Contacts of the strand formed by residues 297 - 303 (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 ILE 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.5 5.7 - - - +
158A HIS* 2.6 46.2 - - + -
159A ARG* 4.0 1.6 - - - +
261A ILE* 5.0 2.5 - - - +
293A LEU* 3.9 1.6 - - - +
294A ASN* 2.3 54.7 + - - +
295A ASN 3.1 17.0 - - - +
296A GLY* 1.3 82.9 - - - +
298A SER* 1.3 57.1 + - - +
299A HIS* 3.2 12.6 - - - +
300A CYS* 2.9 32.1 - - - +
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Residues in contact with SER 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A HIS* 2.0 42.7 + - - -
160A ILE 5.3 0.4 + - - -
161A ILE* 4.2 15.7 - - - -
271A VAL* 6.1 0.9 - - - -
273A THR* 4.9 2.5 - - - +
291A CYS* 3.0 28.7 - - - -
292A VAL 2.5 13.9 - - - +
293A LEU* 3.6 13.5 - - - +
297A ILE* 1.3 68.4 - - - +
299A HIS* 1.3 50.1 - - - +
300A CYS* 2.2 27.8 + - - -
301A ASN 3.8 2.3 + - - -
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASP* 4.9 2.7 - - - -
266A CYS* 2.3 39.4 - - + -
292A VAL* 2.8 25.7 + - + +
294A ASN* 2.3 57.4 - - + +
297A ILE* 3.2 3.8 - - - +
298A SER* 1.3 65.2 - - - +
300A CYS* 1.3 54.5 + - - +
301A ASN* 2.3 40.6 + - - +
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A HIS* 4.0 13.2 - - - -
291A CYS* 5.6 0.2 - - - -
297A ILE* 2.9 28.5 - - - -
298A SER* 2.2 17.7 + - - -
299A HIS* 1.3 66.5 - - - +
301A ASN* 1.3 68.2 + - - +
302A ILE* 5.6 0.9 - - - -
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Residues in contact with ASN 301 (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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291A CYS* 3.1 3.6 - - - -
292A VAL* 2.8 47.7 + - + +
298A SER 3.8 1.4 + - - -
299A HIS* 2.3 41.0 + - - +
300A CYS* 1.3 81.6 + - - +
302A ILE* 1.3 66.3 + - - +
303A VAL* 4.0 2.2 - - + -
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Residues in contact with ILE 302 (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* 4.6 15.7 - - + +
274A MET 4.4 13.2 - - - +
278A PHE* 4.2 32.3 - - + -
289A LEU* 4.3 22.0 - - + -
290A PRO 2.6 24.2 - - - +
291A CYS* 4.4 14.1 - - + -
300A CYS 5.6 0.2 - - - -
301A ASN* 1.3 80.2 - - - +
303A VAL* 1.3 62.4 + - - +
304A LYS* 3.6 15.3 + - - +
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Residues in contact with VAL 303 (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* 3.8 35.7 - - + -
278A PHE* 6.3 0.2 - - - -
279A TYR* 5.6 0.3 + - - -
289A LEU* 4.7 4.0 - - - +
290A PRO* 3.6 30.6 + - + +
292A VAL* 4.1 12.1 - - + -
301A ASN* 4.1 2.4 + - + +
302A ILE* 1.3 75.7 - - - +
304A LYS* 1.3 71.0 + - - +
305A MET* 3.8 15.1 + - + +
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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