Contacts of the strand formed by residues 173 - 182 (chain B) in PDB entry 4GJ0
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 LYS 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASN* 3.0 19.9 + - - -
170B PHE 3.1 15.5 + - - +
172B ARG* 1.3 86.6 - - + +
174B CYS* 1.3 64.9 + - - +
175B TYR* 3.4 22.7 - - + +
200B SER* 3.0 19.8 + - - -
202B HIS* 4.3 6.7 - - + -
206B GLU* 2.9 27.2 + - - +
283B ASP* 2.9 37.5 + - - -
284B ARG 3.4 11.0 - - - +
285B LEU* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B THR 3.5 0.2 - - - -
163B CYS* 2.0 53.2 - - + -
164B PRO* 4.1 5.2 - - + -
167B TRP* 3.6 16.4 - - + -
168B ILE 3.3 6.3 - - - +
173B LYS* 1.3 71.5 - - - +
175B TYR* 1.3 63.2 + - - +
283B ASP* 3.1 7.8 - - - +
284B ARG* 2.8 37.4 + - + +
285B LEU 4.0 4.0 - - - -
286B ALA* 3.5 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS 4.6 0.2 - - - +
167B TRP* 3.4 6.9 - - - -
168B ILE* 2.7 43.4 + - - +
170B PHE* 3.6 29.7 + - + -
171B GLN* 5.5 0.9 + - - +
173B LYS* 3.4 36.6 - - + +
174B CYS* 1.3 76.4 - - - +
176B TYR* 1.3 61.1 + - - +
177B PHE* 3.8 21.7 + - + -
199B VAL* 3.9 17.0 - - + -
206B GLU* 2.4 39.4 + - + +
209B PHE* 3.5 16.8 - + + -
210B LEU* 3.8 20.9 - - + -
281B VAL* 4.7 1.8 - - + -
282B CYS 3.2 6.5 - - - +
283B ASP* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS* 3.7 48.0 + - + +
167B TRP* 3.6 38.3 - + + -
175B TYR* 1.3 73.9 - - - +
177B PHE* 1.3 64.5 + - - +
178B GLY* 3.5 26.2 + - - -
179B LYS 5.6 0.5 + - - -
194B MET* 4.0 27.0 - - + +
280B TRP* 3.8 23.6 - + - -
281B VAL* 3.3 7.6 - - - +
282B CYS* 2.8 37.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS 5.5 0.8 + - - -
168B ILE* 4.1 22.9 - - + -
175B TYR* 3.8 21.5 - - + -
176B TYR* 1.3 79.9 - - - +
178B GLY* 1.3 64.3 + - - +
179B LYS* 3.9 9.6 + - + +
209B PHE* 4.0 12.8 - + - -
210B LEU* 3.9 28.7 - - + -
213B HIS* 3.4 51.8 - + + +
214B ALA* 4.5 2.7 - - - -
215B SER 5.8 0.2 - - - -
262B MET* 5.7 0.2 - - + -
280B TRP 4.0 2.5 - - - -
281B VAL* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR* 3.5 24.0 + - - -
177B PHE* 1.3 75.1 - - - +
179B LYS* 1.3 65.6 + - - +
279B ALA* 3.3 7.4 - - - +
280B TRP* 2.8 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR* 5.6 0.6 + - - -
177B PHE* 3.9 8.9 + - + +
178B GLY* 1.3 83.3 - - - +
180B GLY* 1.3 61.5 + - - +
182B LYS* 4.8 1.4 + - - -
215B SER* 3.0 33.0 + - - +
217B THR* 5.1 2.2 + - - -
278B GLY 3.4 13.9 + - - +
279B ALA* 4.2 3.8 - - + +
280B TRP* 3.8 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 1.3 76.0 - - - +
181B THR* 1.3 66.4 + - - -
182B LYS* 3.4 10.8 + - - +
277B LEU 3.4 5.9 - - - +
278B GLY* 3.0 13.0 + - - +
280B TRP* 3.2 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLY* 1.3 69.6 - - - -
182B LYS* 1.3 70.2 + - - +
276B LYS* 3.6 37.7 - - + +
277B LEU 3.2 9.2 - - - +
278B GLY* 4.2 6.1 - - - -
193C ASP* 3.4 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS 4.8 0.4 + - - -
180B GLY* 3.7 13.5 + - - +
181B THR* 1.3 86.3 + - - +
183B GLN* 1.3 63.3 - - - +
186B HIS* 3.5 31.7 + - + +
187B ALA* 4.0 12.8 - - + +
190B ALA* 4.0 5.8 - - - -
220B TRP* 2.7 24.8 + - - -
276B LYS* 4.1 3.6 - - - -
277B LEU 2.8 24.5 + - - +
280B TRP* 3.3 38.9 - - + +
193C ASP* 4.2 4.5 - - - -
301C GOL 3.1 42.7 + - - -
----------------------------------------------------------
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