Contacts of the strand formed by residues 285 - 295 (chain A) in PDB entry 3LDH
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 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A THR 4.1 0.7 - - - -
275A VAL* 2.5 51.2 + - + +
281A ILE* 2.1 52.5 - - + -
284A ASN* 1.3 70.7 - - - +
286A PHE* 1.3 60.3 + - - +
287A LEU* 2.8 13.1 + - + +
319A ALA* 3.8 24.5 - - + +
322A LEU* 5.4 7.2 - - + -
323A TRP* 2.3 48.5 - - + +
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Residues in contact with PHE 286 (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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143A THR* 3.1 29.0 + - - +
144A ASP* 3.9 1.0 + - - -
146A ASN* 3.5 21.8 - - - -
147A LYS* 3.8 35.3 - - + +
150A TRP* 3.5 37.0 - + - -
157A MET* 4.0 8.3 - - + -
160A ILE* 3.2 28.9 - - + -
272A SER* 3.8 2.9 - - - +
273A THR* 2.6 30.1 - - - -
274A MET* 2.8 42.2 - - + -
284A ASN 3.7 2.2 + - - -
285A VAL* 1.3 68.4 - - - +
287A LEU* 1.3 60.6 + - - +
322A LEU* 4.5 4.6 - - - +
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Residues in contact with LEU 287 (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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143A THR* 3.4 8.5 - - - -
193A GLY* 2.9 9.9 - - - +
194A GLN* 4.0 11.4 - - + -
271A VAL 3.0 0.7 - - - +
272A SER* 2.5 36.9 - - - -
273A THR* 3.2 7.2 + - - -
275A VAL* 4.0 16.8 - - + +
281A ILE* 5.0 0.2 - - + -
285A VAL* 2.8 16.7 + - + +
286A PHE* 1.3 75.6 - - - +
288A SER* 1.3 93.3 + - - +
289A LEU* 3.4 7.9 + - + +
315A LEU* 4.2 23.6 - - + +
318A SER* 4.8 4.0 - - - -
319A ALA* 4.2 30.7 - - + +
322A LEU* 5.1 6.5 - - + -
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 3.8 0.9 - - - +
164A GLY* 4.2 0.5 - - - -
165A CYS* 2.3 50.0 + - - +
192A ILE* 3.6 13.6 - - - +
193A GLY 1.8 61.9 + - - +
194A GLN* 2.9 8.5 - - - +
270A PRO* 5.7 0.4 - - - -
271A VAL 2.9 6.0 + - - -
272A SER* 4.7 0.2 - - - -
287A LEU* 1.3 82.6 - - - +
289A LEU* 1.3 59.1 + - - +
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Residues in contact with LEU 289 (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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192A ILE* 4.6 9.4 - - + -
270A PRO* 4.2 2.6 - - - +
271A VAL* 2.5 40.7 + - - +
273A THR* 4.0 12.4 + - - +
275A VAL* 3.3 33.9 - - + -
278A PHE* 5.5 7.9 - - + -
279A TYR* 5.6 6.3 - - + +
287A LEU* 3.4 8.2 + - + +
288A SER* 1.3 76.8 - - - +
290A PRO* 1.3 116.8 - - + +
291A CYS* 3.3 3.3 + - - +
302A ILE* 4.3 13.0 - - + -
303A VAL 4.7 3.8 - - - +
305A MET* 4.8 5.6 - - + -
315A LEU* 4.9 16.6 - - + -
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Residues in contact with PRO 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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190A TRP* 5.2 9.0 - - + -
192A ILE* 4.5 13.2 - - + -
268A VAL* 4.5 15.9 - - + -
269A HIS 3.5 12.8 - - - +
270A PRO* 4.3 2.8 - - + -
289A LEU* 1.3 107.4 - - + +
291A CYS* 1.3 52.3 + - - +
302A ILE* 2.6 39.5 - - - +
303A VAL* 3.6 31.6 - - + +
305A MET* 4.2 14.6 - - + -
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Residues in contact with CYS 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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268A VAL* 4.3 0.2 - - - -
269A HIS* 2.9 27.5 + - - +
271A VAL* 3.6 22.7 - - + -
273A THR* 3.8 24.5 - - + +
289A LEU 3.3 1.3 + - - +
290A PRO* 1.3 73.7 - - - +
292A VAL* 1.3 66.1 + - - +
293A LEU* 4.2 3.4 + - - +
298A SER* 3.0 42.4 - - - -
300A CYS* 5.6 0.4 - - - -
301A ASN 3.1 15.0 - - - +
302A ILE* 3.9 7.9 - - + +
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Residues in contact with VAL 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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266A CYS* 3.8 21.5 - - + +
267A ARG 3.3 14.6 - - - +
268A VAL* 3.4 33.7 - - + -
291A CYS* 1.3 77.8 - - - +
293A LEU* 1.3 52.6 + - - +
298A SER* 2.5 38.1 - - - +
299A HIS* 2.8 23.5 + - + +
301A ASN* 2.8 27.3 + - + +
303A VAL* 4.1 9.6 - - + -
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Residues in contact with LEU 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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161A ILE* 5.0 9.0 - - + -
257A LEU* 3.1 21.5 - - + +
260A THR* 1.4 65.9 - - + +
261A ILE* 3.8 14.4 - - + +
266A CYS* 3.2 24.6 + - - -
267A ARG 3.6 5.9 + - - +
269A HIS* 5.0 10.3 - - + -
270A PRO 4.9 7.0 - - - +
271A VAL* 4.8 20.6 - - + -
291A CYS 4.9 6.5 - - - +
292A VAL* 1.3 77.4 - - - +
294A ASN* 1.3 62.8 - - - +
298A SER* 3.6 13.0 - - - +
299A HIS* 4.0 0.7 - - - -
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Residues in contact with ASN 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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260A THR 4.0 2.5 - - - -
261A ILE* 3.6 12.6 - - - +
264A ASP* 2.3 38.0 - - - +
266A CYS* 4.0 3.1 - - - -
293A LEU* 1.3 75.4 - - - +
295A ASN* 1.3 51.6 + - - +
296A GLY 2.8 17.3 + - - -
297A ILE* 2.3 52.2 + - - +
299A HIS* 2.3 76.9 + - + +
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Residues in contact with ASN 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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92A LYS* 1.9 44.7 - - - +
261A ILE 3.6 3.4 - - - -
262A MET 3.4 7.9 + - - -
263A LYS 3.7 3.1 - - - +
264A ASP* 1.7 60.4 + - - +
294A ASN* 1.3 63.6 - - - +
296A GLY* 1.3 58.4 + - - +
297A ILE* 3.1 13.4 - - - +
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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