Contacts of the helix formed by residues 150 - 170 (chain P) in PDB entry 1NK2
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 PRO 150 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P ALA* 6.0 1.3 - - + -
139P ARG* 3.8 9.5 - - + +
140P GLU* 3.1 48.5 - - + +
143P ALA* 3.6 17.9 - - + -
148P LEU 4.3 0.7 - - - +
149P THR* 1.4 86.2 - - + +
151P THR* 1.4 51.5 + - - +
153P VAL* 3.0 8.2 + - + +
154P LYS* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P THR* 4.8 5.8 + - - -
150P PRO* 1.4 79.1 - - - +
152P GLN* 1.4 53.5 + - - +
154P LYS* 3.9 21.5 - - - +
155P ILE* 2.7 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A A 3.5 20.7 + - - +
114P VAL* 3.4 32.5 + - - +
116P PHE* 2.9 47.5 - - + -
124P LEU* 4.1 0.8 - - - +
148P LEU* 3.9 19.3 - - + +
149P THR* 2.3 56.6 + - - +
151P THR* 1.4 69.4 - - - +
153P VAL* 1.4 58.4 + - - +
156P TRP* 3.5 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P LEU* 3.5 19.7 - - + -
139P ARG* 3.4 35.4 - - + +
142P LEU* 4.0 12.3 - - + -
143P ALA* 3.5 34.3 - - - +
146P ILE* 4.5 4.5 - - + -
148P LEU* 4.8 2.3 - - + +
149P THR 3.2 4.4 + - - -
150P PRO 3.0 8.8 + - - +
152P GLN* 1.4 71.5 - - - +
154P LYS* 1.4 70.2 + - - +
156P TRP* 2.8 16.8 + - - +
157P PHE* 2.8 32.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B G 5.0 2.2 + - - +
21B C 3.7 26.5 + - - +
139P ARG* 2.8 47.6 - - - +
150P PRO 2.7 14.3 + - - +
151P THR* 3.5 27.5 - - - +
153P VAL* 1.4 75.8 - - - +
155P ILE* 1.4 52.8 + - - +
157P PHE* 2.7 12.1 + - - +
158P GLN* 2.4 68.1 + - + +
161P ARG* 4.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A A 3.9 9.6 - - + -
8A A 2.8 58.1 - - + +
10A T 6.6 0.4 - - + -
151P THR* 2.7 45.7 + - + +
154P LYS* 1.4 77.2 - - - +
156P TRP* 1.4 53.7 + - - +
158P GLN* 2.8 36.2 - - + +
159P ASN* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 156 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A A 3.9 22.3 + - - -
8A A 4.3 0.6 + - - -
116P PHE* 3.2 37.8 - + + -
121P THR* 4.2 15.1 + - + +
124P LEU* 3.4 48.4 - - + +
125P GLU* 3.6 37.5 - - + -
128P PHE* 3.8 15.9 - - + -
152P GLN 3.5 3.8 + - - +
153P VAL 2.8 14.3 + - - +
155P ILE* 1.4 74.1 - - - +
157P PHE* 1.4 62.2 + + - +
159P ASN* 3.6 7.2 + - + +
160P HIS* 3.3 44.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P LEU* 2.9 38.8 - - + -
127P ARG* 3.1 24.2 - - + -
128P PHE* 2.8 64.3 - + + -
131P GLN 4.3 5.4 - - - -
132P ARG 5.2 0.9 - - - -
134P LEU* 4.2 13.5 - - + -
139P ARG* 5.4 3.1 - - - +
142P LEU* 4.1 4.0 - - + -
153P VAL* 2.8 46.3 + - + -
154P LYS* 2.7 16.9 + - - +
156P TRP* 1.4 70.6 - + - +
158P GLN* 1.4 64.9 + - - +
160P HIS 3.2 7.3 + - - -
161P ARG* 3.2 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A T 5.5 1.2 - - - +
21B C 3.5 47.4 + - - +
22B C 4.0 19.6 + - + +
23B A 5.0 6.3 + - - +
154P LYS* 2.4 49.5 + - + +
155P ILE* 2.8 37.3 - - + +
157P PHE* 1.4 68.8 - - - +
159P ASN* 1.4 65.4 + - - +
160P HIS 2.9 1.9 + - - -
161P ARG* 3.1 32.5 + - - +
162P TYR* 3.8 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A A 3.1 46.1 + - - +
8A A 3.1 38.5 + - - -
24B C 5.3 0.7 + - - -
155P ILE* 2.8 25.3 + - - +
156P TRP* 3.6 7.8 + - - +
157P PHE 3.3 0.4 - - - -
158P GLN* 1.4 72.5 - - - +
160P HIS* 1.4 57.3 + - - +
