Contacts of the strand formed by residues 176 - 191 (chain A) in PDB entry 5A19
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 LEU 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 6.1 0.7 - - - -
164A LEU* 3.4 41.1 - - + +
167A LEU* 4.3 1.1 - - + -
168A ARG* 3.4 30.1 - - + +
173A LEU* 3.0 41.4 + - + +
174A PRO 3.7 7.4 - - - +
175A TRP* 1.3 107.8 - - + +
177A ARG* 1.3 62.9 + - - +
207A VAL* 3.4 31.9 - - + -
208A GLN 4.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 3.1 32.0 + - - -
97A LYS* 3.6 32.6 - - + +
168A ARG* 3.6 9.1 + - - +
175A TRP 4.1 8.3 - - - +
176A LEU* 1.3 80.7 - - - +
178A PRO* 1.4 74.4 - - + +
179A ASP 3.4 6.4 + - - +
180A SER* 5.4 0.2 - - - -
207A VAL* 4.1 8.3 - - - +
208A GLN* 3.0 42.4 + - - +
209A HIS* 2.9 28.9 + - - -
210A ASP* 3.5 21.9 - - + +
211A GLU* 4.7 4.0 - - - +
251A VAL* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLY* 4.5 0.2 - - - -
27A GLU 4.2 4.7 + - - -
28A GLY* 3.1 33.1 + - - +
90A ILE 3.7 24.2 - - - +
91A GLY 3.9 21.5 - - - +
92A TYR* 3.8 24.7 - - + -
97A LYS* 5.1 3.8 - - + -
168A ARG* 3.6 22.8 + - - +
177A ARG* 1.4 93.1 - - + +
179A ASP* 1.3 60.7 + - - +
180A SER* 3.5 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 3.6 13.9 - - - +
29A HIS* 3.3 27.6 - - - +
30A PRO* 4.0 6.1 - - - +
92A TYR* 3.3 19.0 + - - +
177A ARG 3.4 1.4 - - - +
178A PRO* 1.3 76.2 - - - +
180A SER* 1.3 66.4 + - - +
181A LYS* 4.8 1.0 - - - +
207A VAL* 3.6 2.8 - - - +
208A GLN* 2.9 40.4 + - + +
250A PHE* 3.8 19.0 - - - -
253A GLY* 3.8 0.9 - - - -
254A GLY* 2.9 21.4 + - - +
258A ASP* 5.7 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.5 4.0 - - - +
26A GLY* 3.0 32.3 + - - +
29A HIS* 4.2 0.5 - - - +
161A ASN* 2.7 25.6 + - - +
164A LEU* 3.8 16.4 - - - +
177A ARG 5.4 0.2 - - - -
178A PRO 3.5 5.7 + - - -
179A ASP* 1.3 79.7 + - - +
181A LYS* 1.3 72.0 + - - +
206A SER 3.3 7.6 - - - -
207A VAL* 3.7 19.3 - - - -
250A PHE* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.3 14.4 + - - +
24A SER 3.6 7.6 - - - +
25A VAL* 3.9 20.9 - - + -
29A HIS* 3.9 9.9 - - + -
161A ASN* 4.1 0.7 - - - -
179A ASP* 4.8 1.3 - - - +
180A SER* 1.3 81.6 - - - +
182A THR* 1.3 65.0 + - - +
204A VAL* 5.5 1.1 - - - +
205A ILE* 3.5 2.9 - - - +
206A SER* 2.8 43.5 + - - +
250A PHE* 6.0 4.5 - - + -
403A PPK 2.9 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 3.3 7.6 - - - +
24A SER 3.0 28.1 + - - +
157A ALA* 2.8 28.6 + - - +
160A LEU* 3.7 30.3 - - + -
161A ASN* 2.9 28.3 + - - +
164A LEU* 4.5 2.2 - - + -
181A LYS* 1.3 80.9 - - - +
183A GLN* 1.3 61.7 + - - +
204A VAL* 3.2 9.6 - - - -
205A ILE* 4.3 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.6 24.5 - - + +
22A SER 3.5 15.5 - - - +
