Contacts of the helix formed by residues 584 - 594 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A LYS* 5.9 1.8 + - - -
584B ASP* 5.0 7.3 - - - +
575C LYS* 2.9 32.1 + - - +
609C LEU 5.5 1.2 + - - -
554D LYS* 4.4 2.2 - - - +
582D GLU 3.8 1.2 + - - -
583D ILE* 1.3 78.0 - - - +
585D ASN* 1.3 66.7 + - - +
586D SER* 3.3 7.4 - - - +
587D GLU* 3.1 13.0 + - + +
588D LEU* 3.0 17.5 + - - +
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Residues in contact with ASN 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D LEU* 3.9 16.0 - - + +
553D GLN* 3.4 36.4 + - - +
554D LYS* 2.8 37.9 + - - +
557D LEU* 3.3 18.6 - - - +
584D ASP* 1.3 71.3 - - - +
586D SER* 1.4 55.9 + - - +
588D LEU* 3.2 4.6 + - - +
589D LEU* 3.0 33.9 + - - +
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Residues in contact with SER 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A THR 4.5 12.3 + - - -
574A GLY* 6.0 1.2 + - - -
584D ASP* 3.3 5.5 + - - +
585D ASN* 1.4 75.9 - - - +
587D GLU* 1.3 62.0 + - - +
589D LEU* 3.3 13.9 + - - +
590D TYR* 3.2 21.0 + - - +
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Residues in contact with GLU 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C LEU 5.2 0.9 - - - +
610C GLN 4.6 3.9 - - - +
611C ALA* 3.4 30.1 - - + +
612C HIS* 2.7 48.5 + - - +
583D ILE* 3.6 19.5 - - + -
584D ASP* 3.1 16.0 + - + +
586D SER* 1.3 76.7 - - - +
588D LEU* 1.3 57.2 + - - +
590D TYR* 3.3 14.0 + - - +
591D MSE 3.0 45.4 + - - +
597D SER* 5.4 1.6 - - - -
601D LYS* 4.7 5.9 - - - -
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Residues in contact with LEU 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D LYS* 4.0 7.9 - - - +
557D LEU* 3.9 31.4 - - + -
561D LEU* 4.0 20.1 - - + +
580D LEU 3.2 24.9 - - - +
581D LEU* 4.0 16.2 - - + -
583D ILE* 3.4 25.8 - - + +
584D ASP 3.0 12.2 + - - +
585D ASN* 3.2 8.5 + - - +
587D GLU* 1.3 75.8 - - - +
589D LEU* 1.3 55.0 + - - +
591D MSE 3.3 27.1 + - + +
592D LEU* 2.9 33.1 + - - +
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Residues in contact with LEU 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D LEU* 3.7 38.0 - - + +
541D THR 4.1 6.3 - - - +
542D ALA* 3.8 29.4 - - + +
545D LEU* 3.7 19.1 - - + -
557D LEU* 3.9 20.6 - - + -
585D ASN* 3.0 23.4 + - + +
586D SER* 3.6 11.7 - - - +
588D LEU* 1.3 71.1 - - - +
590D TYR* 1.4 65.6 + - - +
592D LEU* 3.4 17.5 + - + +
593D GLU* 3.6 15.1 + - - +
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Residues in contact with TYR 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C HIS* 3.4 57.1 - + + +
586D SER 3.2 12.8 + - - +
587D GLU* 3.4 16.2 - - - +
588D LEU 3.3 0.2 - - - -
589D LEU* 1.4 76.3 - - - +
591D MSE 1.4 58.8 - - - +
593D GLU* 3.0 23.1 + - + +
594D SER* 3.0 27.2 + - - -
597D SER* 3.3 32.1 + - - -
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Residues in contact with MSE 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D LEU* 5.0 2.0 - - + -
580D LEU* 3.9 20.0 - - + -
583D ILE* 3.9 23.1 - - + -
587D GLU* 3.0 45.6 + - - +
588D LEU* 3.3 20.6 + - + +
590D TYR* 1.4 76.8 - - + +
592D LEU* 1.4 64.2 + - - +
593D GLU 3.2 0.9 + - - -
594D SER* 3.3 23.2 + - - +
597D SER* 4.5 13.0 - - - +
598D LEU* 3.6 31.7 - - + +
601D LYS* 3.9 31.4 - - + -
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Residues in contact with LEU 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D LEU* 4.3 15.7 - - + +
557D LEU* 3.9 29.6 - - + +
560D ARG* 3.7 35.7 - - + -
561D LEU* 3.6 29.6 - - + +
564D LEU* 3.8 28.7 - - + +
588D LEU 2.9 14.4 + - - +
589D LEU* 3.6 15.5 - - + +
590D TYR 3.3 0.4 - - - -
591D MSE 1.4 74.4 - - - +
593D GLU* 1.4 69.1 + - + +
594D SER 5.3 0.2 - - - -
598D LEU* 5.4 0.2 - - - -
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Residues in contact with GLU 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D THR* 4.0 28.6 + - + +
540D LEU 5.7 3.8 - - - +
589D LEU 3.6 10.5 + - - +
590D TYR* 3.0 10.7 + - + +
592D LEU* 1.4 94.7 - - + +
594D SER* 1.3 57.6 + - - +
595D PRO* 3.6 10.2 - - - +
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Residues in contact with SER 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590D TYR* 3.0 33.2 + - - -
591D MSE 3.3 10.2 + - - +
592D LEU 3.6 0.2 - - - -
593D GLU* 1.3 78.3 - - - +
595D PRO* 1.4 65.5 - - - +
596D GLU* 4.2 2.9 + - - +
597D SER* 3.2 28.2 + - - -
598D LEU 3.0 17.7 + - - -
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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