Contacts of the strand formed by residues 287 - 295 (chain D) in PDB entry 2LDX
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 287 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D ASP* 3.5 22.2 - - - +
143D THR* 3.3 35.2 - - + -
144D TYR* 3.7 21.1 - + + -
147D TRP* 3.3 53.6 - + + -
154D VAL* 4.0 13.9 - - + -
157D VAL 4.9 0.2 - - - -
273D THR* 5.0 0.9 - - - -
274D THR* 3.1 14.6 - - - +
275D LEU* 3.4 40.8 - - + -
285D GLU 3.5 11.0 + - - -
286D VAL* 1.3 73.7 - - - +
288D LEU* 1.3 59.1 + - - +
322D LEU* 3.5 17.5 - - - +
326D GLN* 4.1 4.0 + - - +
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASP* 4.1 6.3 - - - -
190D GLY* 3.1 33.4 - - - +
273D THR* 3.8 5.6 - - - -
274D THR* 2.7 26.7 + - - +
276D VAL* 3.1 44.6 - - + +
282D ILE* 4.0 12.6 - - + -
286D VAL* 4.4 5.8 - - + -
287D PHE* 1.3 73.7 - - - +
289D SER* 1.3 91.7 + - - +
290D ILE* 3.6 3.3 + - + -
315D LEU* 3.3 15.7 - - + -
318D SER* 5.0 0.2 - - - -
319D ALA* 4.7 6.1 - - - +
322D LEU* 3.4 22.9 - - + -
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Residues in contact with SER 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D GLY* 4.1 0.9 - - - -
162D CYS* 2.7 38.6 + - - +
189D LEU* 3.3 16.3 - - - +
190D GLY 3.2 3.4 + - - -
271D PRO* 4.5 2.4 - - - +
272D VAL* 2.9 32.1 + - - -
273D THR* 3.6 10.2 - - - +
288D LEU* 1.3 85.6 - - - +
290D ILE* 1.3 73.8 + - - +
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Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 4.8 1.3 - - + -
270D HIS 3.3 3.9 - - - +
271D PRO* 4.1 3.6 - - - -
272D VAL 2.9 8.8 + - - +
274D THR* 4.7 7.6 + - - +
276D VAL* 4.0 22.0 - - + -
279D PHE* 6.1 7.4 - - + -
280D HIS* 4.9 7.6 - - + +
288D LEU* 3.6 15.9 + - + +
289D SER* 1.3 90.4 + - - +
291D PRO* 1.3 77.4 - - + +
292D CYS* 2.7 37.2 + - - -
302D PHE* 4.6 13.9 - - + -
303D VAL 4.1 11.2 - - - +
305D VAL* 5.8 2.9 - - + -
307D MET* 5.3 6.5 - - + -
315D LEU* 4.1 20.4 - - + -
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Residues in contact with PRO 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ALA* 5.6 1.3 - - + -
187D TRP* 3.1 44.9 - - + +
189D LEU* 4.1 10.8 - - + -
269D VAL* 4.0 3.1 - - + -
270D HIS 3.0 10.3 - - - +
271D PRO* 4.0 0.7 - - + -
290D ILE* 1.3 90.8 - - + +
292D CYS* 1.3 52.0 + - - +
303D VAL* 2.6 63.7 + - + +
305D VAL* 3.4 22.0 - - + -
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Residues in contact with CYS 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D VAL* 3.1 7.9 - - - -
270D HIS* 2.4 56.6 + - - +
272D VAL* 3.1 27.6 - - + -
274D THR* 3.9 20.0 - - - -
290D ILE* 2.7 35.7 - - - -
291D PRO 1.3 68.6 - - - +
293D VAL* 1.3 59.8 + - - +
294D LEU* 4.0 1.5 - - + +
299D ILE* 3.3 25.6 - - + -
301D ASP 3.5 6.3 - - - +
302D PHE* 4.2 4.3 - - - +
303D VAL 4.3 0.2 - - - +
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Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.1 13.9 - - + -
178C GLY 4.4 8.7 - - - +
179C VAL* 4.5 7.2 - - + -
267D LYS* 3.1 42.8 - - + +
269D VAL* 3.6 23.3 - - + +
292D CYS* 1.3 72.2 - - - +
294D LEU* 1.3 63.4 + - - +
299D ILE* 3.5 4.2 - - - -
300D THR* 2.9 31.6 + - + -
301D ASP* 3.0 41.3 + - - +
302D PHE 5.4 0.9 - - - +
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Residues in contact with LEU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D ILE* 4.6 7.6 - - + -
258D LEU* 3.1 37.9 - - + +
261D SER* 3.3 20.2 + - - +
262D ILE* 4.7 9.2 - - + -
267D LYS* 3.0 28.3 + - - -
268D ARG 3.4 7.9 + - - +
270D HIS* 3.3 28.7 - - + -
272D VAL* 4.0 15.5 - - + -
292D CYS* 4.0 3.8 - - + +
293D VAL* 1.3 80.0 - - - +
295D GLY* 1.3 58.1 + - - +
298D GLY 3.3 6.5 - - - +
299D ILE* 3.8 28.0 - - + -
300D THR* 5.6 0.4 - - - -
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Residues in contact with GLY 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D SER 4.2 7.0 - - - -
262D ILE* 3.3 17.2 - - - +
265D ASN* 3.0 14.1 - - - -
267D LYS* 4.4 8.1 - - - -
293D VAL 4.4 0.4 + - - -
294D LEU* 1.3 74.0 - - - +
296D GLU* 1.3 66.3 + - - +
297D SER* 3.1 3.4 - - - -
298D GLY 2.9 18.8 + - - +
300D THR* 5.1 6.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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