Contacts of the strand formed by residues 180 - 184 (chain b) in PDB entry 5W97
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 ASN 180 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294a THR 4.5 0.2 + - - -
295a VAL* 3.0 27.3 + - - +
296a GLY* 3.7 11.6 - - - -
152b MET 3.7 0.7 - - - +
153b LEU* 3.4 4.5 - - - -
154b VAL* 2.8 45.5 + - - +
172b THR* 3.4 20.7 - - + +
173b ASP 3.2 18.7 + - - +
175b ILE* 3.6 11.3 - - - +
178b ARG* 2.7 28.8 + - - +
179b LEU* 1.3 73.0 - - - +
181b GLN* 1.3 59.1 - - - +
23h GLN* 3.8 2.5 - - - +
24h ASN* 4.2 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88b ASP 5.9 1.2 + - - -
91b ASN* 4.5 16.9 - - - +
151b ARG* 2.8 47.3 + - + -
152b MET 3.4 4.7 - - - -
153b LEU* 3.8 6.1 - - + -
172b THR* 4.9 0.9 - - - -
180b ASN* 1.3 72.9 - - - +
182b THR* 1.3 66.8 + - - +
183b THR* 5.5 1.7 - - + +
16h PHE* 6.3 0.6 - - - -
21h PRO 5.4 2.2 + - - -
22h ASN 4.0 7.1 + - - -
23h GLN* 3.0 49.2 + - - +
25h GLN* 3.5 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151b ARG* 3.9 2.9 - - - -
152b MET* 3.0 51.4 + - + +
154b VAL* 5.0 2.9 - - + -
163b TRP* 4.8 6.5 - - + -
170b LEU* 3.7 24.0 - - + +
171b LYS 5.6 0.3 + - - -
172b THR* 3.5 25.6 + - - +
180b ASN 4.2 0.4 + - - -
181b GLN* 1.3 78.7 - - - +
183b THR* 1.3 73.9 + - - +
23h GLN* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16b ILE* 6.1 0.3 - - - +
87b MET 4.1 19.2 + - - +
88b ASP 4.9 2.9 - - - +
89b GLU 4.8 0.2 - - - +
91b ASN* 3.3 39.1 + - - +
149b THR* 4.3 12.3 - - - +
150b ILE 3.4 9.4 - - - -
151b ARG* 4.8 1.6 - - - +
170b LEU* 3.3 23.7 - - - +
181b GLN* 5.5 3.1 - - + +
182b THR* 1.3 79.7 + - - +
184b LEU* 1.3 63.7 + - - +
185b MET* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144b LEU* 4.1 15.3 - - + -
148b MET 3.4 2.9 - - - +
149b THR* 3.7 1.4 - - - -
150b ILE* 2.9 61.4 + - + +
152b MET* 3.7 23.6 - - + -
163b TRP* 3.8 12.6 - - + -
168b LEU* 4.4 14.4 - - + -
170b LEU* 3.5 28.5 - - + -
183b THR* 1.3 78.5 + - - +
185b MET* 1.3 69.4 + - - +
186b SER 4.7 2.7 - - - +
211b LEU* 4.0 12.1 - - + -
213b LEU* 4.8 7.0 - - + -
----------------------------------------------------------
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