Contacts of the strand formed by residues 287 - 295 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C ASP* 3.5 21.5 - - - +
143C THR* 3.3 35.0 - - + -
144C TYR* 3.7 22.2 - + + -
147C TRP* 3.3 52.5 - + + -
154C VAL* 4.0 14.4 - - + -
273C THR* 5.0 0.9 - - - -
274C THR* 3.1 13.5 - - - +
275C LEU* 3.4 37.9 - - + -
285C GLU 3.5 13.5 - - - -
286C VAL* 1.3 74.4 - - - +
288C LEU* 1.3 59.3 + - - +
322C LEU* 3.5 17.5 - - - +
326C GLN* 4.1 4.6 + - - +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ASP* 4.1 6.5 - - - -
190C GLY* 3.1 32.8 - - - +
273C THR* 3.8 5.6 - - - -
274C THR 2.7 26.2 + - - +
276C VAL* 3.1 44.5 - - + +
282C ILE* 4.0 13.0 - - + -
286C VAL* 4.4 5.4 - - + -
287C PHE* 1.3 74.4 - - - +
289C SER* 1.3 92.4 + - - +
290C ILE* 3.6 3.5 + - + -
315C LEU* 3.3 16.4 - - + -
319C ALA* 4.7 5.8 - - - +
322C LEU* 3.4 21.1 - - + -
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Residues in contact with SER 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLY* 4.1 0.9 - - - -
162C CYS* 2.7 38.6 + - - +
189C LEU* 3.3 15.6 - - - +
190C GLY 3.2 3.6 + - - -
271C PRO* 4.5 2.6 - - - +
272C VAL* 2.9 32.6 + - - -
273C THR* 3.6 9.5 - - - +
288C LEU* 1.3 84.4 - - - +
290C ILE* 1.3 75.3 + - - +
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Residues in contact with ILE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 4.8 2.2 - - + -
270C HIS 3.3 3.9 - - - +
271C PRO* 4.1 4.0 - - - -
272C VAL 2.9 8.2 + - - +
274C THR* 4.7 7.4 + - - +
276C VAL* 4.0 22.0 - - + -
279C PHE* 6.1 7.0 - - + -
280C HIS* 4.9 8.1 - - + +
288C LEU* 3.6 16.8 + - + +
289C SER* 1.3 91.0 + - - +
291C PRO* 1.3 78.1 - - + +
292C CYS* 2.7 37.1 + - - -
302C PHE* 4.6 13.5 - - + -
303C VAL 4.1 10.8 - - - +
305C VAL* 5.8 3.4 - - + -
307C MET* 5.3 6.1 - - + -
315C LEU* 4.1 19.7 - - + -
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Residues in contact with PRO 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C TRP* 3.1 44.9 - - + +
189C LEU* 4.1 10.3 - - + -
269C VAL* 4.0 2.5 - - + -
270C HIS 3.0 9.9 - - - +
271C PRO* 4.9 0.4 - - + -
290C ILE* 1.3 91.7 - - + +
292C CYS* 1.3 52.3 + - - +
303C VAL* 2.6 65.6 + - + +
305C VAL* 3.4 22.0 - - + -
206D ALA* 5.6 1.8 - - + -
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Residues in contact with CYS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C VAL* 3.1 7.6 - - - -
270C HIS* 2.4 56.6 + - - +
272C VAL* 3.1 27.6 - - + -
274C THR* 3.9 19.5 - - - -
290C ILE* 2.7 35.2 - - - -
291C PRO 1.3 67.9 - - - -
293C VAL* 1.3 58.8 + - - +
294C LEU* 4.0 1.5 - - + +
299C ILE* 3.3 25.8 - - + -
301C ASP 3.5 5.8 - - - +
302C PHE* 4.2 4.5 - - - +
303C VAL 4.3 0.2 - - - +
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 4.1 13.0 - - + -
267C LYS* 3.1 42.8 - - + +
269C VAL* 3.6 23.6 - - + +
292C CYS* 1.3 72.6 - - - +
294C LEU* 1.3 64.3 + - - +
299C ILE* 3.5 4.0 - - - -
300C THR* 2.9 31.3 + - + -
301C ASP* 3.0 40.2 + - - +
302C PHE 5.4 0.7 - - - +
178D GLY 4.4 8.7 - - - +
179D VAL* 4.5 7.0 - - + -
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ILE* 4.6 7.2 - - + -
258C LEU* 3.1 37.7 - - + +
261C SER* 3.3 20.5 + - - +
262C ILE* 4.7 8.7 - - + -
267C LYS* 3.0 27.7 + - - -
268C ARG 3.4 8.1 + - - +
270C HIS* 3.3 28.9 - - + -
272C VAL* 4.0 14.8 - - + -
292C CYS* 4.1 4.3 - - + +
293C VAL* 1.3 81.1 - - - +
295C GLY* 1.3 57.6 + - - +
298C GLY 3.3 6.7 - - - +
299C ILE* 3.8 27.4 - - + -
300C THR* 5.6 0.2 - - - -
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Residues in contact with GLY 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C SER 4.2 6.5 - - - -
262C ILE* 3.3 17.9 - - - +
265C ASN* 3.0 13.9 - - - -
267C LYS* 4.4 8.3 - - - -
293C VAL 4.3 0.4 - - - -
294C LEU* 1.3 73.2 - - - +
296C GLU* 1.3 67.0 + - - +
297C SER* 3.1 3.8 - - - -
298C GLY 2.9 18.1 + - - +
300C THR* 5.2 7.4 + - - -
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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