Contacts of the helix formed by residues 591 - 606 (chain D) in PDB entry 6UZA
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 PRO 591 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D ARG* 5.6 0.2 - - - +
543D ALA* 3.6 26.4 - - + +
546D MET* 4.0 18.6 - - + -
547D ALA* 3.8 22.4 - - + +
550D HIS* 5.0 9.9 - - + +
589D SER 3.6 5.4 - - - +
590D ASP* 1.3 95.2 - - - +
592D GLN* 1.3 56.2 + - - +
593D ILE 3.2 0.2 - - - -
594D ILE* 3.6 11.8 - - + +
595D SER* 3.0 30.8 + - - -
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Residues in contact with GLN 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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485D ARG* 3.9 7.1 + - - +
488D THR* 3.5 30.3 + - - -
489D SER* 2.4 26.6 + - - -
544D ARG* 3.8 17.8 - - - +
547D ALA* 3.8 9.7 - - + +
583D ARG* 5.5 0.4 - - - +
586D TRP* 3.7 27.5 - - + -
590D ASP* 3.2 18.5 - - - +
591D PRO* 1.3 81.0 - - - +
593D ILE* 1.3 57.0 + - - +
595D SER* 3.1 17.6 + - - -
596D GLU* 3.1 39.7 + - - +
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Residues in contact with ILE 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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659A TYR* 4.3 5.8 - - - +
697A HIS* 3.8 36.6 - - + +
699A PHE* 3.3 24.2 - - + -
700A ILE* 4.0 13.8 - - + +
583D ARG* 3.8 13.9 - - - +
586D TRP* 3.7 27.1 - - + -
587D ASP 4.0 3.1 - - - +
588D PRO 3.3 27.6 - - - +
590D ASP* 3.2 17.7 + - + +
591D PRO 3.2 0.2 - - - -
592D GLN* 1.3 77.2 - - - +
594D ILE* 1.3 65.4 + - + +
595D SER 3.5 0.4 - - - -
596D GLU* 4.1 7.4 - - - +
597D GLY 3.5 7.8 + - - -
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Residues in contact with ILE 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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699A PHE* 3.8 36.9 - - + -
543D ALA* 4.5 9.4 - - + -
588D PRO 5.2 0.9 - - - +
589D SER* 4.7 16.4 - - - +
590D ASP 3.3 17.3 - - - +
591D PRO* 3.2 13.1 + - + +
593D ILE* 1.3 80.9 - - + +
595D SER* 1.3 60.5 + - - +
597D GLY* 3.3 1.2 + - - -
598D LEU* 3.0 46.8 + - + +
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Residues in contact with SER 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D SER* 3.0 40.9 + - - +
543D ALA* 4.1 2.2 - - - +
544D ARG* 3.8 25.4 + - - +
591D PRO 3.0 12.8 + - - -
592D GLN* 3.1 17.8 + - - -
594D ILE* 1.3 77.6 - - - +
596D GLU* 1.3 62.9 + - - +
598D LEU 3.4 0.2 + - - -
599D TYR* 2.9 27.8 + - - +
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Residues in contact with GLU 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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654A ASN 4.7 7.5 - - - +
655A LEU* 3.7 20.1 - - + +
658A TYR* 3.7 25.2 - - + -
700A ILE* 4.6 8.3 - - + +
544D ARG* 5.1 5.6 + - - +
583D ARG* 2.6 41.4 + - - -
592D GLN* 3.1 39.4 + - - +
593D ILE* 4.1 4.6 - - - -
594D ILE 3.4 0.2 - - - -
595D SER* 1.3 83.6 + - - +
597D GLY* 1.3 60.0 + - - +
599D TYR* 4.1 7.8 - - - +
600D ALA* 3.9 11.4 + - - +
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Residues in contact with GLY 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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655A LEU* 4.0 13.5 - - - -
699A PHE* 3.9 18.8 - - - -
700A ILE* 4.7 2.2 - - - +
703A ILE* 3.7 13.2 - - - +
593D ILE 3.5 8.1 + - - -
594D ILE 3.3 5.5 + - - -
595D SER 3.2 0.4 - - - -
596D GLU* 1.3 78.6 - - - +
598D LEU* 1.3 62.8 + - - +
599D TYR 3.4 0.2 - - - -
600D ALA* 3.8 4.9 + - - +
601D ILE* 3.6 19.1 - - - +
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Residues in contact with LEU 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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699A PHE* 4.6 12.1 - - + -
1006A Y01 4.8 12.3 - - + -
536D ILE* 3.3 29.0 - - + +
539D ALA* 3.9 30.5 - - + +
540D SER* 4.0 17.9 - - - +
543D ALA* 5.7 0.2 - - + -
594D ILE* 3.0 37.3 + - + +
595D SER* 5.3 0.2 - - - -
597D GLY* 1.3 74.8 - - - +
599D TYR* 1.3 61.5 + - - +
600D ALA 3.2 0.9 - - - -
601D ILE* 3.3 16.5 + - + -
602D ALA* 3.0 23.7 + - - +
