Contacts of the helix formed by residues 589 - 600 (chain D) in PDB entry 6AH0
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 589 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2333A LEU* 5.3 8.3 + - - +
542D ALA 3.4 13.7 - - - -
543D PRO 5.5 2.5 - - - -
544D MET 6.3 1.1 - - - -
588D CYS* 1.3 75.5 - - - +
590D PRO* 1.3 66.1 - - - +
591D GLU 3.1 3.4 - - - -
592D LYS* 2.9 17.5 + - - +
593D TRP* 3.2 8.7 + - - -
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Residues in contact with PRO 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D ILE* 5.4 4.6 - - - -
542D ALA 4.2 4.9 - - - -
543D PRO* 5.8 0.8 - - - -
588D CYS 3.9 1.6 - - - +
589D THR* 1.3 69.7 - - - +
591D GLU* 1.3 62.1 + - - +
593D TRP* 3.3 4.4 + - - +
594D ASP* 2.9 18.7 + - - -
627D VAL* 5.6 8.2 - - - +
628D LEU* 5.8 7.9 - - - +
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Residues in contact with GLU 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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2333A LEU 5.5 0.7 - - - -
589D THR 3.0 1.2 + - - -
590D PRO* 1.3 75.6 - - - +
592D LYS* 1.3 53.2 + - - +
594D ASP* 2.6 23.5 + - - +
595D ILE* 2.9 12.5 + - - -
627D VAL* 6.1 2.4 - - - +
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Residues in contact with LYS 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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2333A LEU 4.2 17.0 + - - -
2334A TYR* 5.4 4.9 - - - +
2335A ALA 5.4 3.4 - - - +
588D CYS* 6.3 0.2 - - - +
589D THR 2.9 10.1 + - - +
591D GLU* 1.3 72.7 - - - +
593D TRP* 1.3 62.5 + - - +
595D ILE* 4.1 0.4 - - - +
596D ILE* 3.0 23.4 + - - -
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Residues in contact with TRP 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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588D CYS* 6.0 1.0 - - - +
589D THR 3.2 10.0 + - - -
590D PRO* 3.3 4.7 + - - -
591D GLU 3.2 0.6 - - - -
592D LYS* 1.3 74.4 - - - +
594D ASP* 1.3 58.2 + - - +
596D ILE* 3.8 1.0 - - - +
597D THR* 2.9 25.3 + - - -
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Residues in contact with ASP 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 PRO 2.9 9.9 + - - -
591D GLU* 2.6 15.9 + - - +
593D TRP* 1.3 69.2 - - - +
595D ILE* 1.3 63.8 + - - +
597D THR* 3.3 1.8 + - - +
598D ARG* 2.9 19.1 + - - -
631D LEU* 6.4 2.0 - - - +
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Residues in contact with ILE 595 (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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591D GLU 2.9 14.8 + - - -
592D LYS* 4.1 1.6 - - - +
594D ASP* 1.3 70.2 - - - +
596D ILE* 1.3 56.4 + - - +
598D ARG* 2.7 23.9 + - - +
599D LYS* 2.9 11.3 + - - -
989D SER 5.5 5.4 - - - -
990D HIS* 5.2 11.5 - - - +
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Residues in contact with ILE 596 (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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592D LYS 3.0 16.2 + - - -
593D TRP* 3.8 1.1 - - - +
595D ILE* 1.3 74.7 - - - +
597D THR* 1.3 56.7 + - - +
599D LYS* 3.7 1.9 + - - +
600D GLY 3.2 4.0 + - - -
601D GLY* 2.9 31.1 + - - +
602D GLU* 3.5 5.7 + - - -
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Residues in contact with THR 597 (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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593D TRP 2.9 17.6 + - - -
594D ASP 3.8 1.1 - - - -
595D ILE 3.1 0.4 - - - -
596D ILE* 1.3 77.2 - - - +
598D ARG* 1.3 61.8 + - - +
599D LYS 3.2 0.4 - - - -
600D GLY* 3.2 12.5 + - - -
602D GLU* 4.6 10.5 - - - +
603D ARG 5.9 0.2 - - - +
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Residues in contact with ARG 598 (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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594D ASP 2.9 10.7 + - - -
595D ILE* 2.7 15.2 + - - +
597D THR* 1.3 72.8 - - - +
599D LYS* 1.3 57.4 + - - +
903D ALA* 5.7 4.7 - - - +
906D VAL 5.9 1.6 - - - -
907D LEU* 5.8 4.8 - - - +
989D SER 5.6 6.5 - - - -
990D HIS* 5.3 8.1 + - - +
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Residues in contact with LYS 599 (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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595D ILE 2.9 11.5 + - - -
596D ILE* 4.2 2.5 - - - +
598D ARG* 1.3 77.7 - - - +
600D GLY* 1.3 58.3 + - - +
601D GLY 3.6 1.1 - - - -
990D HIS* 5.4 7.3 - - - +
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Residues in contact with GLY 600 (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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596D ILE 3.2 1.0 + - - -
597D THR 3.2 15.8 + - - -
599D LYS* 1.3 79.8 - - - +
601D GLY* 1.3 57.6 + - - +
602D GLU 2.9 7.2 - - - -
603D ARG* 2.9 23.8 + - - -
604D THR 3.8 3.6 + - - -
1537D THR* 5.7 5.2 - - - -
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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