Contacts of the strand formed by residues 219 - 225 (chain A) in PDB entry 1RL3
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 VAL 219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER* 3.2 7.8 + - - -
156A PHE* 2.7 42.1 + - + +
177A GLN 3.3 9.0 - - - +
178A GLY* 3.6 4.3 - - - -
179A GLU 3.3 35.4 - - - +
180A MET* 3.9 14.8 - - + -
215A ALA* 4.1 6.7 - - + -
217A THR 2.8 24.7 - - - +
218A ASN* 1.3 76.0 - - - +
220A LYS* 1.3 60.1 + - - +
221A LEU* 3.8 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 5.7 2.7 - - - +
125A ALA* 4.9 7.2 - - - -
153A PRO* 3.1 34.0 - - - +
154A VAL 3.4 8.7 - - - +
155A SER* 4.4 7.2 - - - +
176A ASP* 3.1 38.0 + - + +
177A GLN* 3.3 21.4 + - + +
219A VAL* 1.3 73.9 - - - +
221A LEU* 1.3 81.8 + - - +
222A TRP* 3.3 26.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PRO* 3.5 0.5 - - - +
154A VAL* 2.7 40.9 + - + +
156A PHE* 4.4 9.2 - - + -
162A VAL* 4.3 16.4 - - + -
173A TYR* 3.7 24.7 - - + -
174A VAL 3.4 7.4 - - - +
175A ILE* 3.6 32.8 - - + -
176A ASP 4.0 1.8 - - - +
180A MET* 4.4 4.5 - - + -
198A PHE* 3.8 16.8 - - + -
219A VAL* 3.8 23.8 - - + +
220A LYS* 1.3 105.5 + - - +
222A TRP* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 5.1 3.4 - - + -
122A THR* 4.0 11.4 - - + -
125A ALA* 3.8 4.9 - - + -
126A LEU* 3.3 56.8 - - + -
129A ALA* 3.6 18.8 - - + +
151A MET* 4.1 18.2 - - + -
152A PHE* 3.1 33.0 - - - +
153A PRO* 3.5 27.6 - - + -
154A VAL* 4.2 3.1 - - - -
173A TYR* 3.2 5.9 - - - +
174A VAL* 2.9 48.5 + - + +
176A ASP* 2.4 44.5 + - + -
220A LYS* 3.3 22.2 - - - -
221A LEU* 1.3 74.3 - - - +
223A GLY* 1.3 60.1 + - - +
224A ILE* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A MET* 3.6 3.9 - - - +
152A PHE* 3.1 51.2 + - - -
154A VAL* 4.1 1.0 - - - +
172A PHE 3.1 11.2 - - - -
173A TYR* 4.3 9.0 - - - -
222A TRP* 1.3 74.8 - - - +
224A ILE* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.6 31.4 - - + -
150A ALA* 4.0 14.1 - - + +
151A MET* 4.0 20.0 - - + -
152A PHE* 3.7 5.4 - - - -
171A ASN* 2.3 36.2 - - - +
172A PHE* 3.1 42.6 + - + +
223A GLY* 1.3 77.1 - - - +
225A ASP* 1.3 80.8 + - - +
228A SER* 3.7 14.6 - - - -
229A TYR* 4.4 11.4 - - + +
233A LEU* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TYR* 4.5 5.3 + - - +
114A LYS* 3.4 40.1 - - - +
150A ALA 4.0 5.5 - - - +
152A PHE* 4.5 5.7 - - + -
170A ASP 3.7 6.7 - - - -
171A ASN* 3.7 3.6 - - - +
224A ILE* 1.3 76.4 - - - +
226A ARG* 1.3 65.2 + - + +
227A ASP* 2.9 17.4 + - + +
228A SER* 2.9 55.1 + - - -
229A TYR* 3.1 8.8 + - - +
----------------------------------------------------------
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