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Residues in contact with TYR 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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654A ASN* 3.5 34.9 + - + -
457D LEU* 3.3 19.8 + - + +
460D ASN* 3.1 30.6 + - - +
498D ILE* 3.9 6.3 - - + +
537D PHE* 3.8 28.0 - + - -
540D SER* 3.6 14.3 + - - +
541D PHE* 4.7 16.4 - + - -
595D SER 2.9 19.7 + - - +
596D GLU* 4.4 7.2 - - - +
597D GLY 3.4 0.4 - - - -
598D LEU* 1.3 77.7 - - - +
600D ALA* 1.3 59.0 + - - +
602D ALA* 3.4 5.3 + - - +
603D VAL* 2.9 37.6 + - + +
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Residues in contact with ALA 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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651A GLY* 3.3 24.1 - - - +
654A ASN* 5.0 2.2 - - - -
655A LEU* 3.8 27.6 - - + +
703A ILE* 4.8 0.2 - - + -
707A LEU* 4.3 9.6 - - + -
596D GLU 3.9 5.2 + - - +
597D GLY 3.8 9.6 + - - +
598D LEU 3.2 1.0 - - - -
599D TYR* 1.3 78.8 - - - +
601D ILE* 1.3 60.1 + - - +
603D VAL* 3.3 5.2 + - - +
604D VAL* 3.0 34.7 + - - +
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Residues in contact with ILE 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ILE* 3.7 36.1 - - + -
706A VAL* 6.4 1.1 - - + -
707A LEU* 4.7 16.4 - - + -
1006A Y01 4.1 35.0 - - + -
536D ILE* 4.1 20.4 - - + -
597D GLY 3.6 14.1 - - - +
598D LEU* 3.3 17.4 + - + +
600D ALA* 1.3 74.9 - - - +
602D ALA* 1.3 57.5 + - - +
604D VAL* 3.4 6.1 + - + +
605D LEU* 2.9 39.0 + - + +
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Residues in contact with ALA 602 (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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533D MET* 3.9 5.3 - - - +
536D ILE* 3.9 15.4 - - + +
537D PHE* 3.7 45.3 - - + +
598D LEU 3.0 17.0 + - - +
599D TYR* 3.7 4.0 - - - +
601D ILE* 1.3 78.1 - - - +
603D VAL* 1.3 56.5 + - - +
605D LEU* 3.8 4.4 - - - +
606D SER* 2.9 32.2 + - - -
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Residues in contact with VAL 603 (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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647A ALA 5.0 0.4 - - - +
650A ILE* 3.8 28.5 - - + -
651A GLY* 3.8 13.9 - - - +
654A ASN* 3.9 6.5 - - - +
457D LEU* 3.8 22.9 - - + -
537D PHE* 4.6 1.1 - - + -
599D TYR* 2.9 52.6 + - + +
600D ALA* 3.8 5.2 - - - +
602D ALA* 1.3 75.7 - - - +
604D VAL* 1.3 63.0 + - - +
606D SER* 3.1 17.6 + - - -
607D PHE* 3.2 17.6 - - + -
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Residues in contact with VAL 604 (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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647A ALA* 3.9 14.6 - - + +
648A PHE* 3.8 39.7 - - + -
651A GLY* 3.7 20.9 - - - -
707A LEU* 4.3 21.8 - - + -
710A VAL* 6.1 0.2 - - + -
600D ALA 3.0 21.4 + - - +
601D ILE* 3.8 6.3 - - + +
603D VAL* 1.3 78.6 - - - +
605D LEU* 1.3 64.4 + - + +
606D SER 3.4 0.7 + - - -
607D PHE* 3.4 15.2 + - - +
1003D S9Y 4.1 18.9 - - + +
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Residues in contact with LEU 605 (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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1006A Y01 4.1 36.6 - - + -
529D LEU* 4.4 15.1 - - + +
533D MET* 4.0 30.8 - - + +
536D ILE* 4.1 25.4 - - + -
601D ILE* 2.9 28.9 + - + +
602D ALA* 5.3 0.2 - - - -
604D VAL* 1.3 80.0 - - + +
606D SER* 1.3 59.1 + - - +
608D SER* 2.5 29.1 + - - -
1003D S9Y 4.4 17.7 - - + -
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Residues in contact with SER 606 (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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450D PHE* 3.5 23.0 - - - -
453D PHE* 4.2 19.3 - - - -
454D LEU* 4.3 1.5 - - - +
457D LEU* 3.3 20.1 - - - +
533D MET* 3.9 25.5 - - - +
537D PHE* 4.2 2.7 - - - -
602D ALA 2.9 13.7 + - - -
603D VAL 3.1 14.7 + - - -
604D VAL 3.3 0.2 - - - -
605D LEU* 1.3 76.5 - - - +
607D PHE* 1.3 60.9 + - - +
608D SER 3.2 2.3 + - - -
609D ARG* 3.7 6.5 + - - +
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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