Contacts of the helix formed by residues 588 - 609 (chain B) in PDB entry 4GT4
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 GLU 588 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ALA* 5.3 9.3 - - + +
587B LEU* 1.3 76.8 - - - +
589B PRO* 1.3 69.8 - - + +
590B PRO* 3.3 12.8 - - + +
591B ASP* 2.9 40.3 + - - +
592B PHE* 3.4 7.7 - - - -
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Residues in contact with PRO 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LEU 4.5 1.6 - - - +
588B GLU* 1.3 86.9 - - + +
590B PRO* 1.3 69.0 - - + +
591B ASP 3.3 0.5 + - - -
592B PHE* 3.4 23.3 + - + +
593B VAL* 3.7 15.5 + - - +
686B PHE* 5.8 0.7 - - - -
802B NO3 5.5 7.9 - - - +
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Residues in contact with PRO 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B GLU* 3.4 17.3 - - + +
589B PRO* 1.3 97.6 - - + +
591B ASP* 1.3 59.8 + - - +
593B VAL* 3.4 8.9 + - + +
594B HIS* 2.9 29.6 + - - +
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Residues in contact with ASP 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ALA 4.5 2.1 - - - +
587B LEU* 3.7 20.0 - - + +
588B GLU* 2.9 40.0 + - - +
590B PRO* 1.3 80.3 - - - +
592B PHE* 1.3 56.2 + - + +
594B HIS* 3.3 8.3 + - - +
595B LEU* 2.9 35.6 + - + +
627B LEU* 3.9 23.7 - - + +
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Residues in contact with PHE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B LEU* 4.7 9.2 - - + -
587B LEU* 3.8 25.6 - - + -
588B GLU 3.4 21.5 - - - -
589B PRO* 3.7 15.0 - - + +
590B PRO 3.3 0.2 - - - -
591B ASP* 1.3 76.6 - - + +
593B VAL* 1.3 63.0 + - - +
595B LEU* 3.2 9.2 + - + +
596B VAL* 3.0 29.4 + - - +
685B VAL* 3.6 40.2 - - + -
686B PHE* 3.8 20.9 - + + -
688B TYR* 3.5 39.0 - + - -
802B NO3 3.5 23.8 - - - -
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Residues in contact with VAL 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B PRO 3.7 14.4 - - - +
590B PRO* 3.4 9.6 + - + +
591B ASP 3.4 0.2 - - - -
592B PHE* 1.3 74.9 - - - +
594B HIS* 1.3 58.2 + - - +
596B VAL* 3.3 8.4 - - - +
597B ALA* 2.9 33.6 + - + +
686B PHE* 4.7 10.5 - - + -
720B TRP* 4.4 27.6 - - + -
746B LEU* 3.8 26.2 - - + +
749B TRP 4.2 15.3 - - - +
750B GLY* 4.3 8.5 - - - -
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Residues in contact with HIS 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B PRO 2.9 17.7 + - - +
591B ASP* 3.4 9.2 - - - +
593B VAL* 1.3 78.1 - - - +
595B LEU* 1.3 58.3 + - - +
597B ALA* 3.6 5.7 - - - +
598B GLN* 2.9 70.8 + - + +
626B LYS 4.4 7.4 + - - -
627B LEU* 4.1 23.4 + - + -
628B ASN* 5.4 0.4 - - - -
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Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LEU* 4.0 31.0 - - + -
564B PHE* 5.7 0.9 - - + -
565B LEU* 4.8 8.1 - - + -
587B LEU* 5.5 6.3 - - + -
591B ASP* 2.9 24.6 + - + +
592B PHE* 3.4 12.6 - - + +
594B HIS* 1.3 75.6 - - - +
596B VAL* 1.3 62.2 + - + +
598B GLN* 3.1 9.5 + - - +
599B ILE* 3.0 33.4 + - + +
627B LEU* 3.8 36.3 - - + +
629B VAL* 3.7 29.1 - - + +
685B VAL* 4.6 11.0 - - + -
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Residues in contact with VAL 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B PHE 3.0 18.8 + - - +
593B VAL* 3.3 21.5 - - + +
595B LEU* 1.3 75.3 - - - +
597B ALA* 1.3 56.1 + - - +
599B ILE* 3.5 8.2 + - + -
600B ALA 2.9 16.3 + - - -
678B TYR* 2.5 30.3 + - + +
681B VAL* 5.4 1.6 - - + -
682B LEU* 3.6 25.6 - - + -
685B VAL* 3.9 33.7 - - + -
686B PHE* 4.4 8.7 - - + -
720B TRP* 6.1 0.4 - - + -
746B LEU* 3.7 18.8 - - + -
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Residues in contact with ALA 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B VAL* 2.9 21.3 + - + +
594B HIS* 3.6 7.9 - - - +
596B VAL* 1.3 75.9 - - - +
598B GLN* 1.3 60.8 + - - +
600B ALA* 3.2 2.0 + - - +
601B ALA 2.9 23.6 + - - -
743B HIS* 3.2 20.5 - - + +
746B LEU* 3.7 31.4 - - + +
747B ARG* 4.8 6.7 - - + +
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Residues in contact with GLN 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ASN* 3.2 30.0 + - - +
594B HIS* 2.9 53.3 + - + +
595B LEU* 3.4 10.6 - - - +
597B ALA* 1.3 76.3 - - + +
599B ILE* 1.3 62.5 + - - +
601B ALA* 3.1 3.2 + - - +
602B GLY 2.9 19.2 + - - -
627B LEU 2.9 23.2 + - - -
628B ASN* 3.2 17.7 + - - -
629B VAL* 2.9 33.4 + - + +
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Residues in contact with ILE 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LEU* 4.0 19.1 - - + -
595B LEU 3.0 19.9 + - - +
596B VAL* 3.8 8.1 - - - +
598B GLN* 1.3 75.7 - - - +
