Contacts of the strand formed by residues 155 - 161 (chain D) in PDB entry 3RZL
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 155 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D THR* 3.6 32.1 - - + -
115D TYR 3.4 10.5 - - - -
120D LEU* 4.5 11.2 - - + -
121D THR 4.9 0.4 - - - -
122D TYR* 3.6 40.4 - + + -
129D LEU 4.7 2.7 - - - -
131D PRO* 3.6 35.0 - - + -
134D TRP* 4.0 4.9 - - - -
153D PHE 3.8 0.6 - - - -
154D ASN* 1.3 84.0 - - - +
156D VAL* 1.3 78.5 + - - +
157D LEU* 4.3 2.2 - - + -
252D THR 3.7 0.2 - - - +
253D PHE* 3.3 5.9 - - - +
254D ARG* 2.7 53.3 + - + +
256D ILE* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ALA 3.9 0.3 - - - +
114D THR* 3.3 7.1 - - - -
115D TYR* 2.7 64.8 + - + +
134D TRP* 3.7 14.6 - - + -
138D LEU* 4.3 11.2 - - + -
155D PHE* 1.3 80.4 - - - +
157D LEU* 1.3 71.4 + - - +
158D ILE* 3.9 3.4 + - + +
251D LEU* 4.0 18.2 - - + -
252D THR 3.2 16.6 - - - +
253D PHE* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D GLN* 4.3 25.6 - - + +
113D ALA 3.6 14.6 - - - +
114D THR* 3.7 16.4 - - + -
122D TYR* 3.8 25.8 - - + +
124D PHE* 5.1 4.7 - - + -
129D LEU* 5.3 4.5 - - + -
155D PHE* 4.3 5.6 - - + -
156D VAL* 1.3 74.2 - - - +
158D ILE* 1.3 67.0 + - - +
159D ASN* 4.1 19.9 + - - +
173D ASP* 5.2 1.1 - - - +
250D ASN* 3.6 1.6 + - - +
251D LEU* 3.5 3.3 - - - -
252D THR* 2.7 48.7 + - - +
254D ARG* 3.9 20.2 - - - +
265E C 5.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D VAL* 4.0 20.0 - - + -
91D TYR* 3.5 29.8 - - + +
112D GLN* 3.1 9.2 - - - +
113D ALA* 2.7 39.6 + - + +
115D TYR* 3.7 33.7 - - + -
138D LEU* 4.2 16.6 - - + -
156D VAL* 4.4 7.0 - - + +
157D LEU* 1.3 77.1 - - - +
159D ASN* 1.3 66.0 + - - +
249D VAL* 3.7 18.6 - - + -
250D ASN 3.3 3.6 - - - +
251D LEU* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 3.7 7.9 + - - -
111D LYS 3.5 4.0 - - - +
112D GLN* 2.9 36.4 + - - +
157D LEU* 4.2 20.0 + - - +
158D ILE* 1.3 76.4 - - - +
160D ARG* 1.3 58.5 + - - +
161D TYR* 3.5 32.1 + - + +
168D ILE* 4.6 10.7 - - - +
249D VAL* 3.4 0.7 - - - -
250D ASN* 2.6 53.8 + - + +
252D THR* 5.1 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLU* 2.7 42.8 + - - -
91D TYR* 3.2 43.9 - - + +
110D ARG* 3.6 6.2 - - - +
111D LYS* 3.2 47.7 + - + +
158D ILE 4.2 0.2 - - - -
159D ASN* 1.3 72.3 - - - +
161D TYR* 1.3 65.5 + - - +
162D LYS* 3.5 33.2 + - - +
166D ASP* 4.1 0.3 - - - +
247D PRO* 3.6 18.2 - - + +
248D ARG 3.1 5.6 - - - +
249D VAL* 3.5 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 3.7 10.8 - - + -
159D ASN* 3.5 40.0 + - + +
160D ARG* 1.3 73.9 - - - +
162D LYS* 1.3 63.1 + - - +
163D ASP* 3.1 1.7 + - - +
166D ASP* 3.6 15.0 - - + -
167D HIS* 3.4 45.8 - - - -
168D ILE* 3.5 18.9 - - - +
193D ARG* 3.7 15.9 - - - +
238D LEU* 3.6 18.2 - - + +
246D ALA 4.3 0.2 - - - +
247D PRO* 3.1 1.2 - - - +
248D ARG* 2.6 77.6 + - + +
250D ASN* 4.5 2.9 + - + +
----------------------------------------------------------
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