Contacts of the strand formed by residues 151 - 156 (chain B) in PDB entry 4JHN
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 THR 151 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B HIS* 3.1 14.1 + - - -
118B GLN* 4.6 0.2 - - - -
147B ALA* 3.3 0.7 - - - -
148B GLY* 3.1 42.8 + - - -
149B SER 3.6 10.2 + - - +
150B ASN* 1.3 85.0 - - - +
152B SER* 1.3 64.1 - - - +
164B TRP 3.6 5.2 - - - -
166B ASP* 3.5 23.8 - - + +
171B GLN* 3.6 20.0 - - + +
172B ILE* 3.9 12.6 - - + -
197B CYS* 3.8 11.3 - - - +
198B GLY 4.2 2.3 + - - -
199B TYR 5.1 2.0 - - - +
202B SER* 4.9 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B HIS* 2.8 20.6 + - - -
100B LEU* 3.7 6.6 - - - +
118B GLN 2.7 21.5 + - - -
146B SER 3.6 6.3 - - - -
151B THR* 1.3 71.6 - - - +
153B ALA* 1.3 62.4 + - - +
163B MET* 3.2 9.4 - - - +
164B TRP* 2.9 64.2 + - - +
172B ILE* 4.5 0.2 - - - +
197B CYS* 4.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.0 1.8 - - - +
145B LEU* 3.4 8.9 - - - +
146B SER* 2.8 37.2 + - - +
152B SER* 1.3 76.9 - - - +
154B ALA* 1.3 61.9 + - - +
155B LEU 4.4 0.2 - - - -
161B LEU* 4.3 1.1 - - + -
162B PHE 3.3 9.4 - - - +
163B MET* 4.0 2.7 - - + -
164B TRP* 4.1 4.3 - - - -
195B ILE* 3.5 35.7 - - + -
197B CYS* 3.6 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 5.8 0.4 - - + -
136B PHE* 3.7 33.9 - - + -
142B ILE* 4.4 9.9 - - + -
144B GLN 3.5 5.4 - - - +
145B LEU* 3.8 16.6 - - + -
153B ALA* 1.3 75.4 - - - +
155B LEU* 1.3 59.7 + - - +
160B ARG 3.8 1.6 - - - +
161B LEU* 3.6 3.7 - - - -
162B PHE* 2.8 36.3 + - - -
164B TRP* 3.9 4.9 - - + -
195B ILE* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ILE* 3.6 3.9 - - - -
143B LYS* 2.7 39.9 + - + -
144B GLN* 2.8 37.5 + - + +
154B ALA* 1.3 73.6 - - - +
156B THR* 1.3 63.3 + - - +
159B GLY 4.0 1.6 - - - -
160B ARG 3.5 17.9 - - - +
161B LEU* 4.3 4.0 - - + +
192B VAL* 3.4 37.2 - - + +
193B SER* 3.6 33.7 - - - +
194B TRP* 3.6 8.1 - - - +
195B ILE* 4.1 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B HIS* 4.0 19.1 - - + -
141B LYS 3.1 11.2 - - - +
142B ILE* 4.3 6.7 - - + +
143B LYS* 3.9 6.4 - - - +
154B ALA 5.3 0.2 - - - +
155B LEU* 1.3 82.5 - - - +
157B GLU* 1.3 65.2 + - - +
158B ASP* 2.6 27.8 + - - -
159B GLY* 3.1 13.9 + - - -
160B ARG* 2.9 42.9 + - - +
162B PHE* 3.9 21.8 - - + -
192B VAL 4.7 0.3 - - - +
----------------------------------------------------------
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