Contacts of the helix formed by residues 485 - 496 (chain C) in PDB entry 2LVN
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 SER 485 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460C MET* 5.2 0.4 - - - -
480C LEU* 3.6 2.0 - - - +
483C THR* 3.0 5.9 + - - -
484C ARG* 1.3 80.7 - - - +
486C VAL* 1.3 59.9 + - - +
487C GLU* 3.7 14.0 + - - +
488C ILE* 2.9 34.2 + - - +
489C THR* 2.8 31.6 + - - -
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Residues in contact with VAL 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C MET* 3.3 53.7 - - + +
463C GLN* 5.4 7.0 - - + +
464C ILE* 3.5 26.7 - - + -
467C MET* 5.6 4.9 - - + -
480C LEU* 4.0 2.5 - - + -
485C SER* 1.3 71.5 + - - +
487C GLU* 1.3 75.0 + - + +
489C THR* 3.8 2.4 - - - -
490C THR* 2.7 38.9 + - - +
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Residues in contact with GLU 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C MET* 5.9 1.9 - - - +
485C SER* 3.1 11.6 - - - +
486C VAL* 1.3 100.9 - - + +
488C ILE* 1.3 62.2 + - + +
490C THR* 4.2 4.2 - - - -
491C ASP* 3.6 16.6 + - - +
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Residues in contact with ILE 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C THR* 3.6 21.3 - - + +
485C SER* 2.9 28.4 + - - +
487C GLU* 1.3 77.8 - - + +
489C THR* 1.3 54.6 + - - +
491C ASP* 2.9 8.4 + - + +
492C ASN* 2.5 56.1 + - - +
495C GLU* 5.9 0.4 - - - +
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Residues in contact with THR 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ILE* 3.5 27.4 - - + -
476C VAL* 3.7 9.6 - - + -
479C ASP* 2.7 40.2 + - + +
480C LEU* 3.5 20.3 - - + +
483C THR* 3.0 5.2 + - - -
485C SER 2.8 23.1 + - - -
488C ILE* 1.3 71.7 - - - +
490C THR* 1.3 56.1 + - - +
492C ASN* 3.1 3.6 - - - +
493C ILE* 2.8 33.8 + - + +
498C ILE* 3.8 5.7 - - + +
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Residues in contact with THR 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ILE* 3.9 9.0 - - - +
467C MET* 3.9 19.4 - - + +
468C PHE* 3.3 39.9 - - + -
486C VAL* 2.7 23.5 + - - +
487C GLU* 4.2 4.9 - - - -
489C THR* 1.3 76.2 - - - +
491C ASP* 1.3 62.7 + - - +
493C ILE* 3.2 25.9 - - - +
494C LEU* 3.3 13.4 + - + +
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Residues in contact with ASP 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C GLU 3.6 11.7 + - - +
488C ILE* 2.9 10.8 + - + +
490C THR* 1.3 76.4 - - - +
492C ASN* 1.3 60.1 + - - +
494C LEU* 3.1 18.8 + - - +
495C GLU* 2.9 49.0 + - - +
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Residues in contact with ASN 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C ASP* 2.9 37.4 + - - +
482C LEU* 5.7 0.2 - - - +
483C THR* 3.3 22.0 - - - +
488C ILE* 2.5 24.7 + - - +
489C THR 3.1 11.2 - - - +
491C ASP* 1.3 69.2 - - - +
493C ILE* 1.3 65.8 + - - +
495C GLU* 3.0 19.8 + - - +
497C ARG* 2.9 56.1 + - + +
498C ILE* 4.8 0.7 - - + -
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Residues in contact with ILE 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C ILE* 3.6 30.5 - - + -
468C PHE* 4.6 15.3 - - + -
470C GLN* 5.3 3.6 - - - +
471C VAL* 3.5 37.7 - - + -
476C VAL* 4.9 0.7 - - + -
489C THR 2.8 21.8 + - - +
490C THR* 3.2 13.0 - - - +
492C ASN* 1.3 74.7 - - - +
494C LEU* 1.3 64.4 + - + +
496C GLY* 3.0 20.1 + - - -
498C ILE* 3.5 39.2 - - + +
500C VAL* 5.6 1.1 - - + -
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C PHE* 4.3 24.7 - - + -
470C GLN* 5.6 2.9 - - - +
490C THR* 3.3 25.6 - - + +
491C ASP* 3.1 23.0 + - - +
493C ILE* 1.3 81.2 - - + +
495C GLU* 1.3 59.7 + - - +
496C GLY 3.2 0.4 + - - -
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Residues in contact with GLU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C ILE* 5.9 0.5 - - - +
491C ASP* 2.9 32.1 + - - +
492C ASN* 3.0 22.8 + - - +
494C LEU* 1.3 76.5 - - + +
496C GLY* 1.3 58.7 + - - +
497C ARG* 2.8 35.9 + - - +
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Residues in contact with GLY 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C ILE 3.0 13.4 + - - -
494C LEU 3.2 1.2 - - - -
495C GLU* 1.3 79.6 - - - +
497C ARG* 1.3 64.9 + - - +
498C ILE 3.2 5.4 - - - -
499C GLN* 2.9 32.9 + - - +
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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