600B ALA* 1.3 57.1 + - - +
602B GLY 3.3 0.7 + - - -
603B MET* 2.9 29.4 + - + +
616B LEU* 4.3 15.7 - - + -
621B VAL* 4.0 18.8 - - + -
629B VAL* 3.8 16.8 - - + -
631B ILE* 3.5 20.8 - - + +
678B TYR* 3.7 21.5 - - + -
681B VAL* 3.9 24.0 - - + -
685B VAL* 5.0 1.8 - - + -
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Residues in contact with ALA 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B VAL 2.9 19.2 + - - +
597B ALA 3.4 5.8 - - - +
599B ILE* 1.3 78.7 - - - +
601B ALA* 1.3 56.7 + - - +
603B MET* 3.4 5.5 + - - +
604B GLU* 2.9 28.8 + - - +
678B TYR* 3.4 20.3 - - + +
739B PHE* 4.0 7.8 - - + +
742B ILE* 4.0 9.9 - - + -
743B HIS* 3.9 24.9 - - + +
746B LEU* 4.1 2.0 - - + -
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Residues in contact with ALA 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B HIS* 3.8 11.7 + - + +
535B ASN* 3.6 14.6 - - - +
597B ALA 2.9 8.0 + - - +
598B GLN* 3.1 8.7 + - - +
600B ALA* 1.3 72.7 - - - +
602B GLY* 1.3 67.0 + - - +
604B GLU* 3.1 8.8 + - - +
605B TYR* 2.9 22.5 + - - +
743B HIS* 3.5 34.9 - - + +
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Residues in contact with GLY 602 (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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533B HIS* 4.1 7.2 - - - -
535B ASN* 3.8 20.9 - - - +
536B VAL* 4.0 2.9 - - - +
598B GLN 2.9 10.9 + - - -
599B ILE 3.7 3.4 - - - -
601B ALA* 1.3 76.1 - - - +
603B MET* 1.3 56.5 + - - +
605B TYR* 3.2 4.7 + - - +
606B LEU* 2.9 30.7 + - - +
631B ILE* 3.7 15.7 - - - -
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Residues in contact with MET 603 (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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599B ILE* 2.9 23.4 + - + +
600B ALA 3.9 0.2 - - - +
602B GLY* 1.3 72.6 - - - +
604B GLU* 1.3 60.1 + - - +
606B LEU* 4.0 17.8 - - + +
607B SER* 2.9 34.8 + - - +
611B VAL 5.3 2.0 - - - +
613B HIS* 4.2 13.0 - - + +
616B LEU* 3.8 31.2 - - + -
631B ILE* 3.6 17.9 - - + -
674B ASP* 3.8 27.4 - - + +
678B TYR* 4.8 0.4 - - + -
739B PHE* 3.5 43.9 - - + -
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Residues in contact with GLU 604 (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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600B ALA 2.9 14.0 + - - +
601B ALA* 3.1 10.8 + - - +
603B MET* 1.3 76.9 - - - +
605B TYR* 1.3 57.1 + - - +
607B SER* 3.1 7.3 + - - +
608B SER* 2.9 34.8 + - - -
739B PHE* 3.7 11.2 - - + +
740B LYS* 3.3 45.7 - - + +
743B HIS* 3.6 28.6 + - - +
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Residues in contact with TYR 605 (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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530B ARG 3.7 5.5 + - - -
531B LEU* 3.5 27.0 - - + -
532B GLN* 2.9 39.5 + - - +
533B HIS* 3.5 46.0 - + + +
536B VAL* 4.3 9.4 - - + -
601B ALA 2.9 8.2 + - - +
602B GLY 3.5 7.6 - - - +
604B GLU* 1.3 78.0 - - - +
606B LEU* 1.3 68.4 + - + +
608B SER* 2.7 20.8 + - - -
609B HIS* 3.1 46.8 + + - -
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Residues in contact with LEU 606 (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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531B LEU* 4.2 25.8 - - + -
536B VAL* 4.1 25.4 - - + -
602B GLY 2.9 19.2 + - - +
603B MET* 4.0 20.4 - - + +
605B TYR* 1.3 83.0 - - + +
607B SER* 1.3 59.1 + - - +
609B HIS* 3.2 8.9 + - - -
611B VAL* 2.9 49.9 + - + +
613B HIS* 4.3 10.1 - - + -
631B ILE* 4.2 25.1 - - + -
633B ASP* 4.7 12.6 - - + -
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Residues in contact with SER 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B MET* 2.9 24.2 + - - +
604B GLU* 3.1 12.3 + - - +
606B LEU* 1.3 73.6 - - - +
608B SER* 1.3 63.7 + - - +
610B HIS* 3.1 17.0 + - - -
611B VAL 4.1 10.3 + - - +
671B ILE* 3.9 41.5 - - - +
739B PHE* 3.8 12.7 - - - +
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Residues in contact with SER 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B GLU* 2.9 19.0 + - - -
605B TYR* 2.7 22.9 + - - -
607B SER* 1.3 78.5 + - - +
609B HIS* 1.3 68.2 + - - +
610B HIS* 3.2 15.2 + - - -
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Residues in contact with HIS 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ARG* 5.0 4.8 + - - +
531B LEU* 4.0 25.9 - - + +
605B TYR* 3.1 60.7 + + - +
606B LEU* 3.2 5.6 + - - +
607B SER 3.1 1.0 - - - -
608B SER* 1.3 89.4 + - - +
610B HIS* 1.3 75.2 + - - +
611B VAL* 3.3 9.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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