Contacts of the strand formed by residues 209 - 216 (chain A) in PDB entry 1SBB
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 HIS 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TRP 4.6 0.4 + - - -
163A VAL* 3.4 3.6 - - - +
164A ASN* 2.7 51.4 + - - +
165A GLY 5.0 2.9 + - - -
202A PHE* 5.7 0.2 - - - -
208A ASN* 1.3 72.4 - - - +
210A PHE* 1.3 80.0 + - - +
211A ARG* 3.8 17.1 - - + +
240A GLU* 3.6 28.7 + - + +
241A ALA 3.5 5.8 - - - -
242A TRP* 3.5 47.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 5.2 1.8 - - + -
145A LEU* 3.6 28.9 - - + -
161A TRP* 4.9 3.1 - - + -
162A TRP 4.0 2.7 - - - -
163A VAL* 3.8 16.8 - - + +
196A LEU* 4.1 5.4 - - + -
198A VAL* 3.9 22.0 - - + -
202A PHE* 3.2 41.1 - + - -
203A TRP* 3.7 34.5 - + - -
208A ASN* 3.6 25.6 - - + -
209A HIS* 1.3 86.3 - - - +
211A ARG* 1.3 61.8 + - - +
239A ALA 4.5 0.4 - - - -
240A GLU* 3.2 0.9 - - - -
241A ALA* 2.7 45.5 + - + +
242A TRP 4.5 0.2 - - - -
243A GLY 4.3 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A SER 3.9 0.2 - - - +
161A TRP* 3.3 12.3 - - - -
162A TRP* 2.9 46.0 + - + +
209A HIS* 3.8 7.9 - - + -
210A PHE* 1.3 77.8 - - - +
212A CYS* 1.3 64.5 + - - +
213A GLN* 3.2 43.9 + - + +
236A ASN* 3.3 7.9 + - - -
238A SER* 2.9 26.6 + - - -
239A ALA 3.3 6.3 - - - -
240A GLU* 3.0 35.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 4.3 2.8 - - - +
129A LEU* 4.3 1.1 - - + -
147A CYS* 2.0 52.3 - - + -
159A LEU* 3.3 28.7 - - - -
160A SER 3.4 3.8 - - - -
161A TRP* 3.9 14.6 - - + -
211A ARG* 1.3 73.5 - - - +
213A GLN* 1.3 60.1 + - - +
214A VAL* 4.0 2.4 + - - -
237A ILE 3.7 0.7 - - - +
238A SER* 3.4 4.9 - - - -
239A ALA* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLU 3.4 1.1 - - - +
159A LEU* 3.1 6.1 - - - +
160A SER* 2.8 49.0 + - - +
162A TRP* 3.1 46.5 + - + +
211A ARG* 3.2 42.7 - - - +
212A CYS* 1.3 72.1 - - - +
214A VAL* 1.3 62.0 + - - +
215A GLN 4.2 0.2 - - - -
236A ASN* 3.0 26.6 + - - +
237A ILE 3.5 3.6 - - - -
238A SER* 3.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 4.3 15.9 - - + +
127A VAL* 3.6 44.4 - - + -
149A ALA* 4.3 13.2 - - + -
157A VAL* 4.5 13.7 - - + -
158A GLU 3.1 6.1 - - - +
159A LEU* 3.8 24.2 - - + -
192A LEU* 5.8 0.9 - - + -
212A CYS* 4.4 1.6 - - - -
213A GLN* 1.3 81.5 - - - +
215A GLN* 1.3 64.0 + - - +
216A PHE* 3.7 0.5 + - - +
235A GLN 3.4 3.1 - - - +
236A ASN* 3.1 6.4 + - - +
237A ILE* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A HIS 3.5 0.9 - - - +
157A VAL* 2.9 28.1 - - - -
158A GLU* 2.7 39.5 + - + +
214A VAL* 1.3 71.3 - - - +
216A PHE* 1.3 74.0 + - - +
217A HIS* 2.8 29.9 + - - -
235A GLN* 3.7 24.7 - - - +
236A ASN* 3.7 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 3.9 10.1 - - + -
123A THR 3.0 25.4 - - - -
124A PRO* 3.7 22.7 - - + -
125A PRO* 3.4 29.8 - - + -
152A PHE* 3.8 4.9 - - + -
153A PHE 3.5 12.1 - - - -
154A PRO 3.6 22.2 - - - -
156A HIS 3.4 3.6 - - - -
157A VAL* 3.8 17.5 - - + -
214A VAL 3.7 0.6 + - - -
215A GLN* 1.3 81.0 + - - +
217A HIS* 1.3 76.1 + - - +
218A GLY* 4.1 10.5 - - - -
232A PRO* 5.2 5.4 - - + -
234A THR* 3.8 25.9 - - - +
235A GLN* 3.2 15.7 + - - +
----------------------------------------------------------
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