Contacts of the helix formed by residues 586 - 595 (chain B) in PDB entry 1LV5
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 THR 586 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582B LYS* 3.1 30.5 + - + +
584B GLN 2.7 4.8 + - - -
585B SER* 1.3 78.6 + - - +
587B TYR* 1.3 90.0 + - + +
590B GLY* 3.2 25.1 + - - -
591B LEU* 4.1 0.5 + - - +
26E G 6.2 1.8 - - - +
8F T 4.9 15.3 + - - +
9F G 3.5 32.5 + - - -
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Residues in contact with TYR 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B LYS* 3.6 19.5 - - + -
583B LEU* 3.5 10.5 + - + +
584B GLN 3.4 0.8 + - - -
586B THR* 1.3 96.8 - - + +
588B ILE* 1.3 64.0 + - - +
591B LEU* 3.0 42.9 + - + +
622B ASN 5.2 0.9 - - - -
625B ASN* 2.4 45.7 + - - -
626B ILE* 3.4 30.5 - - + -
627B PRO* 3.1 28.9 - - + -
636B ILE* 4.7 15.0 - - + -
26E G 5.7 0.3 + - - -
27E C 2.9 29.1 + - - -
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Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B LEU* 3.5 42.5 - - + +
503B MET* 3.9 9.9 - - + -
504B GLY* 4.0 5.8 - - - -
507B LEU* 4.4 9.0 - - + -
583B LEU 2.8 24.7 + - - +
584B GLN* 3.1 27.1 - - - +
587B TYR* 1.3 71.8 - - - +
589B GLU* 1.3 69.0 + - + +
591B LEU* 3.8 1.9 - - - +
592B LEU* 3.0 37.7 + - + +
636B ILE* 3.2 30.7 - - + -
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Residues in contact with GLU 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B GLN* 3.1 31.0 + - + +
585B SER* 3.3 35.6 - - - +
588B ILE* 1.3 82.4 - - + +
590B GLY* 1.3 60.8 + - - +
592B LEU* 3.6 8.6 + - - +
593B LYS* 3.1 31.2 + - + +
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Residues in contact with GLY 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B SER 3.3 4.3 + - - -
586B THR 3.2 20.6 + - - -
588B ILE 3.1 0.8 - - - -
589B GLU* 1.3 76.9 - - - +
591B LEU* 1.3 64.1 + - - +
593B LYS* 3.0 20.4 + - - +
594B VAL* 3.2 15.7 + - - +
621B PRO* 5.9 0.9 - - - -
9F G 4.9 8.7 - - - -
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Residues in contact with LEU 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B VAL* 5.7 1.3 - - + -
500B LEU* 4.3 20.0 - - + -
586B THR 4.1 0.8 + - - -
587B TYR* 3.0 31.9 + - - +
588B ILE 3.8 1.6 - - - +
590B GLY* 1.3 74.6 - - - +
592B LEU* 1.3 55.3 + - - +
594B VAL* 3.4 5.4 + - + +
595B VAL* 2.7 38.4 + - + +
602B VAL* 4.6 6.7 - - + -
621B PRO* 4.0 26.9 - - + -
622B ASN 5.6 0.4 - - - +
623B LEU* 4.2 8.3 - - + -
626B ILE* 4.7 10.1 - - + -
636B ILE* 4.2 14.8 - - + -
640B PHE* 3.7 35.9 - - + -
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Residues in contact with LEU 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B THR* 4.1 25.6 - - + -
500B LEU* 4.1 26.5 - - + -
501B GLU* 4.1 27.8 - - + +
588B ILE* 3.0 38.2 + - + +
589B GLU* 3.9 7.2 - - - +
590B GLY 3.2 0.2 - - - -
591B LEU* 1.3 77.1 - - - +
593B LYS* 1.3 60.5 + - + +
595B VAL* 3.3 21.2 - - + +
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Residues in contact with LYS 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B GLU* 3.1 17.7 - - + +
590B GLY* 3.0 12.4 + - - +
592B LEU* 1.3 81.2 - - + +
594B VAL* 1.3 58.0 + - - +
595B VAL 3.4 4.6 + - - +
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Residues in contact with VAL 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ASN* 5.6 0.4 - - - +
590B GLY 3.2 11.0 + - - +
591B LEU* 3.4 13.2 + - - +
593B LYS* 1.3 75.6 - - - +
595B VAL* 1.3 63.0 + - - +
596B ARG* 4.1 4.2 + - - +
601B LYS 4.5 0.2 - - - +
602B VAL* 4.3 12.4 - - + +
603B HIS 4.8 4.0 + - - +
620B GLU* 3.7 28.5 - - + +
621B PRO* 3.3 50.3 - - + -
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Residues in contact with VAL 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B VAL* 4.3 15.9 - - + -
497B THR* 4.1 24.0 - - + -
500B LEU* 5.3 0.7 - - + -
591B LEU* 2.7 24.0 - - + +
592B LEU* 3.3 20.8 - - + +
593B LYS 4.3 4.3 - - - +
594B VAL* 1.3 80.1 - - - +
596B ARG* 1.3 63.9 + - - +
597B PRO* 3.2 14.4 - - + +
600B LYS* 4.7 7.4 - - - -
601B LYS 3.7 7.4 - - - +
602B VAL* 3.1 24.0 - - + -
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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