Contacts of the strand formed by residues 177 - 187 (chain B) in PDB entry 5T78
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 177 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 4.0 21.1 - - + +
147B GLY* 3.9 37.5 - - - +
148B TYR 3.7 9.2 - - - +
149B PHE* 4.1 6.5 - - + -
172B VAL 3.7 0.2 - - - +
173B LEU* 3.5 7.2 - - - +
174B GLN* 2.9 32.4 + - - +
175B SER* 3.1 10.6 + - - +
176B ASP* 1.3 86.5 - - + +
178B TYR* 1.3 60.8 + - - +
179B THR* 4.9 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLY 2.9 24.4 + - - -
148B TYR* 2.8 49.8 + - + +
149B PHE* 3.6 30.7 - + - -
150B PRO* 4.4 0.7 - - + -
151B GLU* 3.8 44.2 - - + +
171B ALA* 3.9 11.0 - - + -
172B VAL 3.2 18.6 - - - -
173B LEU* 3.8 31.9 - - + +
177B LEU* 1.3 71.9 - - - +
179B THR* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 5.2 13.7 - - + +
183A THR* 5.7 7.2 - - + +
144B LEU* 4.1 22.2 - - + -
145B VAL 3.3 12.3 - - - +
146B LYS* 3.8 20.7 + - + +
147B GLY* 3.6 9.5 + - - -
148B TYR* 4.2 0.9 - - - -
170B PRO 4.2 1.2 - - - +
171B ALA* 3.4 2.3 - - - -
172B VAL* 2.9 34.4 + - - +
174B GLN* 6.2 0.2 - - - +
177B LEU* 4.9 2.3 + - - +
178B TYR* 1.3 78.1 + - - +
180B LEU* 1.3 65.4 + - - +
181B SER* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.8 4.2 - - - +
145B VAL* 2.9 52.6 + - + +
148B TYR* 3.3 21.7 - - - +
151B GLU* 4.6 3.1 - - - +
153B VAL* 3.6 20.0 - - + +
155B VAL* 4.0 15.5 - - + -
168B THR* 4.1 11.4 - - + -
169B PHE* 3.3 21.3 - - - +
170B PRO 4.6 2.2 - - - -
171B ALA* 3.8 13.0 - - + +
179B THR* 1.3 77.5 - - - +
181B SER* 1.3 78.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.9 1.5 - - - +
140A PHE* 3.7 25.5 - - - -
181A SER* 3.8 13.3 + - - -
183A THR* 4.4 6.9 + - - -
127B LEU* 5.1 1.8 - - - -
143B CYS 3.3 11.9 - - - -
144B LEU* 3.9 13.5 - - - +
168B THR* 3.8 2.1 - - - +
169B PHE* 2.8 42.6 + - - +
179B THR* 5.5 0.3 - - - +
180B LEU* 1.3 83.1 + - - +
182B SER* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.8 4.9 - - - -
142B GLY* 3.1 6.4 - - - -
143B CYS* 3.0 32.9 + - - +
155B VAL* 3.7 26.2 - - - +
157B TRP* 3.1 24.2 + - - -
166B VAL* 4.1 2.8 - - - +
167B HIS 3.6 7.2 + - - -
168B THR* 3.1 23.4 + - - +
180B LEU* 4.5 0.4 - - - +
181B SER* 1.3 73.9 - - - +
183B SER* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.5 23.8 - - - -
142A ASN* 3.2 23.0 + - - -
140B THR* 3.7 7.8 - - - +
141B LEU 3.5 4.9 - - - -
157B TRP* 4.6 0.2 - - - -
165B GLY 4.1 0.6 + - - -
166B VAL* 3.2 7.1 - - - +
167B HIS* 3.0 42.4 + - - +
169B PHE* 3.9 14.0 - - - -
182B SER* 1.3 73.9 - - - +
184B VAL* 1.3 63.3 + - - +
185B THR* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL 4.0 0.3 - - - +
140B THR* 3.4 0.7 - - - -
141B LEU* 2.7 49.1 + - + +
157B TRP* 3.6 44.6 - - + -
162B LEU* 4.1 24.0 - - + -
164B SER 4.7 1.6 - - - +
165B GLY 3.1 5.2 - - - +
166B VAL* 3.6 21.8 - - + -
183B SER* 1.3 74.9 + - - +
185B THR* 1.3 70.2 + - - +
186B VAL* 4.2 5.5 + - + -
196B VAL* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 4.8 3.8 + - - -
138B MET* 3.5 28.6 - - + +
139B VAL 3.2 15.7 - - - +
140B THR* 3.0 24.4 + - - +
162B LEU* 5.4 0.2 - - - +
164B SER 4.2 3.3 - - - +
165B GLY* 2.9 28.9 + - - -
167B HIS* 6.1 1.0 - - - -
183B SER* 4.4 3.3 + - - -
184B VAL* 1.3 76.1 - - - +
186B VAL* 1.3 68.3 + - - +
187B PRO* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B MET* 3.5 6.5 - - - +
139B VAL* 2.8 51.9 + - + +
141B LEU* 4.9 9.9 - - + -
162B LEU* 3.7 39.9 - - + -
184B VAL* 4.2 7.6 - - + +
185B THR* 1.3 79.6 - - - +
187B PRO* 1.3 78.8 - - + +
190B THR* 4.0 13.7 - - + -
191B TRP* 4.1 15.9 - - + -
196B VAL* 5.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER 3.4 13.5 - - - +
138B MET* 3.9 13.9 - - + -
139B VAL* 4.0 0.6 - - - +
186B VAL* 1.3 93.7 - - + +
188B SER* 1.3 57.8 + - - +
189B SER* 4.2 10.1 - - - +
190B THR* 2.8 44.6 + - - +
191B TRP 3.6 3.1 + - - -
----------------------------------------------------------
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