Contacts of the helix formed by residues 454 - 468 (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 ASN 454 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453C SER* 1.3 87.4 - - - +
455C SER* 1.3 64.0 + - - +
456C GLN 3.2 3.1 - - - +
457C LEU* 3.0 17.5 + - + +
458C ASN* 2.9 34.5 + - - +
481C GLN* 3.0 33.0 + - - +
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Residues in contact with SER 455 (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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453C SER* 3.4 7.8 + - - -
454C ASN* 1.3 79.0 + - - +
456C GLN* 1.3 63.6 + - - +
458C ASN* 3.3 11.7 + - - +
459C ALA* 2.9 31.0 + - - +
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Residues in contact with GLN 456 (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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453C SER 5.2 0.4 + - - -
454C ASN 3.2 1.0 - - - -
455C SER* 1.3 81.1 - - - +
457C LEU* 1.3 64.0 + - + +
459C ALA* 3.3 7.8 + - - +
460C MET* 2.9 39.9 + - + +
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Residues in contact with LEU 457 (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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454C ASN* 3.0 23.1 + - + +
456C GLN* 1.3 79.0 - - + +
458C ASN* 1.3 67.2 + - - +
460C MET* 3.4 27.8 + - + +
461C ALA* 3.2 23.2 + - - +
477C LEU* 3.9 5.6 - - + +
480C LEU* 3.6 32.0 - - + +
481C GLN* 3.1 39.7 - - + +
484C ARG* 4.3 19.7 - - + +
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Residues in contact with ASN 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ASN* 2.9 31.3 + - - +
455C SER* 3.6 10.6 + - - +
457C LEU* 1.3 78.8 - - - +
459C ALA* 1.3 58.6 + - - +
461C ALA* 3.4 7.8 + - - +
462C HIS 3.4 0.3 + - - -
473C TYR* 2.7 32.0 + - + +
477C LEU* 3.3 31.8 - - + +
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Residues in contact with ALA 459 (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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455C SER 2.9 18.1 + - - +
456C GLN* 3.7 10.3 - - - +
458C ASN* 1.3 74.0 - - - +
460C MET* 1.3 61.8 + - - +
462C HIS* 3.0 12.7 - - - +
463C GLN* 2.9 28.6 + - - +
473C TYR* 4.7 0.4 - - - -
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Residues in contact with MET 460 (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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456C GLN* 2.9 26.7 + - + +
457C LEU* 3.5 31.2 - - + +
459C ALA* 1.3 75.9 - - + +
461C ALA* 1.3 62.6 + - - +
462C HIS 3.1 0.9 + - - -
463C GLN* 3.2 24.0 + - - +
464C ILE 3.6 5.4 + - - -
480C LEU* 3.4 26.0 - - + -
484C ARG 3.6 18.2 - - - +
485C SER* 5.2 0.2 - - - -
486C VAL* 3.3 34.6 - - + +
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Residues in contact with ALA 461 (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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457C LEU 3.2 5.7 + - - +
458C ASN 3.7 2.0 - - - +
459C ALA 3.3 0.2 - - - -
460C MET* 1.3 78.6 - - - +
462C HIS* 1.3 56.5 + - - +
463C GLN 3.3 0.2 - - - -
464C ILE* 3.3 4.7 + - - +
465C GLN* 2.8 30.0 + - - +
473C TYR* 3.9 8.5 - - + +
476C VAL* 3.6 31.1 - - + +
477C LEU* 3.5 32.8 - - + -
480C LEU* 4.1 6.9 - - + +
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Residues in contact with HIS 462 (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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458C ASN 3.4 2.8 + - - -
459C ALA* 3.0 21.2 + - - +
461C ALA* 1.3 80.0 - - - +
463C GLN* 1.3 62.8 + - - +
465C GLN* 3.2 3.9 + - + +
466C GLU* 3.0 56.2 + - + +
473C TYR* 3.5 32.5 - + - +
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Residues in contact with GLN 463 (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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459C ALA* 2.9 29.4 + - - +
460C MET* 3.2 18.8 + - - +
462C HIS* 1.3 87.0 + - - +
464C ILE* 1.3 59.4 + - + +
466C GLU* 3.1 11.2 + - - +
467C MET* 2.9 39.1 + - + +
486C VAL* 5.4 6.9 - - + +
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Residues in contact with ILE 464 (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 3.8 5.6 - - - +
461C ALA 3.3 6.2 + - - +
462C HIS 3.3 0.4 - - - -
463C GLN* 1.3 76.1 - - + +
465C GLN* 1.3 51.4 + - - +
467C MET* 3.6 10.0 - - + +
468C PHE* 2.6 40.5 + - + +
471C VAL* 4.9 0.7 - - + -
476C VAL* 3.7 19.1 - - + -
480C LEU* 3.9 4.3 - - + -
486C VAL* 3.5 40.2 - - + +
489C THR* 3.5 30.1 - - + -
490C THR* 3.9 13.2 - - - +
493C ILE* 3.6 29.6 - - + -
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Residues in contact with GLN 465 (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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461C ALA 2.8 16.1 + - - +
462C HIS* 3.5 6.5 - - + +
464C ILE* 1.3 77.3 - - - +
466C GLU* 1.3 68.9 + - - +
468C PHE 3.8 4.6 + - - -
469C PRO* 3.2 47.7 - - - +
471C VAL* 2.9 32.7 + - - +
473C TYR* 3.6 42.8 - - + +
476C VAL* 4.8 1.8 - - - +
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Residues in contact with GLU 466 (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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462C HIS* 3.0 44.6 + - - +
463C GLN* 3.3 11.7 - - - +
464C ILE 3.1 0.2 - - - -
465C GLN* 1.3 88.5 - - - +
467C MET* 1.3 64.1 + - + +
469C PRO* 3.8 8.0 - - - +
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Residues in contact with MET 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C GLN* 2.9 19.8 + - + +
464C ILE* 3.8 22.7 - - + +
466C GLU* 1.3 79.2 - - + +
468C PHE* 1.3 81.7 + - + +
469C PRO* 3.4 7.6 - - - +
486C VAL* 5.6 5.6 - - + -
487C GLU* 5.9 2.2 - - - +
490C THR* 3.9 22.2 - - + +
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Residues in contact with PHE 468 (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* 2.6 20.8 + - + +
465C GLN* 3.4 7.0 + - - +
467C MET* 1.3 96.4 - - + +
469C PRO* 1.3 58.3 - - - +
470C GLN* 3.0 40.9 + - + +
471C VAL* 3.3 27.1 - - + +
490C THR* 3.3 33.7 - - + -
493C ILE* 4.6 12.3 - - + -
494C LEU* 4.3 25.1 - - + -
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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