Contacts of the strand formed by residues 287 - 295 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B ASP* 3.5 22.6 - - - +
143B THR* 3.3 35.0 - - + -
144B TYR* 3.7 21.3 - + + -
147B TRP* 3.3 53.6 - + + -
154B VAL* 4.0 14.4 - - + -
273B THR* 5.0 0.9 - - - -
274B THR* 3.1 13.5 - - - +
275B LEU* 3.4 38.4 - - + -
285B GLU 3.5 14.1 + - - -
286B VAL* 1.3 75.2 - - - +
288B LEU* 1.3 59.4 - - - +
322B LEU* 3.5 17.3 - - - +
326B GLN* 4.1 4.4 + - - +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ASP* 4.1 6.1 - - - -
190B GLY* 3.1 33.4 - - - +
273B THR* 3.8 5.2 - - - -
274B THR 2.8 26.3 + - - +
276B VAL* 3.1 44.6 - - + +
282B ILE* 4.0 13.5 - - + -
286B VAL* 4.4 5.4 - - + -
287B PHE* 1.3 74.2 - - - +
289B SER* 1.3 92.4 + - - +
290B ILE* 3.6 3.0 + - + -
315B LEU* 3.3 16.4 - - + -
318B SER* 5.0 0.2 - - - -
319B ALA* 4.7 6.3 - - - +
322B LEU* 3.4 21.5 - - + -
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLY* 4.1 1.1 - - - -
162B CYS* 2.7 38.4 + - - +
189B LEU* 3.3 15.8 - - - +
190B GLY 3.2 3.6 + - - -
271B PRO* 4.5 2.3 - - - +
272B VAL* 2.9 31.9 + - - -
273B THR* 3.6 10.0 - - - +
288B LEU* 1.3 84.7 - - - +
290B ILE* 1.3 73.6 + - - +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.9 1.3 - - + -
270B HIS 3.3 3.7 - - - +
271B PRO* 4.1 4.0 - - - -
272B VAL 2.9 9.3 + - - +
274B THR* 4.7 6.7 + - - +
276B VAL* 4.0 20.2 - - + -
279B PHE* 6.1 6.7 - - + -
280B HIS* 4.9 8.1 - - + +
288B LEU* 3.6 17.7 + - + +
289B SER* 1.3 90.5 - - - +
291B PRO* 1.3 80.5 - - + +
292B CYS* 2.7 37.1 + - - -
302B PHE* 4.6 13.2 - - + -
303B VAL 4.1 10.1 - - - +
305B VAL* 5.8 3.1 - - + -
307B MET* 5.3 6.3 - - + -
315B LEU* 4.1 19.5 - - + -
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Residues in contact with PRO 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ALA* 5.6 1.6 - - + -
187B TRP* 3.1 45.5 - - + +
189B LEU* 4.1 10.5 - - + -
269B VAL* 4.0 2.7 - - + -
270B HIS 3.0 9.4 - - - +
271B PRO* 4.9 0.4 - - + -
290B ILE* 1.3 91.6 - - + +
292B CYS* 1.3 53.0 + - - +
303B VAL* 2.6 65.0 + - + +
305B VAL* 3.4 21.3 - - + -
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Residues in contact with CYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B VAL* 3.1 6.7 - - - +
270B HIS* 2.4 56.4 + - - +
272B VAL* 3.1 28.0 - - + -
274B THR* 3.9 18.8 - - - -
290B ILE* 2.7 36.1 - - - -
291B PRO 1.3 67.6 - - - +
293B VAL* 1.3 60.2 + - - +
294B LEU* 3.9 1.4 + - + +
299B ILE* 3.3 25.8 - - + -
301B ASP 3.5 6.5 - - - +
302B PHE* 4.2 4.0 - - - +
303B VAL 4.3 0.2 - - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLY 4.4 8.7 - - - +
179A VAL* 4.5 7.0 - - + -
267B LYS* 3.1 43.1 - - + +
269B VAL* 3.6 23.3 - - + +
292B CYS* 1.3 73.1 - - - +
294B LEU* 1.3 61.3 - - - +
299B ILE* 3.5 4.2 - - - -
300B THR* 2.9 31.2 + - + -
301B ASP* 3.0 41.6 + - - +
302B PHE 5.4 0.9 - - - +
8C ILE* 4.1 13.9 - - + -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ILE* 4.6 8.1 - - + -
258B LEU* 3.1 38.4 - - + +
261B SER* 3.3 21.2 + - - +
262B ILE* 4.7 8.3 - - + -
267B LYS* 3.0 28.2 + - - -
268B ARG 3.4 8.3 + - - +
270B HIS* 3.3 28.3 - - + -
272B VAL* 4.0 14.6 - - + -
292B CYS* 4.0 4.3 - - + +
293B VAL* 1.3 80.0 - - - +
295B GLY* 1.3 57.5 + - - +
298B GLY 3.3 6.5 - - - +
299B ILE* 3.7 27.1 - - + -
300B THR* 5.6 0.2 - - - -
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B SER 4.2 7.0 - - - -
262B ILE* 3.3 17.4 - - - +
265B ASN* 3.0 14.4 - - - -
267B LYS* 4.4 7.8 - - - +
293B VAL 4.3 0.4 + - - -
294B LEU* 1.3 73.6 - - - +
296B GLU* 1.3 68.0 + - - +
297B SER* 3.1 3.6 - - - -
298B GLY 2.9 19.1 + - - +
300B THR* 5.1 6.8 + - - -
17C LEU* 5.9 0.2 - - - -
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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