Contacts of the helix formed by residues 312 - 322 (chain A) in PDB entry 3LKB
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 THR 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.6 10.3 - - - -
310A ARG* 3.8 19.3 - - + +
311A ILE* 1.3 77.4 - - - +
313A ASN* 1.3 71.3 + - - +
314A GLU* 2.8 20.0 + - + +
315A THR* 2.9 27.6 + - + +
316A VAL* 2.8 32.1 + - - +
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Residues in contact with ASN 313 (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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76A ILE 4.8 1.1 - - - +
77A PRO* 3.4 28.3 - - + +
97A LEU 3.3 16.4 + - - -
98A ARG* 3.1 32.7 + - - +
99A ILE* 3.9 14.3 - - + +
100A PRO* 3.6 7.1 - - + +
312A THR* 1.3 88.3 + - - +
314A GLU* 1.3 70.8 + - - +
317A TYR* 3.0 28.4 + - - +
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Residues in contact with GLU 314 (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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98A ARG* 5.5 13.0 - - + -
310A ARG* 5.8 2.7 + - - +
312A THR* 2.8 12.2 + - + +
313A ASN* 1.3 93.2 + - - +
315A THR* 1.3 65.7 + - + +
317A TYR* 3.3 7.9 + - - +
318A GLN* 3.1 28.5 + - + +
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Residues in contact with THR 315 (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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304A ALA* 3.5 10.2 - - - +
308A PHE* 3.6 33.3 - - + -
310A ARG* 3.1 54.6 + - + +
312A THR* 2.9 28.6 + - + -
314A GLU* 1.3 77.3 - - + +
316A VAL* 1.3 58.6 + - - +
318A GLN* 3.1 6.0 + - - +
319A ALA* 3.0 27.9 + - - +
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Residues in contact with VAL 316 (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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77A PRO* 3.9 20.0 - - + +
78A VAL* 3.7 21.1 - - + -
100A PRO* 4.0 4.5 - - + -
300A ALA* 4.2 4.9 - - + -
301A ILE* 3.1 32.1 - - + -
304A ALA* 4.2 14.8 - - + -
311A ILE* 4.6 3.6 - - + -
312A THR 2.8 19.2 + - - +
313A ASN 4.1 0.2 - - - +
315A THR* 1.3 76.2 + - - +
317A TYR* 1.3 65.1 + - - +
319A ALA* 3.3 5.9 + - - +
320A ILE* 3.0 38.4 + - + +
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Residues in contact with TYR 317 (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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100A PRO* 3.9 11.9 - - + +
117A ASP* 3.6 27.6 + - + +
118A TYR* 3.6 32.3 - + + -
120A PHE* 4.1 13.2 - + - -
313A ASN 3.0 22.0 + - - +
314A GLU* 3.4 7.2 - - - +
315A THR 3.3 0.2 - - - -
316A VAL* 1.3 76.4 - - - +
318A GLN* 1.3 80.4 + - - +
320A ILE* 3.0 20.2 + - - +
321A VAL* 3.1 38.6 + - + +
347A LYS* 3.4 32.0 + - - +
350A HIS* 5.5 0.3 - - - -
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Residues in contact with GLN 318 (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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307A ARG* 3.7 11.7 + - - +
308A PHE* 4.0 26.0 - - + -
314A GLU* 3.1 19.1 + - + +
315A THR 3.1 7.4 + - - +
317A TYR* 1.3 96.5 - - - +
319A ALA* 1.3 66.0 + - - +
321A VAL* 3.7 13.5 + - - +
322A GLY* 3.2 17.7 + - - -
347A LYS* 4.9 8.3 - - - +
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Residues in contact with ALA 319 (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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300A ALA* 3.3 31.9 - - - +
303A ARG* 3.8 23.0 + - + -
304A ALA* 3.9 4.7 - - - +
307A ARG* 4.0 13.0 + - - +
308A PHE* 5.2 1.1 - - + -
315A THR 3.0 12.7 + - - +
316A VAL 3.5 7.9 - - - +
318A GLN* 1.3 78.2 - - - +
320A ILE* 1.3 61.8 + - - +
322A GLY* 3.5 2.3 + - - -
323A MET* 3.4 22.2 + - - +
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Residues in contact with ILE 320 (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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78A VAL* 5.5 0.9 - - + -
100A PRO* 3.8 27.6 - - + -
102A ILE* 5.0 14.4 - - + -
120A PHE* 3.6 45.5 - - + -
296A ILE* 5.2 6.5 - - + -
300A ALA* 3.7 17.0 - - + -
316A VAL* 3.0 26.1 + - + +
317A TYR* 3.0 9.1 + - - +
319A ALA* 1.3 77.5 - - - +
321A VAL* 1.3 58.0 + - - +
322A GLY 3.2 0.9 - - - -
323A MET* 3.1 31.9 + - + +
345A PHE* 3.4 20.8 - - + +
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Residues in contact with VAL 321 (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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120A PHE* 4.1 12.8 - - + -
317A TYR* 3.1 50.7 + - + +
318A GLN* 3.7 18.8 - - - +
320A ILE* 1.3 75.3 - - - +
322A GLY* 1.3 58.0 + - - +
323A MET 3.4 0.7 - - - -
324A ASN* 3.1 15.9 + - - -
345A PHE* 3.6 2.2 - - - +
346A THR* 3.7 12.0 - - - +
347A LYS* 3.8 48.1 + - + +
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Residues in contact with GLY 322 (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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307A ARG* 4.8 8.3 - - - -
318A GLN 3.2 17.2 + - - -
319A ALA 3.9 3.8 - - - -
320A ILE 3.2 0.4 - - - -
321A VAL* 1.3 77.4 - - - +
323A MET* 1.3 56.2 + - - +
324A ASN* 3.0 16.5 + - - +
327A ASN* 2.9 24.8 - - - +
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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