162P TYR* 4.4 3.3 + - - +
163P LYS* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 160 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P GLU* 6.0 2.0 - - + -
128P PHE* 3.2 55.2 - + + -
129P ARG* 4.9 14.9 + - - -
156P TRP* 3.3 31.3 + + + +
157P PHE 3.2 2.0 + - - +
158P GLN 2.9 3.2 + - - -
159P ASN* 1.4 76.3 - - - +
161P ARG* 1.4 56.7 + - - +
163P LYS* 2.9 40.9 + - + +
164P THR* 3.0 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B C 3.7 36.8 - - - +
22B C 6.4 1.1 - - - -
23B A 5.0 0.2 - - - -
128P PHE* 3.6 12.1 - - + -
132P ARG* 2.6 37.7 + - + +
133P TYR* 3.0 44.4 - - - +
134P LEU 5.0 0.6 - - - +
139P ARG* 5.0 9.5 - - - +
154P LYS* 4.6 4.4 + - - +
157P PHE* 3.2 38.9 + - - +
158P GLN* 3.1 22.0 + - - +
160P HIS* 1.4 75.8 - - - +
162P TYR* 1.4 56.2 + - - +
164P THR* 2.8 25.9 - - + +
165P LYS* 3.1 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B C 4.8 3.4 - - + +
23B A 2.8 77.2 + + + +
24B C 3.2 25.2 + + - -
158P GLN 3.8 7.9 + - - +
159P ASN* 4.8 3.4 - - - +
160P HIS 3.4 0.4 - - - -
161P ARG* 1.4 75.6 - - - +
163P LYS* 1.4 67.2 + - + +
165P LYS* 3.2 16.8 + - + +
166P ARG* 2.9 72.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A C 3.2 41.3 + - - +
159P ASN* 2.9 32.8 + - + +
160P HIS* 2.9 30.1 + - + +
162P TYR* 1.4 81.6 - - + +
164P THR* 1.4 65.4 + - - +
166P ARG* 3.6 13.1 + - - +
167P ALA* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P PHE* 4.9 9.9 - - + -
132P ARG* 5.1 9.7 + - - +
160P HIS* 3.0 21.7 + - + +
161P ARG* 2.8 34.8 - - + +
163P LYS* 1.4 76.5 - - - +
165P LYS* 1.4 72.1 + - + +
167P ALA* 2.8 33.5 + - - +
168P GLN* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B A 5.0 9.4 - - - +
132P ARG* 3.4 24.6 - - - +
161P ARG 3.1 22.7 - - - +
162P TYR* 3.2 14.3 + - + +
164P THR* 1.4 93.5 + - + +
166P ARG* 1.4 54.7 + - - +
168P GLN* 2.9 29.1 + - + +
169P ASN* 3.0 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A A 6.0 0.4 - - - +
24B C 4.2 12.1 - - - +
25B T 3.3 34.3 + - - +
162P TYR* 2.9 64.1 + - + +
163P LYS* 3.6 16.5 - - - +
165P LYS* 1.4 74.3 - - - +
167P ALA* 1.4 66.1 + - - +
168P GLN 2.9 2.2 - - - -
169P ASN* 2.9 27.5 + - + +
170P GLU* 3.3 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P LYS 3.2 8.9 + - - +
164P THR* 2.8 20.6 + - - +
166P ARG* 1.4 75.8 - - - +
168P GLN* 1.4 58.5 + - + +
170P GLU* 2.9 29.8 + - - +
171P LYS* 3.5 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164P THR* 3.1 28.3 + - - +
165P LYS* 2.9 20.1 + - + +
167P ALA* 1.4 74.8 - - - +
169P ASN* 1.4 59.2 + - - +
170P GLU 3.1 1.8 - - - -
171P LYS* 3.0 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 169 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P LYS 3.0 6.5 + - - +
166P ARG* 2.9 23.3 + - + +
168P GLN* 1.4 75.7 - - - +
170P GLU* 1.4 54.6 + - - +
173P TYR* 2.7 51.7 + - - +
174P GLU* 3.2 33.3 - - + +
175P GLY 4.6 0.7 + - - -
176P HIS* 6.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166P ARG 3.3 3.7 + - - +
167P ALA* 2.9 21.4 + - - +
169P ASN* 1.4 79.8 - - - +
171P LYS* 1.4 62.3 + - + +
172P GLY 3.1 9.7 + - - -
173P TYR* 3.4 13.6 + - - +
174P GLU* 5.0 2.2 - - - +
----------------------------------------------------------
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