Contacts of the helix formed by residues 395 - 400 (chain A) in PDB entry 3LPK
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 GLY 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ASP 3.3 9.0 - - - -
292A THR 3.2 14.4 - - - -
293A THR 3.7 0.2 - - - -
294A ASN 3.2 15.9 + - - -
295A LEU* 4.3 2.2 - - - +
393A VAL* 3.0 12.2 + - - -
394A MET* 1.3 76.2 - - - +
396A ALA* 1.3 66.0 + - - -
397A VAL 3.3 2.9 - - - -
398A ILE* 3.1 6.1 + - - +
399A MET* 3.0 20.6 + - - +
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Residues in contact with ALA 396 (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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71A SER* 4.1 24.5 - - - +
74A GLY* 6.4 0.2 - - - -
75A TYR* 4.5 6.5 - - + -
215A LEU* 4.4 13.4 - - + +
289A ASP 3.8 2.0 + - - -
290A SER* 4.4 11.9 - - - +
292A THR 2.7 16.8 + - - +
293A THR* 3.2 5.8 + - - +
395A GLY* 1.3 71.2 - - - -
397A VAL* 1.3 57.8 + - - +
399A MET* 3.2 9.2 + - - +
400A GLU* 2.8 35.6 + - - +
456A Z76 5.3 1.3 - - - -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.9 21.3 - - - +
293A THR* 2.9 29.4 + - + +
294A ASN 4.1 0.4 - - - -
295A LEU* 3.9 9.6 - - + +
365A GLN* 3.3 43.5 - - - +
366A TYR* 4.8 2.7 - - - -
368A ARG* 4.3 6.1 - - + -
384A ALA* 3.8 39.0 - - + +
396A ALA* 1.3 75.6 - - - +
398A ILE* 1.3 71.2 + - + +
400A GLU* 3.8 15.2 - - - +
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Residues in contact with ILE 398 (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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295A LEU* 3.6 48.9 - - + -
346A LEU* 5.2 5.4 - - + -
359A ILE* 4.6 3.4 - - + -
361A ILE* 3.2 45.1 - - + +
366A TYR* 5.3 1.3 - - + -
394A MET* 4.2 28.3 - - + -
395A GLY 3.1 13.6 + - - +
397A VAL* 1.3 81.0 - - + +
399A MET* 1.3 66.1 + - + +
400A GLU 3.1 1.6 - - - -
401A GLY 3.1 11.3 + - - -
402A PHE* 3.2 20.6 - - + -
415A PHE* 5.9 0.7 - - + -
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Residues in contact with MET 399 (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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94A THR* 4.8 0.2 - - - -
213A LEU* 4.0 22.9 - - + +
215A LEU* 3.9 24.3 + - + +
288A VAL* 4.0 16.4 - - + -
289A ASP 4.0 2.9 - - - -
290A SER* 3.7 33.4 - - - -
394A MET* 4.0 7.6 - - + +
395A GLY 3.0 15.7 + - - +
396A ALA 3.2 6.5 + - - +
398A ILE* 1.3 78.3 - - + +
400A GLU* 1.3 58.7 + - - +
402A PHE* 2.8 30.0 + - - +
404A VAL* 4.2 21.3 - - + -
406A PHE* 4.0 27.4 - - + -
415A PHE* 6.2 2.5 - - + -
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Residues in contact with GLU 400 (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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71A SER* 3.3 27.4 + - - -
75A TYR* 2.5 28.0 + - + +
215A LEU* 3.2 30.5 - - + +
217A GLY* 3.5 23.9 + - - +
364A GLN 5.6 0.7 - - - +
365A GLN* 4.7 9.7 + - + +
396A ALA 2.8 23.6 + - - +
397A VAL* 3.8 15.9 - - - +
398A ILE 3.1 0.8 - - - -
399A MET* 1.3 76.4 - - - +
401A GLY* 1.3 59.9 + - - +
402A PHE 3.3 0.4 + - - -
418A SER* 4.0 4.2 + - - -
420A CYS 4.6 1.2 - - - +
421A HIS* 3.6 17.5 - - - +
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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