Contacts of the strand formed by residues 159 - 176 (chain A) in PDB entry 1TLY
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 GLU 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 3.1 16.3 - - - -
148A GLN* 2.8 29.0 + - - +
155A ALA 3.7 3.3 - - - +
156A ASN* 2.9 42.3 - - - +
157A GLU 3.7 3.1 - - - +
158A ASN* 1.3 76.3 - - - +
160A TRP* 1.3 72.3 + - - +
161A ASP* 3.4 4.3 + - + -
194A ASP* 3.1 29.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 3.9 31.6 - - + -
145A ALA* 4.4 12.3 - - + -
146A LYS* 3.3 39.9 - - - -
147A TYR* 3.8 24.7 - + + -
159A GLU* 1.3 81.0 - - - +
161A ASP* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 2.6 56.8 + - - +
148A GLN* 4.8 0.6 - - + +
156A ASN* 3.1 24.6 + - - +
159A GLU* 3.4 15.9 + - + +
160A TRP* 1.3 74.6 - - - +
162A GLY* 1.3 59.2 + - - +
192A GLY 4.1 1.0 - - - +
193A SER* 2.5 26.4 + - - -
194A ASP* 2.6 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 5.5 0.9 - - - -
145A ALA* 4.9 0.2 - - - +
146A LYS* 3.4 22.1 + - - +
161A ASP* 1.3 83.4 + - - +
163A TYR* 1.3 74.4 + - - -
191A TRP 3.5 9.9 - - - -
192A GLY 3.6 9.2 + - - -
193A SER* 3.6 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 4.5 5.1 - - - -
144A TYR 3.3 18.2 - - - +
145A ALA* 3.9 17.3 - - + -
162A GLY* 1.3 86.0 - - - -
164A ARG* 1.3 63.1 + - - +
190A ASP* 3.3 6.1 - - - +
191A TRP* 2.7 73.6 + + + -
192A GLY* 4.4 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 4.4 3.4 + - - -
107A ASN* 2.7 42.6 - - - +
109A ILE* 4.3 6.3 - - - +
124A TYR* 3.3 41.5 + - + -
143A VAL* 3.2 2.9 - - - +
144A TYR* 2.8 56.1 + - + -
163A TYR* 1.3 76.5 - - - +
165A PHE* 1.3 69.4 + - - +
188A ASN* 3.5 33.8 + - - +
189A PHE 3.2 4.3 - - - -
190A ASP* 2.6 42.6 + - - +
191A TRP* 3.7 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET* 3.3 53.2 - - + -
142A ASN 3.0 24.9 - - - -
143A VAL* 3.7 17.7 - - + +
164A ARG* 1.3 75.0 - - - +
166A LYS* 1.3 59.3 + - - +
167A ILE* 4.0 24.0 - - + -
187A THR 3.6 2.1 - - - +
188A ASN* 3.6 1.0 - - - -
189A PHE* 2.8 59.2 + + + +
191A TRP* 3.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 4.6 2.8 + - - -
81A GLU* 3.4 35.5 + - - +
107A ASN* 3.1 29.5 - - - +
141A MET* 3.3 3.6 - - - -
142A ASN* 2.8 49.8 + - - +
144A TYR* 3.2 37.2 - - + +
164A ARG* 4.0 0.8 - - + -
165A PHE* 1.3 76.1 - - - +
167A ILE* 1.3 64.8 + - - +
168A LYS* 3.8 19.2 - - - +
186A PHE* 5.3 5.6 - - + -
187A THR 3.3 5.2 - - - +
188A ASN* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.0 19.5 - - + -
140A SER 3.3 10.5 - - - +
141A MET* 4.0 18.2 - - + -
165A PHE* 4.0 17.7 - - + -
166A LYS* 1.3 75.4 - - - +
168A LYS* 1.3 62.7 + - - +
169A TYR* 4.6 14.8 - - + -
186A PHE* 3.0 3.0 - - - +
187A THR* 2.8 54.2 + - - +
189A PHE* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 4.6 13.9 - - - +
81A GLU* 3.0 36.3 + - - +
138A SER 4.7 0.2 - - - -
139A LEU* 3.7 0.6 - - - -
140A SER* 2.9 50.0 + - - +
142A ASN* 5.2 2.2 - - - +
166A LYS* 3.8 19.3 - - + +
167A ILE* 1.3 72.1 - - - +
169A TYR* 1.3 63.5 + - - +
184A ILE* 6.0 1.8 - - + -
185A GLY 3.2 4.7 - - - +
186A PHE* 3.2 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A MET* 5.1 6.3 - - + -
138A SER 3.1 15.0 - - - +
139A LEU* 3.7 19.7 - - + -
167A ILE* 4.6 18.2 - - + -
168A LYS* 1.3 78.8 - - - +
170A PHE* 1.3 58.1 + - - +
171A VAL* 4.8 9.2 - - + -
183A TYR* 3.2 43.8 + + - -
184A ILE* 3.5 7.1 - - - +
185A GLY* 2.6 54.3 + - - -
186A PHE* 5.0 1.1 + - - -
187A THR* 5.5 3.6 + - - -
218A HIS* 3.9 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A MET* 3.2 5.7 - - - -
138A SER* 2.9 53.7 + - - -
169A TYR* 1.3 72.1 - - - +
171A VAL* 1.3 67.7 + - - +
172A PRO* 3.5 28.9 - - + -
182A SER* 3.5 32.5 - - - -
183A TYR 3.7 1.3 - - - -
184A ILE* 3.8 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO 4.3 7.0 - - - +
137A MET* 3.6 32.8 - - + -
169A TYR* 4.8 7.9 - - + -
170A PHE* 1.3 85.1 - - - +
172A PRO* 1.3 77.1 - - + +
173A ILE* 3.3 7.6 + - + +
182A SER* 4.4 1.8 - - - -
183A TYR* 2.8 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 3.5 25.4 - - + +
137A MET* 4.5 0.9 - - - -
170A PHE* 3.5 29.8 - - + +
171A VAL* 1.3 91.3 - - - +
173A ILE* 1.3 64.0 + - - +
181A LEU 4.5 0.2 - - - +
182A SER* 4.1 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 3.6 15.9 - - + +
172A PRO* 1.3 75.5 - - - +
174A THR* 1.3 84.5 + - + +
181A LEU* 3.1 35.4 + - + +
182A SER* 3.7 21.8 - - - -
183A TYR* 3.7 14.4 - - + +
220A LEU* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 1.3 101.7 - - + +
175A ASP* 1.3 72.7 + - - +
176A LEU* 4.0 2.8 - - - +
180A GLN* 3.6 1.9 - - - +
181A LEU* 2.7 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 1.3 85.2 + - - +
176A LEU* 1.3 61.1 + - - +
178A GLY 5.4 2.5 - - - +
179A GLY 3.2 8.1 - - - +
180A GLN* 3.1 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 4.0 5.0 + - - +
175A ASP* 1.3 75.5 - - - +
177A TRP* 1.3 131.6 + - + +
178A GLY 3.2 1.5 - - - +
179A GLY* 2.8 27.6 + - - +
181A LEU* 4.2 28.0 - - + +
222A LEU* 3.7 18.5 - - + +
----------------------------------------------------------
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