE* 4.2 22.7 - - + -
153A SER 3.0 18.5 + - - +
154A LEU 3.1 5.8 + - - +
156A GLN* 1.3 78.0 - - - +
158A LEU* 1.3 61.8 + - - +
160A PHE* 3.2 5.0 + - - +
161A ILE* 3.1 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.2 9.9 - - + -
24A ALA* 4.5 4.3 - - + -
25A LEU* 3.7 35.9 - - + -
154A LEU* 3.0 33.7 + - + +
155A LYS* 3.9 3.4 - - - +
157A VAL* 1.3 75.9 - - - +
159A GLN* 1.3 56.4 + - - +
161A ILE* 3.7 3.6 - - + +
162A ALA* 2.8 35.8 + - - +
155C LYS* 3.7 34.3 - - + +
158C LEU* 4.2 14.0 - - + +
159C GLN* 4.2 23.3 - - + +
162C ALA* 4.1 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LYS* 3.0 32.2 + - - +
156A GLN* 3.4 12.4 - - - +
158A LEU* 1.3 75.0 - - - +
160A PHE* 1.3 68.3 + - + +
162A ALA* 3.2 5.2 + - - +
163A LEU* 3.1 31.4 + - + +
113B ARG* 4.4 4.1 - - - +
120B ASN* 3.2 47.7 + - - +
24C ALA* 3.2 46.4 - - + +
25C LEU* 5.1 0.2 - - - +
154C LEU* 5.0 0.2 - - - +
158C LEU* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 4.3 8.1 - + + -
142A PHE* 3.4 51.6 - + + -
143A ILE 4.3 5.8 - - - -
144A ILE* 3.8 24.5 - - + -
156A GLN* 3.3 21.5 - - + -
157A VAL 3.2 7.4 + - - +
159A GLN* 1.3 81.2 - - + +
161A ILE* 1.3 65.9 + - - +
163A LEU* 3.3 3.1 + - - +
164A GLN* 3.1 26.7 + - - +
167A LEU* 4.0 2.8 - - + +
110B GLN* 3.4 25.1 - - - +
113B ARG* 3.6 27.8 - - + -
114B ALA* 4.0 6.3 - - - -
120B ASN* 4.0 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.7 24.9 - - + -
25A LEU* 3.8 13.9 - - + -
95A PHE* 4.6 5.2 - - + -
157A VAL* 3.1 36.9 + - + +
158A LEU* 3.9 5.8 - - - +
160A PHE* 1.3 73.8 - - - +
162A ALA* 1.3 66.8 + - - +
163A LEU 3.3 0.3 + - - -
164A GLN 3.4 18.7 + - - +
165A PRO* 3.5 8.0 - - + +
167A LEU* 4.0 25.4 - - + -
168A SER* 3.7 25.1 - - - +
162C ALA* 3.8 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU 2.8 14.0 + - - +
159A GLN 3.2 10.5 + - - +
161A ILE* 1.3 78.2 - - - +
163A LEU* 1.3 62.0 + - - +
165A PRO* 4.2 10.2 - - - +
25C LEU* 4.0 15.2 - - + +
158C LEU* 4.3 8.1 - - + +
161C ILE* 3.8 28.2 - - + +
162C ALA* 3.9 17.6 - - - +
165C PRO* 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLN* 3.1 18.4 + - + +
160A PHE 3.8 4.3 - - - +
161A ILE 3.1 0.4 - - - -
162A ALA* 1.3 81.7 - - - +
164A GLN* 1.3 57.7 + - + +
165A PRO* 3.8 5.5 - - - +
110B GLN* 3.1 51.0 - - + +
113B ARG* 4.2 1.8 - - - +
24C ALA 3.6 19.3 - - - +
25C LEU* 4.1 34.3 - - + +
26C LYS* 5.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 3.7 25.0 - - - -
160A PHE 3.1 11.9 + - - +
161A ILE 3.5 3.6 - - - +
163A LEU* 1.3 77.1 - - - +
165A PRO* 1.3 66.9 - - - +
166A SER* 3.1 16.2 + - - +
167A LEU* 3.1 42.3 - - + +
110B GLN* 4.8 18.0 - - + +
----------------------------------------------------------
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