Contacts of the helix formed by residues 584 - 594 (chain B) in PDB entry 4IVE
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 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572A LEU* 6.1 0.2 - - - +
575A LYS* 2.7 27.4 + - - +
609A LEU 5.2 6.3 + - - +
554B LYS* 4.5 2.2 - - - +
582B GLU 3.8 0.6 + - - -
583B ILE* 1.4 79.4 - - - +
585B ASN* 1.3 65.1 + - - +
586B SER* 3.3 8.5 - - - +
587B GLU* 3.1 12.7 + - + +
588B LEU* 3.0 18.0 + - - +
575C LYS* 5.9 0.7 + - - -
584D ASP* 5.0 7.1 - - - +
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Residues in contact with ASN 585 (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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545B LEU* 3.9 16.7 - - + +
553B GLN* 3.5 35.8 + - - +
554B LYS* 2.8 37.7 + - - +
557B LEU* 3.3 20.5 - - - +
584B ASP* 1.3 71.3 - - - +
586B SER* 1.4 56.6 + - - +
588B LEU* 3.3 4.7 + - - +
589B LEU* 3.0 34.3 + - - +
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Residues in contact with SER 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B ASP* 3.3 6.4 - - - +
585B ASN* 1.4 75.3 - - - +
587B GLU* 1.3 62.2 + - - +
589B LEU* 3.3 14.0 + - - +
590B TYR* 3.2 21.3 + - - +
570C PRO 5.3 4.7 + - - -
571C THR* 4.2 15.5 + - - +
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Residues in contact with GLU 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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609A LEU 5.3 0.7 - - - +
610A GLN 4.8 3.5 - - - +
611A ALA* 3.4 24.2 - - + +
612A HIS* 3.3 41.0 + - - +
583B ILE* 3.6 19.1 - - + -
584B ASP* 3.1 16.0 + - + +
586B SER* 1.3 77.2 - - - +
588B LEU* 1.3 58.1 + - - +
590B TYR* 3.3 26.6 + - - +
591B MSE 3.0 37.7 + - - +
597B SER* 4.0 6.9 + - - -
601B LYS* 4.8 3.9 - - - -
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Residues in contact with LEU 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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554B LYS* 4.1 5.4 - - - +
557B LEU* 3.9 30.5 - - + -
561B LEU* 3.7 20.5 - - + +
580B LEU 3.2 24.7 - - - +
581B LEU* 4.0 18.4 - - + -
583B ILE* 3.4 26.0 - - + +
584B ASP 3.0 12.3 + - - +
585B ASN* 3.3 7.8 + - - +
587B GLU* 1.3 77.3 - - - +
589B LEU* 1.3 55.7 + - - +
591B MSE 3.3 26.4 + - + +
592B LEU* 3.0 33.1 + - - +
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Residues in contact with LEU 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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540B LEU* 3.7 44.7 - - + +
541B THR 4.3 4.9 - - - +
542B ALA* 3.7 32.1 - - + +
545B LEU* 3.8 15.9 - - + -
557B LEU* 3.9 15.0 - - + -
585B ASN* 3.0 21.9 + - + +
586B SER* 3.3 12.3 + - - +
588B LEU* 1.3 75.6 - - - +
590B TYR* 1.4 62.9 + - - +
592B LEU* 3.4 17.0 + - + +
593B GLU* 3.4 15.6 + - - +
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Residues in contact with TYR 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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612A HIS* 4.2 22.2 - - + +
586B SER 3.2 11.7 + - - +
587B GLU* 3.5 29.8 - - - +
589B LEU* 1.4 75.9 - - - +
591B MSE 1.3 53.2 + - - +
593B GLU* 3.0 31.7 + - - +
594B SER* 2.8 53.0 + - - -
596B GLU* 4.5 8.0 + - - -
597B SER* 3.5 27.8 - - - -
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Residues in contact with MSE 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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561B LEU* 4.8 2.5 - - + -
580B LEU* 3.8 20.6 - - + -
583B ILE* 3.9 21.3 - - + -
587B GLU* 3.0 35.2 + - - +
588B LEU* 3.3 21.5 + - + +
590B TYR* 1.3 76.8 - - - +
592B LEU* 1.3 59.8 + - - +
594B SER 3.0 24.0 - - - +
595B PRO* 5.0 0.2 - - - +
597B SER* 3.9 26.5 - - - +
598B LEU* 3.5 28.3 - - + +
601B LYS* 3.8 34.3 - - + -
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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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540B LEU* 4.6 10.8 - - + +
557B LEU* 3.8 31.4 - - + +
560B ARG* 3.7 37.9 - - + -
561B LEU* 3.7 25.6 - - + -
564B LEU* 3.8 32.6 - - + +
588B LEU 3.0 13.4 + - - +
589B LEU* 3.6 13.7 - - + +
590B TYR 3.2 0.4 - - - -
591B MSE 1.3 75.9 - - - +
593B GLU* 1.4 58.8 + - - +
594B SER 5.2 0.4 - - - -
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Residues in contact with GLU 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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539B THR* 6.0 6.1 - - + -
589B LEU 3.4 5.9 + - - +
590B TYR* 3.0 45.5 + - + +
592B LEU* 1.4 78.6 - - - +
594B SER* 1.4 56.8 + - - +
595B PRO* 3.6 10.8 - - - +
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Residues in contact with SER 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B TYR* 2.8 52.3 + - - -
591B MSE 3.0 16.9 - - - +
592B LEU 5.2 0.2 - - - -
593B GLU* 1.4 73.1 - - - +
595B PRO* 1.4 65.7 - - - +
596B GLU* 3.7 10.7 + - - +
597B SER* 3.4 16.7 + - - -
598B LEU 3.2 10.4 + - - -
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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