Contacts of the helix formed by residues 556 - 571 (chain D) in PDB entry 6X34
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 ALA 556 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D LYS* 5.9 6.6 - - + +
519D VAL* 4.3 17.0 - - + -
520D ASN* 5.3 9.2 - - + +
523D TYR* 3.6 28.9 - - + -
550D LYS 5.5 0.2 - - - +
554D LEU 3.6 2.4 + - - -
555D GLU* 1.3 76.1 - - + +
557D SER* 1.3 61.1 + - - +
558D SER 3.5 2.5 - - - +
559D GLY 4.4 2.7 - - - +
560D ILE* 3.4 22.3 + - - +
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Residues in contact with SER 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D LEU* 4.3 6.4 - - - +
553D ARG 4.1 9.6 - - - -
554D LEU 4.4 3.3 + - - -
555D GLU 3.5 0.6 - - - -
556D ALA* 1.3 73.5 - - - +
558D SER* 1.3 60.4 + - - +
559D GLY 3.3 2.5 - - - -
560D ILE* 3.4 7.2 + - - +
561D LEU* 2.9 29.6 + - - +
589D LEU* 4.5 10.9 - - - +
593D HIS* 3.7 34.5 - - - -
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Residues in contact with SER 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D ALA* 3.5 0.8 - - - +
557D SER* 1.3 78.6 - - - +
559D GLY* 1.3 56.9 + - - +
561D LEU* 3.3 13.0 + - - +
562D GLU* 2.9 29.6 + - - +
598D LYS* 6.0 2.3 - - - +
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Residues in contact with GLY 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D TYR* 4.4 19.7 - - - -
527D ALA* 5.0 0.8 - - - +
556D ALA* 4.2 6.1 + - - +
557D SER 3.3 0.4 - - - -
558D SER* 1.3 78.8 - - - +
560D ILE* 1.3 59.1 + - - +
562D GLU* 3.3 10.9 + - - +
563D VAL* 2.9 34.7 + - - +
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Residues in contact with ILE 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D TYR* 3.6 42.4 - - + +
546D TRP* 6.3 2.7 - - + -
547D LEU* 3.9 26.0 - - + +
550D LYS* 4.3 18.8 - - + +
551D LEU* 3.6 36.1 - - + +
556D ALA 3.4 17.9 - - - +
557D SER* 3.4 5.5 + - - +
559D GLY* 1.3 75.8 - - - +
561D LEU* 1.3 58.0 + - - +
563D VAL* 3.6 8.3 - - + +
564D LEU* 2.9 29.7 + - + +
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Residues in contact with LEU 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D LEU* 4.4 7.1 - - + +
557D SER 2.9 17.4 + - - +
558D SER* 3.6 12.3 - - - +
560D ILE* 1.3 76.8 - - - +
562D GLU* 1.3 56.9 + - - +
564D LEU* 3.3 9.1 + - + +
565D TYR* 2.9 28.7 + - + +
586D ILE* 5.7 2.2 - - + -
589D LEU* 4.4 16.2 - - + -
596D ASN* 4.7 8.7 - - + -
598D LYS* 3.7 26.2 - - + +
599D VAL* 3.7 35.9 - - + -
602D VAL* 4.0 21.1 - - + -
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Residues in contact with GLU 562 (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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527D ALA* 4.5 12.6 - - + +
531D ARG* 2.5 33.7 + - - +
558D SER 2.9 17.2 + - - +
559D GLY* 3.7 8.1 - - - +
561D LEU* 1.3 76.1 - - - +
563D VAL* 1.3 58.1 + - - +
565D TYR* 3.3 13.0 + - + +
566D CYS* 2.9 28.6 + - - +
598D LYS* 6.5 0.2 - - - -
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Residues in contact with VAL 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D TYR* 4.3 5.6 - - + +
526D LEU* 3.6 33.4 - - + -
527D ALA* 3.6 22.4 - - + +
530D ILE* 5.4 7.8 - - + +
540D PHE* 5.2 7.4 - - + -
547D LEU* 4.3 22.9 - - + -
559D GLY 2.9 23.2 + - - +
560D ILE* 3.6 11.9 - - + +
562D GLU* 1.3 77.5 - - - +
564D LEU* 1.3 58.2 + - - +
566D CYS* 3.2 6.1 + - - +
567D VAL* 2.9 30.7 + - + +
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Residues in contact with LEU 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 5.2 4.9 - - + -
547D LEU* 3.8 26.7 - - + +
