Contacts of the strand formed by residues 228 - 235 (chain A) in PDB entry 1LAP
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 228 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PRO* 4.3 10.5 - - + +
181A THR* 3.6 34.3 - - + +
184A ALA* 4.0 13.9 - - + -
202A ILE* 3.5 31.6 - - + -
203A ARG 3.3 9.9 - - - +
204A PRO* 5.3 2.0 - - + -
208A ILE* 4.0 5.4 - - - -
216A PHE* 3.7 3.1 - - - -
227A PRO* 1.3 79.9 - - - +
229A PHE* 1.3 73.1 + - - +
230A LEU 4.0 3.1 - - - +
300A ALA 3.8 0.3 - - - +
302A LEU* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ARG* 2.8 53.7 + - + +
207A TRP* 3.8 17.9 - + + -
208A ILE* 3.8 10.2 - - + +
213A MET* 4.0 27.4 - - + -
216A PHE* 4.2 11.0 - + - -
228A VAL* 1.3 74.8 - - - +
230A LEU* 1.3 60.8 + - - +
231A GLU* 3.9 11.2 - - + -
299A LEU* 3.7 28.3 - - + -
300A ALA 3.9 1.3 - - - -
301A PRO* 4.3 13.7 - - + -
342A ALA* 4.3 21.8 - - + -
345A TYR* 3.6 37.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 4.0 22.9 - - + -
184A ALA* 4.1 17.3 - - + +
187A VAL* 3.9 24.0 - - + -
200A VAL* 3.9 12.8 - - + -
201A PHE 3.5 9.0 - - - +
202A ILE* 4.1 11.7 - - + -
228A VAL* 3.9 5.3 - - + -
229A PHE* 1.3 71.7 - - - +
231A GLU* 1.3 60.6 + - - +
232A ILE* 3.8 25.4 - - + -
281A CYS* 4.2 7.0 - - - -
298A GLY 3.4 6.4 - - - +
299A LEU* 3.4 2.3 - - - -
300A ALA* 3.0 42.1 + - + +
302A LEU* 3.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 3.4 4.3 - - - -
201A PHE* 2.7 53.9 + - + +
203A ARG* 2.8 34.9 + - - +
229A PHE* 3.7 8.7 + - + -
230A LEU* 1.3 69.8 - - - +
232A ILE* 1.3 61.9 + - - +
233A HIS* 2.8 30.1 + - - -
297A VAL* 3.6 2.4 - - - +
298A GLY 3.5 3.4 - - - -
299A LEU* 3.6 16.3 - - + +
345A TYR* 2.9 15.5 + - + -
349A PHE* 3.4 25.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 4.1 17.3 - - + -
188A GLU* 5.1 0.4 - - - -
191A LEU* 3.5 21.1 - - + -
199A ASP 3.7 0.2 - - - -
200A VAL* 3.5 42.6 - - + -
230A LEU* 3.8 24.9 - - + -
231A GLU* 1.3 74.7 - - - +
233A HIS* 1.3 62.1 + - - +
281A CYS* 4.9 6.3 - - - -
284A ILE* 3.7 30.3 - - + -
296A ILE 5.4 0.2 - - - +
297A VAL* 3.2 9.5 - - - +
298A GLY* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 3.9 2.6 - - - +
198A THR* 3.1 28.3 - - - +
199A ASP* 2.9 29.0 + - + +
201A PHE* 3.7 31.0 - + - -
231A GLU* 2.8 31.3 + - - -
232A ILE* 1.3 82.5 - - - +
234A TYR* 1.3 60.4 + - - +
235A LYS* 4.0 24.8 + - + -
296A ILE 3.6 3.6 - - - +
297A VAL* 3.8 13.5 - - + +
349A PHE* 3.8 21.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 5.2 0.2 - - + -
195A SER* 3.7 16.6 - - - -
197A LYS* 3.6 23.1 + - + -
198A THR* 3.9 6.5 - - + -
233A HIS* 1.3 74.0 - - - +
235A LYS* 1.3 57.8 + - - +
236A GLY* 3.3 11.3 + - - -
284A ILE* 4.2 18.6 - - + -
287A ALA 4.2 5.2 - - - -
288A ALA* 3.5 38.6 - - + -
291A ASP* 3.4 27.2 + - - -
292A LEU* 3.1 31.0 + - + -
294A ILE* 3.5 13.0 - - + -
295A ASN* 3.4 1.6 - - - +
296A ILE* 2.8 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 2.9 38.0 + - + +
198A THR 5.9 0.2 - - - -
199A ASP* 3.3 28.9 - - + +
233A HIS* 4.2 24.7 + - + -
234A TYR* 1.3 73.9 - - - +
236A GLY* 1.3 59.5 + - - +
237A SER 3.4 4.7 - - - +
240A ALA* 5.5 11.7 + - + -
295A ASN* 3.3 15.0 - - - +
----------------------------------------------------------
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