Contacts of the strand formed by residues 151 - 159 (chain A) in PDB entry 4WB9
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 PHE 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE 5.5 0.7 - - - +
147A ILE* 3.9 28.2 - - + +
148A ASP 3.6 11.7 - - - -
149A GLY* 3.1 22.3 + - - +
150A ASN* 1.3 90.7 - - - +
152A PHE* 1.3 59.8 - - - +
153A THR 4.1 0.2 - - - -
493A THR* 3.9 26.5 - - + -
494A VAL 3.2 7.9 - - - +
495A LYS* 3.8 28.0 - - + -
496A ILE* 3.8 11.9 - - - +
499A LYS* 4.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 4.2 23.8 - - + -
151A PHE* 1.3 72.0 - - - +
153A THR* 1.3 67.7 + - - +
154A TYR* 3.6 33.4 - + + -
492A VAL 3.6 1.6 - - - +
493A THR* 3.4 1.0 - - - -
494A VAL* 2.8 57.5 + - + +
496A ILE* 4.1 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 3.5 5.2 - - - -
145A ILE* 3.0 60.6 + - + +
147A ILE* 3.4 25.0 - - + +
151A PHE 4.1 1.4 + - - -
152A PHE* 1.3 74.8 - - - +
154A TYR* 1.3 65.4 + - - +
491A THR* 3.8 19.5 - - + -
492A VAL 3.3 2.7 - - - +
493A THR* 2.7 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG 3.1 13.5 - - - +
144A THR* 4.1 12.8 - - + -
145A ILE* 4.9 0.7 - - - +
152A PHE* 3.6 33.7 - + + -
153A THR* 1.3 75.0 - - - +
155A THR* 1.3 76.0 + - - +
156A ARG* 4.1 18.1 - - + -
491A THR* 3.5 4.2 - - - +
492A VAL* 2.8 76.4 + - + +
494A VAL* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY* 3.4 19.1 - - - -
143A ARG* 2.8 38.9 + - - +
145A ILE* 4.0 21.8 - - + -
154A TYR* 1.3 85.6 - - - +
156A ARG* 1.4 63.8 + - - +
157A HIS* 4.0 4.7 + - - -
489A VAL* 4.1 17.9 - - + -
490A LYS 3.1 7.0 - - - +
491A THR* 3.8 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 6.0 1.2 - - - +
78A ARG* 4.6 11.1 - - - +
142A GLY* 4.9 0.7 - - - +
154A TYR* 4.1 23.3 - - + -
155A THR* 1.4 76.2 - - - +
157A HIS* 1.3 62.7 + - - +
158A GLU* 2.9 49.9 + - + +
159A PRO* 6.0 0.6 - - - +
489A VAL* 3.5 4.0 - - - -
490A LYS* 2.8 51.0 + - + +
492A VAL* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 3.9 27.0 - - + +
141A GLN 3.3 23.7 + - - +
142A GLY* 3.7 18.7 - - - +
143A ARG* 4.8 12.8 - - + +
155A THR* 4.0 10.2 + - - -
156A ARG* 1.3 77.0 - - - +
158A GLU* 1.3 64.6 + - - +
159A PRO* 4.1 1.2 - - - +
186A CYS 5.4 1.0 - - - +
484A HIS* 5.0 18.0 - + - -
487A THR* 4.0 20.3 + - - +
488A GLU 4.0 3.8 - - - -
489A VAL* 4.0 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 4.7 8.3 + - - +
156A ARG* 2.9 49.8 + - + +
157A HIS* 1.3 74.8 - - - +
159A PRO* 1.4 78.9 - - + +
487A THR* 3.1 7.9 - - - -
488A GLU* 2.7 44.1 + - + +
490A LYS* 2.7 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.4 28.2 - - + -
78A ARG* 4.2 14.8 - - - +
85A ARG* 6.4 0.2 - - - +
156A ARG* 6.0 0.7 - - - +
157A HIS 4.6 0.9 - - - +
158A GLU* 1.4 100.3 - - + +
160A ILE* 1.3 65.1 + - - +
186A CYS 3.3 25.5 - - - +
187A GLY* 3.4 24.0 - - - +
188A ASN* 3.6 7.0 - - - +
486A TYR 3.8 5.6 - - - +
487A THR* 4.9 0.2 - - + -
488A GLU* 4.3 3.3 - - - +
----------------------------------------------------------
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