Contacts of the strand formed by residues 266 - 275 (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 CYS 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A THR* 5.1 0.4 - - - -
264A ASP 4.6 3.1 - - - -
265A LEU* 1.3 83.3 - - - +
267A ARG* 1.3 62.7 + - - +
292A VAL* 3.8 13.5 - - + -
293A LEU 3.2 16.0 + - - -
294A ASN* 4.0 2.0 - - - -
299A HIS* 2.3 58.1 - - + -
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Residues in contact with ARG 267 (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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256A ASP* 3.8 10.9 + - - -
259A GLN* 3.8 20.6 + - - +
260A THR* 3.0 41.1 - - + +
265A LEU* 4.2 17.9 - - + +
266A CYS* 1.3 77.1 - - - +
268A VAL* 1.3 65.5 + - - +
269A HIS* 2.9 35.4 + - + -
292A VAL* 3.3 23.7 - - - +
293A LEU* 3.6 9.7 + - - +
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Residues in contact with VAL 268 (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* 3.8 32.4 - - + -
267A ARG* 1.3 74.6 - - - +
269A HIS* 1.3 74.4 + - - +
290A PRO* 4.5 9.9 - - + -
292A VAL* 3.4 24.2 - - + -
303A VAL* 3.8 26.0 - - + -
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Residues in contact with HIS 269 (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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166A ASN* 6.0 0.4 - - - -
173A ARG* 6.3 1.3 - - - -
190A TRP* 4.6 2.2 - + - -
256A ASP* 3.5 20.9 - - - -
257A LEU* 5.2 14.6 - - + +
260A THR* 4.7 5.6 - - + -
267A ARG* 2.9 44.6 + - + +
268A VAL* 1.3 89.9 + - - +
270A PRO* 1.3 85.8 - - + +
271A VAL* 4.3 1.0 - - - +
290A PRO* 4.2 5.6 - - - -
291A CYS 2.9 34.4 + - - +
293A LEU* 5.0 14.0 - - + +
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Residues in contact with PRO 270 (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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165A CYS* 3.5 25.8 - - + +
166A ASN* 3.4 33.7 - - + +
169A SER* 4.1 9.9 - - - +
190A TRP* 4.3 18.3 - - + -
191A VAL 5.6 1.6 - - - +
192A ILE* 5.9 4.5 - - + -
257A LEU* 5.1 6.1 - - - +
269A HIS* 1.3 112.5 - - + +
271A VAL* 1.3 72.8 + - - +
289A LEU* 3.8 11.9 - - - +
290A PRO* 4.3 2.0 - - + -
293A LEU* 4.9 2.6 - - - +
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Residues in contact with VAL 271 (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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160A ILE 6.1 0.2 - - - +
161A ILE* 2.2 48.0 - - + -
162A GLY 4.2 1.6 - - - +
163A SER* 4.4 16.4 - - - +
164A GLY 5.2 0.4 - - - -
165A CYS 4.8 2.6 - - - +
257A LEU* 5.7 6.1 - - + -
269A HIS 4.3 1.1 - - - +
270A PRO* 1.3 82.4 - - - +
272A SER* 1.3 67.1 + - - +
273A THR* 4.7 1.1 - - + -
288A SER* 2.9 10.9 + - - -
289A LEU 2.5 39.9 + - - +
291A CYS* 3.6 26.5 - - + +
293A LEU* 4.8 9.6 - - + -
298A SER* 6.1 0.4 - - - -
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Residues in contact with SER 272 (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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142A GLY 4.9 0.2 - - - -
143A THR* 3.8 20.0 - - - -
146A ASN* 2.0 52.3 + - - +
160A ILE* 3.8 8.0 - - - +
162A GLY* 3.7 7.9 + - - +
163A SER 4.8 1.7 - - - +
164A GLY 5.2 1.3 - - - -
271A VAL* 1.3 78.9 - - - +
273A THR* 1.3 66.3 + - - +
286A PHE* 3.8 3.7 - - - -
287A LEU* 2.5 26.5 - - - -
288A SER* 4.4 0.7 - - - -
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Residues in contact with THR 273 (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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157A MET* 5.3 12.8 - - + -
160A ILE* 5.1 6.3 - - + +
161A ILE* 6.4 0.4 - - + -
271A VAL* 4.7 2.0 - - + -
272A SER* 1.3 77.4 - - - +
274A MET* 1.3 56.5 + - - +
275A VAL* 4.2 1.5 - - - +
286A PHE* 2.6 54.1 - - + -
287A LEU 3.2 5.7 + - - -
289A LEU* 4.0 24.8 + - - +
290A PRO 4.8 0.5 + - - -
291A CYS* 3.8 32.1 - - + +
298A SER* 4.9 2.9 - - - +
302A ILE* 4.6 17.6 - - + +
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Residues in contact with MET 274 (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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150A TRP* 3.4 27.1 - - + -
157A MET* 3.6 23.7 - - + +
273A THR* 1.3 78.5 - - - +
275A VAL* 1.3 65.5 + - - +
276A LYS* 3.2 48.9 + - + +
278A PHE* 4.0 12.6 - - - -
284A ASN* 3.2 31.9 - - + -
286A PHE* 2.8 27.5 - - + -
302A ILE* 4.4 9.9 - - - +
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Residues in contact with VAL 275 (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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273A THR* 5.8 1.3 - - - +
274A MET* 1.3 74.2 - - - +
276A LYS* 1.3 60.0 + - - +
278A PHE* 4.1 21.8 - - + -
279A TYR* 6.5 1.1 - - + -
281A ILE* 3.1 18.5 - - + +
284A ASN 3.9 2.3 + - - -
285A VAL* 2.5 81.4 + - + +
287A LEU* 4.0 16.4 - - + +
289A LEU* 3.3 35.0 - - + -
315A LEU* 5.5 3.8 - - + -
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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