Contacts of the helix formed by residues 423 - 434 (chain E) in PDB entry 3LVQ
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 ASP 423 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424E LEU* 1.3 68.2 + - - +
425E THR* 3.1 5.9 + - - +
426E LYS* 3.4 40.7 + - - +
427E LEU* 4.2 8.7 + - - +
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Residues in contact with LEU 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ASP* 1.3 78.1 - - - +
425E THR* 1.3 62.8 + - - +
426E LYS 3.8 0.2 + - - -
427E LEU* 3.9 18.6 + - + +
428E LEU* 3.9 20.0 - - + +
488E PRO* 3.8 28.7 - - + -
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Residues in contact with THR 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ASP* 3.1 3.2 + - - +
424E LEU* 1.3 78.0 - - - +
426E LYS* 1.3 66.6 + - - +
427E LEU 3.0 2.9 - - - -
428E LEU* 2.8 11.2 + - + -
429E ILE* 2.8 39.7 + - + +
486E LEU* 3.3 27.6 + - + +
487E GLY 5.2 0.2 - - - -
488E PRO* 4.4 14.2 - - - +
491E LEU* 3.8 22.4 - - + -
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Residues in contact with LYS 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ASP* 3.4 38.1 + - - +
425E THR* 1.3 76.7 - - - +
427E LEU* 1.3 66.9 + - + +
429E ILE* 3.5 11.2 - - - +
430E ALA* 3.2 21.0 + - - +
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Residues in contact with LEU 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ASP* 4.5 8.1 - - - +
424E LEU* 4.0 16.2 - - + +
425E THR 2.8 4.2 + - - -
426E LYS* 1.3 79.1 - - + +
428E LEU* 1.3 56.5 + - + +
430E ALA* 2.9 9.9 + - + +
431E GLU* 2.6 40.5 + - + +
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Residues in contact with LEU 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E LEU* 3.9 25.4 - - + +
425E THR* 2.8 15.6 + - - +
427E LEU* 1.3 71.0 - - + +
429E ILE* 1.3 54.7 + - - +
431E GLU* 3.3 12.1 - - + +
432E VAL* 2.8 40.6 + - - +
488E PRO* 4.1 33.9 - - + +
491E LEU* 3.9 15.5 - - + -
495E LEU* 3.8 22.6 - - + +
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Residues in contact with ILE 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425E THR* 2.8 42.1 + - + +
426E LYS* 3.5 12.1 - - - +
428E LEU* 1.3 71.1 - - - +
430E ALA* 1.3 64.4 + - - +
432E VAL* 3.1 8.5 + - - +
433E LYS* 3.1 48.5 + - - +
481E LEU* 3.8 41.1 - - + +
486E LEU* 4.3 10.3 - - + -
491E LEU* 4.2 10.8 - - + -
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Residues in contact with ALA 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E LYS 3.2 10.6 + - - +
427E LEU* 2.9 11.5 + - + +
429E ILE* 1.3 80.0 - - - +
431E GLU* 1.3 63.0 + - - +
433E LYS* 3.4 10.8 + - - +
434E SER* 3.3 23.8 + - - -
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Residues in contact with GLU 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E LEU* 2.6 22.4 + - + +
428E LEU* 3.3 17.4 - - + +
429E ILE 3.1 0.2 - - - -
430E ALA* 1.3 70.3 - - - +
432E VAL* 1.3 65.3 + - - +
434E SER* 3.0 23.0 + - - -
435E ARG* 3.7 38.7 + - - +
495E LEU* 3.5 15.8 - - + +
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Residues in contact with VAL 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E LEU 2.8 22.1 + - - +
429E ILE* 3.5 7.4 - - - +
431E GLU* 1.3 72.8 - - - +
433E LYS* 1.3 59.5 + - - +
434E SER 3.2 0.9 + - - -
435E ARG* 3.3 10.1 + - - +
438E ASN* 2.8 37.6 + - - +
459E LEU* 4.2 20.2 - - + -
481E LEU* 4.8 9.6 - - + -
491E LEU* 4.0 17.0 - - + -
494E ALA* 3.8 30.7 - - + +
495E LEU* 3.6 24.2 - - + +
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Residues in contact with LYS 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429E ILE* 3.1 36.0 + - + +
430E ALA* 3.7 12.3 - - - +
431E GLU 3.3 0.4 - - - -
432E VAL* 1.3 79.0 - - - +
434E SER* 1.3 57.4 + - - +
435E ARG 3.4 0.6 - - - +
438E ASN* 3.1 32.2 - - - +
439E SER* 4.3 3.8 + - - -
448E ASP* 6.4 2.0 - - + -
449E PRO 5.2 4.7 - - - +
450E THR* 4.6 18.5 - - + +
459E LEU* 4.5 4.9 - - + -
481E LEU* 4.3 25.5 - - + -
482E THR* 5.3 2.8 + - - -
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Residues in contact with SER 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E ALA 3.3 12.3 + - - -
431E GLU* 3.0 23.2 + - - -
432E VAL 3.2 0.2 - - - -
433E LYS* 1.3 74.2 - - - +
435E ARG* 1.3 71.8 + - - +
436E PRO* 4.5 0.7 - - - +
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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