Contacts of the helix formed by residues 152 - 171 (chain d) in PDB entry 5GJQ
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 SER 152 (chain d).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12d TYR* 2.9 7.6 + - - -
150d THR 3.5 3.6 + - - -
151d ILE* 1.3 73.7 - - - +
153d ARG* 1.4 53.8 + - - +
154d GLU* 3.6 14.7 + - - +
155d ARG* 3.1 30.9 + - - +
156d ALA 2.7 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11d ASP* 3.3 29.3 + - - -
12d TYR* 3.4 38.9 + - + +
14d LEU* 5.6 0.4 - - + +
152d SER* 1.4 70.2 - - - +
154d GLU* 1.3 82.7 + - + +
156d ALA* 3.4 2.5 - - - +
157d VAL* 2.9 33.7 + - + +
182d ILE* 4.0 31.2 - - + +
184d ASP* 3.3 27.1 + - - +
189d HIS* 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152d SER* 3.6 15.9 + - - +
153d ARG* 1.3 97.6 + - + +
155d ARG* 1.3 56.8 + - + +
157d VAL* 3.1 9.7 + - - +
158d GLU* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151d ILE* 3.5 21.7 - - + +
152d SER* 3.1 21.7 + - - +
154d GLU* 1.3 73.2 - - + +
156d ALA* 1.3 60.4 + - - +
158d GLU* 2.6 43.1 + - - +
159d LEU* 2.9 30.3 + - - +
162d LYS* 5.1 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7d ILE* 4.0 10.4 - - + +
12d TYR* 3.2 37.0 - - + +
14d LEU* 3.7 14.1 - - + +
151d ILE* 3.6 12.3 - - + +
152d SER 2.7 10.9 + - - +
153d ARG 3.4 6.7 - - - +
154d GLU 3.2 0.2 - - - -
155d ARG* 1.3 74.6 - - - +
157d VAL* 1.3 56.9 + - - +
159d LEU* 3.4 4.2 + - - +
160d LEU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14d LEU* 4.3 13.2 - - + -
153d ARG* 2.9 19.9 + - + +
154d GLU* 3.1 10.7 + - - +
156d ALA* 1.3 74.6 - - - +
158d GLU* 1.3 58.8 + - - +
160d LEU* 3.3 9.8 + - + +
161d ARG* 2.9 45.8 + - - +
180d VAL* 5.3 2.9 - - + -
191d LEU* 4.1 25.6 - - + -
194d ILE* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154d GLU 3.0 13.2 + - - +
155d ARG* 2.6 50.6 + - - +
157d VAL* 1.3 79.3 - - - +
159d LEU* 1.3 62.2 + - - +
161d ARG* 3.1 18.9 + - + +
162d LYS* 3.0 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7d ILE* 4.3 9.2 - - + -
142d ILE* 4.0 20.9 - - + +
143d LEU* 3.6 26.5 - - + -
146d TYR* 3.6 37.9 - - + +
147d TYR* 4.1 15.9 - - + +
151d ILE* 4.0 21.5 - - + -
155d ARG 2.9 17.9 + - - +
156d ALA 3.5 3.4 - - - +
158d GLU* 1.3 74.2 - - - +
160d LEU* 1.3 67.3 + - - +
162d LYS* 2.9 23.4 + - + +
163d CYS* 3.1 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5d ILE* 3.7 38.1 - - + -
7d ILE* 4.3 10.1 - - + -
14d LEU* 3.8 21.8 - - + -
16d ALA* 3.8 21.1 - - + -
156d ALA 2.9 14.1 + - - +
157d VAL* 3.4 12.3 - - + +
159d LEU* 1.3 77.4 - - - +
161d ARG* 1.3 62.7 + - - +
163d CYS* 3.1 8.1 + - - +
164d LEU* 2.9 43.2 + - + +
180d VAL* 4.0 22.0 - - + -
194d ILE* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157d VAL* 2.9 29.8 + - - +
158d GLU* 3.1 19.9 + - + +
160d LEU* 1.3 76.0 - - - +
162d LYS* 1.3 56.6 + - + +
164d LEU* 3.2 7.9 + - - +
165d GLU* 2.8 53.0 + - + +
193d ASN 5.6 1.2 + - - -
194d ILE* 3.5 44.8 - - + +
195d SER 5.4 4.6 + - - +
196d PHE* 5.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142d ILE* 4.2 16.2 - - + +
146d TYR* 4.0 49.9 - - + -
155d ARG* 5.1 6.7 - - - +
158d GLU* 3.0 31.2 + - + +
159d LEU* 2.9 20.9 + - - +
161d ARG* 1.3 74.9 - - - +
163d CYS* 1.3 61.9 + - - +
165d GLU* 3.8 8.9 - - - +
166d GLU* 3.0 22.7 + - - +
