Contacts of the strand formed by residues 287 - 295 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASP* 3.5 22.1 - - - +
143A THR* 3.3 34.8 - - + -
144A TYR* 3.7 22.0 - + + -
147A TRP* 3.3 53.8 - + + -
154A VAL* 4.0 14.6 - - + -
157A VAL 4.9 0.2 - - - -
273A THR* 5.0 1.1 - - - -
274A THR* 3.1 14.6 - - - +
275A LEU* 3.4 42.0 - - + -
285A GLU 3.5 10.5 + - - -
286A VAL* 1.3 74.4 - - - +
288A LEU* 1.3 59.6 + - - +
322A LEU* 3.5 17.8 - - - +
326A GLN* 4.1 4.4 + - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASP* 4.1 6.7 - - - +
190A GLY* 3.1 31.6 - - - +
273A THR* 3.8 5.4 - - - -
274A THR* 2.8 26.4 + - - +
276A VAL* 3.1 44.6 - - + +
282A ILE* 4.0 13.5 - - + -
286A VAL* 4.4 5.2 - - + -
287A PHE* 1.3 74.2 - - - +
289A SER* 1.3 91.8 + - - +
290A ILE* 3.6 3.1 + - + -
315A LEU* 3.3 17.0 - - + -
319A ALA* 4.7 6.1 - - - +
322A LEU* 3.4 22.0 - - + -
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLY* 4.1 0.9 - - - -
162A CYS* 2.7 38.2 + - - +
189A LEU* 3.3 15.6 - - - +
190A GLY 3.2 3.8 + - - -
271A PRO* 4.5 2.1 - - - +
272A VAL* 2.9 32.0 + - - -
273A THR* 3.6 10.0 - - - +
288A LEU* 1.3 86.0 - - - +
290A ILE* 1.3 74.0 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.9 1.6 - - + -
270A HIS 3.3 3.5 - - - +
271A PRO* 4.1 3.8 - - - -
272A VAL 2.9 9.2 + - - +
274A THR* 4.7 7.2 + - - +
276A VAL* 4.0 21.1 - - + -
279A PHE* 6.1 7.2 - - + -
280A HIS* 4.9 7.4 - - + +
288A LEU* 3.6 16.5 + - + -
289A SER* 1.3 90.0 + - - +
291A PRO* 1.3 79.1 - - + +
292A CYS* 2.7 37.1 + - - -
302A PHE* 4.6 13.7 - - + -
303A VAL 4.1 9.9 - - - +
305A VAL* 5.8 2.9 - - + -
307A MET* 5.3 6.5 - - + -
315A LEU* 4.1 19.5 - - + -
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Residues in contact with PRO 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TRP* 3.1 45.3 - - + +
189A LEU* 4.1 11.0 - - + -
269A VAL* 4.0 3.1 - - + -
270A HIS 3.0 10.1 - - - +
271A PRO* 4.1 0.4 - - + -
290A ILE* 1.3 90.4 - - + +
292A CYS* 1.3 50.9 + - - +
303A VAL* 2.6 64.0 + - + +
305A VAL* 3.4 21.8 - - + -
206B ALA* 5.6 1.6 - - + -
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Residues in contact with CYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 3.1 6.7 - - - -
270A HIS* 2.4 56.0 + - - +
272A VAL* 3.1 27.4 - - + -
274A THR* 3.9 18.8 - - - -
290A ILE* 2.7 35.7 - - - -
291A PRO* 1.3 67.9 - - - +
293A VAL* 1.3 59.8 + - - +
294A LEU* 4.0 1.3 - - + +
299A ILE* 3.3 26.0 - - + -
301A ASP 3.5 6.5 - - - +
302A PHE* 4.2 4.7 - - - +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LYS* 3.1 43.5 - - + +
269A VAL* 3.6 23.3 - - + +
292A CYS* 1.3 72.5 - - - +
294A LEU* 1.3 62.8 - - - +
299A ILE* 3.5 3.8 - - - -
300A THR* 2.9 31.5 + - + -
301A ASP* 3.0 42.6 + - - +
302A PHE 5.4 1.1 - - - +
178B GLY 4.4 8.7 - - - +
179B VAL* 4.5 6.7 - - + -
8D ILE* 4.1 13.5 - - + -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS* 5.5 0.2 - - - +
158A ILE* 4.6 9.2 - - + -
258A LEU* 3.1 37.0 - - + +
261A SER* 3.3 21.3 + - - +
262A ILE* 4.7 8.5 - - + -
267A LYS* 3.0 27.3 + - - -
268A ARG 3.4 7.7 + - - +
270A HIS* 3.3 28.9 - - + -
272A VAL* 4.0 15.0 - - + -
292A CYS* 4.0 4.5 - - + +
293A VAL* 1.3 80.2 - - - +
295A GLY* 1.3 58.1 + - - +
298A GLY 3.3 6.7 - - - +
299A ILE* 3.8 27.4 - - + -
300A THR* 5.6 0.4 - - - -
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A SER 4.2 6.1 - - - -
262A ILE* 3.3 17.9 - - - +
265A ASN* 3.0 13.0 - - - -
267A LYS* 4.3 7.8 - - - +
293A VAL 4.3 0.4 + - - -
294A LEU* 1.3 74.7 - - - +
296A GLU* 1.3 68.0 + - - +
297A SER* 3.1 3.4 - - - -
298A GLY 2.9 19.5 + - - +
300A THR* 5.2 6.8 + - - -
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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