23A GLU* 4.1 19.9 - - + +
182A THR* 1.3 76.1 - - - +
184A VAL* 1.3 64.0 + - - +
185A THR* 5.0 3.9 + - - +
202A THR 3.8 0.5 - - - +
203A ILE* 3.3 5.7 - - - -
204A VAL* 2.8 62.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.4 2.1 - - - -
22A SER 2.8 33.6 + - - +
153A THR* 3.6 21.4 - - - +
156A LEU* 4.1 17.9 - - + -
157A ALA* 3.7 25.6 - - - +
160A LEU* 3.8 22.0 - - + -
183A GLN* 1.3 78.6 - - - +
185A THR* 1.3 63.9 + - - +
186A VAL* 3.9 22.7 - - + -
200A VAL* 4.4 13.2 - - + -
202A THR 3.6 1.8 - - - -
203A ILE* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.2 22.2 - - + -
20A PHE 3.4 7.2 - - - +
21A THR* 2.7 31.1 + - - +
183A GLN* 5.0 3.3 + - - +
184A VAL* 1.3 70.9 - - - +
186A VAL* 1.3 57.8 + - - +
200A VAL* 3.7 4.3 - - - +
201A HIS* 2.8 48.5 + - + +
202A THR* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.5 5.5 - - - -
20A PHE 2.9 31.9 + - - +
152A LEU* 4.4 12.1 - - + -
153A THR* 3.6 27.1 - - + +
156A LEU* 4.8 0.7 - - + -
184A VAL* 3.9 15.5 - - + -
185A THR* 1.3 77.4 - - - +
187A GLN* 1.3 74.3 + - - +
188A TYR* 3.5 23.6 - - + -
197A PRO* 4.1 15.5 - - + -
199A ARG 3.5 12.6 - - - +
200A VAL* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.4 39.9 + - - +
18A PHE 3.5 6.7 - - - +
19A LEU* 3.8 19.5 - - + +
185A THR 4.4 0.2 + - - -
186A VAL* 1.3 76.5 - - - +
188A TYR* 1.3 61.4 + - - +
198A ILE* 2.9 38.8 + - + +
199A ARG* 3.0 48.7 + - + +
201A HIS* 4.4 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.2 10.2 - - - -
18A PHE* 2.8 64.9 + + + -
20A PHE* 4.0 3.1 - - + -
145A GLU* 2.6 29.0 + - - -
152A LEU* 3.7 12.3 + - - +
153A THR* 3.8 14.3 + - + +
186A VAL* 3.5 33.9 - - + -
187A GLN* 1.3 73.0 - - - +
189A MET* 1.3 59.5 + - - +
195A VAL* 3.8 23.3 - - + -
196A LEU 3.4 20.4 - - - -
197A PRO* 3.6 15.3 - - + -
198A ILE* 4.0 4.5 - - - -
274A TRP* 3.5 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 4.2 12.1 - - - +
17A THR* 4.6 7.0 - - + -
18A PHE* 4.4 2.7 - - - -
188A TYR* 1.3 77.8 - - - +
190A GLN* 1.3 63.6 + - - +
195A VAL* 3.5 2.8 - - - -
196A LEU* 2.8 66.1 + - + +
198A ILE* 3.6 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 3.9 20.7 + - - +
17A THR 5.7 0.4 - - - -
18A PHE* 4.3 20.6 - - + -
189A MET* 1.3 81.1 - - - +
191A ASP* 1.3 62.5 + - - +
192A ARG 4.1 1.3 - - - +
193A GLY* 5.3 5.6 - - - +
194A ALA 3.4 11.2 - - - +
195A VAL* 4.5 1.1 - - + +
408A PEG 3.5 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLN* 1.3 73.8 - - - +
192A ARG* 1.3 105.6 + - - +
193A GLY 3.3 0.2 - - - -
194A ALA* 2.9 27.9 + - + +
195A VAL* 4.9 0.2 - - - +
196A LEU* 3.7 27.0 - - + +
312A ARG* 3.1 25.9 + - - +
----------------------------------------------------------
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