Contacts of the strand formed by residues 288 - 297 (chain A) in PDB entry 4LL4
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 288 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LYS* 3.9 30.3 - - + +
166A LYS* 3.6 34.3 - - + +
168A VAL* 5.6 0.4 - - + -
178A VAL* 4.1 26.5 - - + +
179A SER* 5.1 0.4 - - - -
180A VAL* 3.8 26.3 - - + +
278A ILE 4.0 0.3 - - - +
279A TYR* 3.0 3.1 - - - -
280A VAL* 2.7 43.9 + - + +
282A VAL* 4.5 7.2 - - + -
287A LYS* 1.3 73.1 - - - +
289A ILE* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LYS* 2.5 36.7 + - - +
277A LEU* 4.6 14.6 - - + -
278A ILE 3.6 4.0 - - - -
279A TYR* 3.7 10.8 - - + -
287A LYS* 3.6 32.2 + - + +
288A VAL* 1.3 73.4 - - - +
290A LEU* 1.3 76.1 + - - +
291A ASP* 4.2 7.0 + - + +
79C GLU 4.1 16.6 - - - +
80C ASP* 4.6 4.3 - - - +
82C PRO* 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA* 3.8 16.8 - - + +
163A LYS* 3.5 36.3 - - - +
164A LYS* 3.5 19.7 - - + +
180A VAL* 3.8 22.4 - - + +
182A ALA* 3.3 34.3 - - + +
276A LEU 3.5 0.7 - - - +
277A LEU* 3.1 6.8 - - - -
278A ILE* 2.6 48.2 + - + +
288A VAL 4.3 0.2 - - - -
289A ILE* 1.3 77.3 - - - +
291A ASP* 1.3 59.2 + - - +
292A LEU* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG* 3.1 24.7 + - - -
275A SER* 2.6 25.7 + - - -
276A LEU 3.6 2.9 - - - -
277A LEU* 3.6 12.6 - - + +
289A ILE* 4.1 7.4 + - + -
290A LEU* 1.3 72.1 - - - +
292A LEU* 1.3 66.7 + - - +
293A PRO* 3.5 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 4.1 24.9 - - + +
162A ALA* 3.8 26.5 - - + +
182A ALA* 4.6 12.3 - - + +
184A ILE* 4.7 15.5 - - + +
276A LEU* 2.6 45.5 + - + +
278A ILE* 3.8 29.8 - - + -
290A LEU* 4.6 4.7 - - + -
291A ASP* 1.3 83.6 + - - +
293A PRO* 1.3 70.3 - - + +
294A LEU* 3.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 5.4 7.7 - - + +
184A ILE* 5.7 0.2 - - - +
187A LYS* 3.1 40.5 - - - +
274A TYR 3.8 8.3 - - - +
275A SER* 4.0 3.8 - - - +
291A ASP* 3.5 13.9 - - - +
292A LEU* 1.3 86.7 - - + +
294A LEU* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 4.9 0.5 - - - +
184A ILE* 4.1 16.8 - - + -
187A LYS* 3.4 9.3 - - - +
189A PHE* 4.0 24.9 - - + -
195A ILE* 3.9 17.3 - - + -
215A ILE* 4.3 6.5 - - + -
273A GLU* 5.5 0.7 - - - -
274A TYR* 3.0 26.0 + - + +
275A SER* 3.6 10.1 - - - +
276A LEU* 3.6 24.9 - - + +
292A LEU 3.7 10.5 - - - +
293A PRO* 1.3 82.4 - - - +
295A VAL* 1.3 65.7 + - - +
296A ILE* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.0 17.5 - - + -
56A TRP* 3.7 26.2 - - + -
65A GLN* 3.3 22.9 - - + +
114A PHE* 4.2 31.9 - - + -
156A LEU* 4.6 7.0 - - + -
187A LYS* 3.0 13.1 + - - +
188A GLY* 3.4 4.3 - - - -
189A PHE 2.8 26.3 + - - +
294A LEU* 1.3 76.3 - - - +
296A ILE* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 3.4 26.9 + - - +
189A PHE* 3.2 19.1 - - + +
191A GLU* 4.4 13.7 - - + +
195A ILE* 5.3 0.2 - - + -
215A ILE* 5.0 3.8 - - + -
257A VAL* 3.8 33.7 - - + -
258A GLN 5.5 1.6 - - - +
274A TYR* 3.7 48.0 + - + +
294A LEU* 3.7 35.4 - - + -
295A VAL* 1.3 79.4 - - - +
297A GLY* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 3.8 10.2 - - - -
63A CYS* 4.1 5.6 - - - -
64A LYS* 3.3 24.5 - - - -
65A GLN* 3.8 2.5 - - - -
189A PHE 3.1 8.3 + - - -
190A CYS* 3.5 3.6 - - - -
191A GLU* 3.0 31.1 + - - +
296A ILE* 1.3 74.9 - - - +
298A SER* 1.3 60.7 + - - -
----------------------------------------------------------
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