548D VAL* 5.0 9.0 - - + -
551D LEU* 4.1 15.5 - - + -
560D ILE* 2.9 17.1 + - + +
561D LEU* 3.8 8.1 - - + +
563D VAL* 1.3 78.2 - - - +
565D TYR* 1.3 62.4 + - - +
567D VAL* 3.3 14.8 - - + +
568D LEU* 3.2 48.3 - - + +
586D ILE* 3.6 31.2 - - + -
602D VAL* 4.3 9.0 - - + -
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Residues in contact with TYR 565 (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* 2.9 17.6 + - + +
562D GLU* 3.6 13.7 - - + +
564D LEU* 1.3 77.4 - - - +
566D CYS* 1.3 64.8 + - + +
568D LEU* 3.7 6.6 + - - +
569D ILE* 3.4 31.7 + - + +
598D LYS* 4.8 4.3 - - + +
601D ASP* 3.6 34.4 - - + +
602D VAL* 3.6 30.6 - - + +
605D SER* 4.9 8.6 + - - -
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Residues in contact with CYS 566 (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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527D ALA* 4.7 3.6 - - + +
530D ILE* 4.8 9.4 - - + +
531D ARG* 3.5 60.1 - - - +
532D GLY 5.1 0.4 - - - -
537D CYS* 5.4 0.2 - - - +
562D GLU* 2.9 17.3 + - + +
563D VAL* 3.2 6.0 + - - +
565D TYR* 1.3 81.9 - - + +
567D VAL* 1.3 62.1 + - - +
568D LEU 3.3 0.2 - - - -
569D ILE* 3.3 23.7 + - - +
570D GLU* 3.8 11.5 + - - +
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Residues in contact with VAL 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D ILE* 5.0 8.3 - - + -
537D CYS* 4.2 25.8 - - + +
540D PHE* 4.1 24.5 - - + -
544D LEU* 5.5 1.1 - - + -
547D LEU* 4.4 8.5 - - + -
563D VAL* 2.9 17.4 + - + +
564D LEU* 3.3 33.9 - - + +
566D CYS* 1.3 78.7 - - - +
568D LEU* 1.3 67.7 + - + +
569D ILE 3.4 0.6 + - - -
570D GLU 4.6 0.7 - - - -
571D SER* 3.7 18.7 + - - +
574D VAL* 4.3 19.8 - - + +
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Residues in contact with LEU 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 6.0 0.4 - - + -
564D LEU* 3.2 37.3 + - + +
565D TYR* 3.7 2.9 + - - +
566D CYS 3.3 0.4 - - - -
567D VAL* 1.3 83.6 - - + +
569D ILE* 1.3 57.3 + - - +
571D SER 4.7 6.9 - - - +
572D PRO* 5.4 3.7 - - - +
574D VAL* 3.7 35.9 - - + -
575D LEU* 4.9 4.4 - - + +
578D ILE* 5.4 1.8 - - + -
602D VAL* 4.0 20.0 - - + -
605D SER* 3.7 29.1 + - - +
606D LEU* 3.7 35.9 - - + +
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Residues in contact with ILE 569 (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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565D TYR* 3.4 29.8 + - + +
566D CYS* 3.3 24.2 - - - +
568D LEU* 1.3 81.2 - - - +
570D GLU* 1.3 71.3 + - + +
571D SER 3.7 1.1 - - - -
572D PRO* 5.4 1.0 - - - +
605D SER* 4.9 14.8 - - - -
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Residues in contact with GLU 570 (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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530D ILE 5.9 1.1 - - - +
532D GLY 5.9 4.9 - - - +
533D ASN 4.7 4.9 - - - +
534D ARG* 5.2 16.9 + - + +
537D CYS* 3.7 23.6 - - + -
566D CYS* 3.8 11.7 + - - +
567D VAL 4.5 0.6 + - - +
569D ILE* 1.3 86.9 - - + +
571D SER* 1.3 60.1 + - - +
572D PRO* 3.9 5.9 - - - +
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Residues in contact with SER 571 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D ARG* 5.0 12.8 - - - +
537D CYS* 4.0 31.3 + - - +
538D ALA* 4.6 4.5 + - - -
567D VAL 3.7 14.8 + - - +
568D LEU* 4.7 3.6 - - - -
569D ILE 5.0 1.8 - - - -
570D GLU* 1.3 79.3 - - - +
572D PRO* 1.3 61.5 - - - +
573D GLU* 3.2 28.6 + - - +
574D VAL* 3.9 12.6 + - - +
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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