Contacts of the strand formed by residues 151 - 156 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D HIS* 3.1 19.8 + - - -
118D GLN* 4.5 0.4 - - - -
147D ALA* 3.3 0.9 - - - -
148D GLY* 3.1 37.8 + - - -
149D SER 3.6 8.9 + - - +
150D ASN* 1.3 82.6 - - - +
152D SER* 1.3 63.2 + - - +
164D TRP 3.6 4.3 - - - -
166D ASP* 3.5 25.8 - - + +
171D GLN* 3.5 20.9 - - + -
172D ILE* 4.0 13.7 - - + -
197D CYS* 3.8 11.2 - - - +
198D GLY 4.1 2.8 + - - -
199D TYR 5.2 1.8 - - - +
202D SER* 4.9 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D HIS* 2.8 21.0 + - - -
100D LEU* 3.7 6.8 - - - +
118D GLN 2.7 21.7 + - - -
146D SER 3.6 6.3 - - - -
147D ALA* 4.4 0.2 - - - +
151D THR* 1.3 72.6 - - - +
153D ALA* 1.3 62.3 + - - +
163D MET* 3.2 9.2 - - - +
164D TRP* 2.9 62.5 + - - +
172D ILE* 4.5 0.3 - - - +
197D CYS* 4.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LEU* 4.0 2.1 - - - +
144D GLN 4.7 0.2 - - - -
145D LEU* 3.5 9.4 - - - +
146D SER* 2.9 34.3 + - - +
152D SER* 1.3 77.9 - - - +
154D ALA* 1.3 61.6 + - - +
161D LEU* 4.3 2.0 - - + -
162D PHE 3.2 10.1 - - - +
163D MET* 4.0 8.1 - - + -
164D TRP* 4.1 4.0 - - - -
195D ILE* 3.9 24.0 - - + -
197D CYS* 3.7 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D VAL* 5.8 0.2 - - + -
136D PHE* 3.7 34.3 - - + -
142D ILE* 4.3 9.4 - - + -
144D GLN 3.5 5.4 - - - -
145D LEU* 3.8 16.6 - - + -
153D ALA* 1.3 75.2 - - - +
155D LEU* 1.3 60.4 + - - +
160D ARG 3.7 1.7 - - - +
161D LEU* 3.6 4.4 - - - +
162D PHE* 2.8 36.4 + - - +
164D TRP* 3.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ILE* 3.6 5.2 - - - -
143D LYS* 2.7 43.3 + - + -
144D GLN* 2.8 34.5 + - + +
154D ALA* 1.3 74.1 - - - +
156D THR* 1.3 61.8 + - - +
159D GLY 4.0 0.7 - - - -
160D ARG 3.5 18.4 - - - +
161D LEU* 4.2 4.5 - - + +
192D VAL* 3.5 39.7 - - + +
193D SER 3.6 33.2 - - - +
194D TRP* 3.7 6.5 - - - +
195D ILE* 4.1 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D GLU 4.7 1.2 + - - -
140D HIS* 3.8 13.1 - - - -
141D LYS* 3.0 33.8 + - - +
142D ILE* 4.3 4.2 - - - +
143D LYS* 4.0 6.1 - - - +
154D ALA 4.2 0.2 - - - -
155D LEU* 1.3 82.7 - - - +
157D GLU* 1.3 63.6 + - - +
158D ASP* 2.7 30.7 + - - +
159D GLY* 3.1 14.2 + - - -
160D ARG* 3.0 44.7 + - + +
162D PHE* 4.9 6.9 - - + -
192D VAL 4.9 0.2 - - - +
----------------------------------------------------------
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