141s ARG* 4.3 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 163 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3d TYR* 4.6 0.9 - - - +
5d ILE* 4.1 16.2 - - + -
139d THR* 3.8 24.9 - - + +
142d ILE* 3.8 18.6 - - - -
143d LEU* 3.6 36.1 - - - -
159d LEU 3.1 15.1 + - - -
160d LEU* 3.4 7.9 - - - +
162d LYS* 1.3 76.3 - - - +
164d LEU* 1.3 60.6 + - + +
166d GLU* 3.2 9.8 - - - +
167d LEU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3d TYR* 3.8 21.1 - - + -
5d ILE* 4.8 1.3 - - + -
16d ALA* 5.1 1.6 - - + -
160d LEU* 2.9 43.0 + - + +
161d ARG* 3.9 3.6 - - - +
163d CYS* 1.3 78.5 - - + +
165d GLU* 1.3 58.4 + - - +
167d LEU* 3.2 9.6 + - + +
168d GLN* 3.0 30.8 + - - +
178d PHE* 3.6 45.5 - - + -
194d ILE* 3.7 27.4 - - + -
196d PHE* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161d ARG* 2.8 39.5 + - - +
162d LYS* 3.8 6.8 - - - +
164d LEU* 1.3 75.4 - - - +
166d GLU* 1.3 64.1 + - - +
168d GLN* 3.0 18.3 + - - +
169d LYS* 3.1 13.5 + - - +
196d PHE* 3.4 28.9 - - + -
141s ARG* 3.8 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138d LEU* 3.7 31.5 - - + +
139d THR* 5.0 0.4 - - + -
142d ILE* 3.6 11.7 - - + -
162d LYS 3.0 14.1 + - - +
163d CYS 3.2 10.8 - - - +
165d GLU* 1.3 75.0 - - - +
167d LEU* 1.3 63.7 + - - +
169d LYS* 3.0 13.8 + - - +
170d ARG* 3.1 26.7 + - + +
136s TYR* 3.7 3.8 - - - +
137s GLY* 3.6 22.2 + - - +
140s ASP* 3.1 39.6 - - - +
141s ARG* 3.8 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3d TYR* 3.7 40.2 - - + -
135d GLY* 3.7 32.1 - - - +
138d LEU* 4.2 8.7 - - + -
139d THR* 4.0 8.5 - - + -
163d CYS 3.0 14.3 + - - +
164d LEU* 3.2 13.2 - - + +
166d GLU* 1.3 77.9 - - - +
168d GLN* 1.3 64.6 + - - +
169d LYS 3.2 0.9 + - - -
171d PHE* 3.2 47.6 + - + +
173d LEU 4.8 2.9 - - - +
174d ASN 5.1 1.7 - - - +
175d LEU* 4.1 17.3 - - + -
178d PHE* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164d LEU 3.0 17.1 + - - +
165d GLU* 3.0 11.9 + - - +
167d LEU* 1.3 77.1 - - - +
169d LYS* 1.3 60.1 + - - +
174d ASN* 3.8 15.3 + - - +
175d LEU* 2.4 32.3 + - - +
176d PRO* 4.1 2.4 - - - +
178d PHE* 3.9 9.1 - - - -
196d PHE* 3.6 47.9 - - + +
174r ASN* 3.7 21.1 + - - +
176r PRO* 6.0 1.6 - - - +
198r LYS* 5.4 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165d GLU 3.1 9.1 + - - +
166d GLU* 3.0 10.6 + - - +
168d GLN* 1.3 81.3 - - - +
170d ARG* 1.3 94.0 + - + +
171d PHE 3.8 2.1 - - - +
27r GLN* 2.9 33.0 + - - +
30r ASP* 3.6 23.8 + - - -
140s ASP* 4.0 19.3 - - + +
141s ARG* 4.8 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138d LEU* 4.1 15.5 - - + -
166d GLU* 3.1 24.8 + - - +
169d LYS* 1.3 101.5 - - + +
171d PHE* 1.3 65.2 + - - +
26r VAL* 3.0 9.9 - - + -
27r GLN* 2.5 60.2 + - - +
28r MET* 4.3 6.5 + - - +
125s THR* 2.7 26.1 + - - -
136s TYR* 2.6 48.3 + - + -
140s ASP* 2.8 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1d MET* 4.4 7.2 - - + -
3d TYR* 5.9 1.8 - - + -
134d TYR* 3.6 35.0 - + + -
135d GLY* 3.8 13.0 - - - -
138d LEU* 4.0 13.9 - - + +
167d LEU* 3.2 36.3 + - + +
169d LYS 4.6 2.4 - - - +
170d ARG* 1.3 81.0 + - - +
172d ILE* 1.3 65.1 + - + +
173d LEU* 3.5 49.0 - - + +
175d LEU* 3.9 26.0 - - + -
25r ILE* 3.5 26.9 - - + -
27r GLN* 5.3 1.0 - - - +
174r ASN* 4.0 10.7 + - - +
----------------------------------------------------------
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