Contacts of the helix formed by residues 594 - 602 (chain A) in PDB entry 1LVK
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 GLN 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A ARG 5.6 4.9 + - - +
592A LEU 3.4 3.0 + - - -
593A GLN* 1.3 74.2 + - - +
595A ASP* 1.4 66.5 + - - +
597A GLU* 2.8 23.8 + - - +
598A LEU* 2.8 53.2 + - + +
601A LYS* 4.2 10.6 + - - +
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Residues in contact with ASP 595 (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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392A ALA* 3.9 24.9 - - + +
395A GLU 4.5 1.6 - - - +
396A PRO* 3.9 9.3 - - + +
397A ARG* 2.9 67.0 + - - +
593A GLN* 3.2 2.8 + - + +
594A GLN* 1.4 77.4 - - - +
596A LEU* 1.3 53.3 + - - +
598A LEU* 3.0 14.9 + - - +
599A CYS* 2.6 36.9 + - - +
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Residues in contact with LEU 596 (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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389A LEU* 4.0 16.6 - - + -
392A ALA* 3.6 30.1 - - + +
393A LEU* 3.7 24.0 - - + -
417A SER* 3.5 29.6 - - - +
421A LEU* 4.3 12.6 - - + -
592A LEU* 4.1 24.9 - - + -
593A GLN* 3.0 22.2 + - + +
595A ASP* 1.3 77.1 - - - +
597A GLU* 1.3 63.3 + - - +
599A CYS* 4.2 1.6 - - - -
600A PHE* 3.1 30.9 + - + +
612A PHE* 4.5 2.0 - - - -
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Residues in contact with GLU 597 (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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428A ARG* 3.0 26.2 + - - -
592A LEU* 3.4 22.8 - - + +
593A GLN 3.3 10.8 + - - +
594A GLN* 2.8 32.1 + - - +
596A LEU* 1.3 76.5 - - - +
598A LEU* 1.3 57.7 + - - +
600A PHE 3.9 0.3 - - - -
601A LYS* 2.9 45.3 + - - +
612A PHE* 2.7 40.9 - - - +
618A ALA* 4.7 3.6 - - - +
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Residues in contact with LEU 598 (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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397A ARG* 3.9 13.5 - - - +
594A GLN* 2.8 38.7 + - + +
595A ASP* 3.2 29.6 - - - +
597A GLU* 1.3 75.1 - - - +
599A CYS* 1.3 66.6 + - - +
601A LYS* 3.4 26.4 + - + +
602A ASP* 3.6 18.6 - - - +
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Residues in contact with CYS 599 (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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384A VAL* 3.8 23.9 - - - +
385A ASN 4.4 2.5 + - - -
388A VAL* 4.1 21.1 - - + -
389A LEU* 3.6 46.2 - - - -
392A ALA* 4.5 5.8 - - + -
595A ASP 2.6 19.5 + - - +
596A LEU* 3.5 8.7 - - - +
598A LEU* 1.3 77.2 - - - +
600A PHE* 1.3 64.9 + - + +
602A ASP* 3.4 17.7 + - - +
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Residues in contact with PHE 600 (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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382A PHE* 3.7 42.2 - + + -
384A VAL* 3.8 15.7 - - + -
389A LEU* 3.3 32.5 - - + -
421A LEU* 3.5 32.3 - - + -
425A LEU* 4.1 9.0 - - + -
596A LEU* 3.1 19.9 + - + +
599A CYS* 1.3 80.4 - - + +
601A LYS* 1.3 66.5 + - - +
602A ASP 3.1 2.9 - - - -
603A SER* 3.0 21.9 + - - -
608A VAL* 4.0 21.4 - - + +
609A THR* 4.8 0.7 - - - -
612A PHE* 3.5 37.6 - + + +
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Residues in contact with LYS 601 (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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594A GLN* 4.2 17.2 + - - +
597A GLU* 2.9 34.3 + - - +
598A LEU* 3.6 17.8 - - + +
599A CYS 3.3 0.2 - - - -
600A PHE* 1.3 77.1 - - - +
602A ASP* 1.4 59.0 + - - +
603A SER 3.2 2.8 + - - -
609A THR* 4.1 7.6 + - - +
612A PHE* 3.5 31.3 - - + +
613A ASN* 2.8 43.6 - - - +
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Residues in contact with ASP 602 (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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383A GLY 3.9 2.8 - - - +
384A VAL* 5.1 2.4 - - - -
388A VAL* 5.3 6.1 - - - +
598A LEU 3.6 16.1 - - - +
599A CYS* 3.4 11.8 + - - +
600A PHE 3.1 0.8 - - - -
601A LYS* 1.4 76.0 - - - +
603A SER* 1.3 67.7 + - - +
604A SER* 3.3 2.3 + - - -
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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