Contacts of the helix formed by residues 556 - 571 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B LYS* 5.9 6.4 - - + +
519B VAL* 4.3 16.4 - - + -
520B ASN* 5.3 9.4 - - + +
523B TYR* 3.6 28.0 - - + -
550B LYS 5.5 0.2 - - - +
554B LEU 3.6 2.2 + - - -
555B GLU* 1.3 76.6 - - + +
557B SER* 1.3 60.3 + - - +
558B SER 3.5 2.5 - - - +
559B GLY 4.4 2.9 - - - +
560B ILE* 3.4 22.3 + - - +
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Residues in contact with SER 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 4.3 5.3 - - - +
553B ARG 4.1 10.3 - - - -
554B LEU 4.4 3.7 + - - -
555B GLU 3.5 0.6 - - - -
556B ALA* 1.3 75.2 - - - +
558B SER* 1.3 60.6 + - - +
559B GLY 3.3 2.0 - - - -
560B ILE* 3.4 6.6 + - - +
561B LEU* 2.9 29.6 + - - +
589B LEU* 4.5 11.7 - - - -
593B HIS* 3.7 33.2 - - - -
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Residues in contact with SER 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ALA* 3.5 0.6 - - - +
557B SER* 1.3 78.4 - - - +
559B GLY* 1.3 57.4 + - - +
561B LEU* 3.3 11.9 + - - +
562B GLU* 2.9 30.0 + - - +
598B LYS* 6.0 2.4 - - - +
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Residues in contact with GLY 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B TYR* 4.4 20.0 - - - -
527B ALA* 5.0 1.4 - - - +
556B ALA* 4.2 5.9 + - - +
557B SER 3.3 0.6 - - - -
558B SER* 1.3 80.3 - - - +
560B ILE* 1.3 59.8 + - - +
562B GLU* 3.3 10.0 + - - +
563B VAL* 2.9 35.0 + - - +
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Residues in contact with ILE 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B TYR* 3.6 43.7 - - + +
546B TRP* 6.3 2.0 - - + -
547B LEU* 3.9 27.1 - - + +
550B LYS* 4.3 19.3 - - + +
551B LEU* 3.6 35.9 - - + +
556B ALA 3.4 17.7 - - - +
557B SER* 3.4 5.8 + - - +
559B GLY* 1.3 76.2 - - - +
561B LEU* 1.3 58.5 + - - +
563B VAL* 3.3 8.2 + - + +
564B LEU* 2.9 28.8 + - + +
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Residues in contact with LEU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 4.4 7.3 - - + +
557B SER 2.9 17.5 + - - +
558B SER* 3.6 12.6 - - - +
559B GLY 3.2 0.2 - - - -
560B ILE* 1.3 77.9 - - - +
562B GLU* 1.3 56.8 + - - +
564B LEU* 3.3 9.0 + - + +
565B TYR* 2.9 27.9 + - + +
586B ILE* 5.7 2.0 - - + -
589B LEU* 4.4 15.3 - - + -
596B ASN* 4.7 9.0 - - + +
598B LYS* 3.7 27.6 - - + +
599B VAL* 3.7 36.6 - - + -
602B VAL* 4.0 20.6 - - + -
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Residues in contact with GLU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B GLU* 6.2 0.2 - - - -
527B ALA* 4.5 12.2 - - + +
531B ARG* 2.5 34.1 + - - +
558B SER 2.9 17.4 + - - +
559B GLY* 3.3 8.2 + - - +
561B LEU* 1.3 76.1 - - - +
563B VAL* 1.3 57.1 + - - +
565B TYR* 3.3 12.1 + - + +
566B CYS* 2.9 28.6 + - - +
598B LYS* 6.5 0.4 - - - -
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Residues in contact with VAL 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B TYR* 4.3 5.8 - - + +
526B LEU* 3.6 34.1 - - + -
527B ALA* 3.6 22.0 - - + +
530B ILE* 5.4 7.4 - - + +
540B PHE* 5.2 7.0 - - + -
547B LEU* 4.3 22.9 - - + -
559B GLY 2.9 23.2 + - - +
560B ILE* 3.6 11.9 - - + +
562B GLU* 1.3 77.0 - - - +
564B LEU* 1.3 55.9 + - - +
566B CYS* 3.2 6.5 + - - +
567B VAL* 2.9 30.8 + - + +
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Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 5.2 5.6 - - + -
547B LEU* 3.8 26.2 - - + +
548B VAL* 5.0 9.6 - - + -
551B LEU* 4.1 14.8 - - + -
560B ILE* 2.9 17.2 + - + +
561B LEU* 3.8 8.7 - - + +
563B VAL* 1.3 78.0 - - - +
565B TYR* 1.3 62.1 + - - +
567B VAL* 3.3 15.6 - - + +
568B LEU* 3.2 47.5 - - + +
586B ILE* 3.6 31.4 - - + -
602B VAL* 4.3 10.8 - - + -
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Residues in contact with TYR 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LEU* 2.9 16.8 + - + +
562B GLU* 3.3 13.0 + - + +
564B LEU* 1.3 78.0 - - - +
566B CYS* 1.3 66.1 + - + +
567B VAL 3.7 0.2 + - - -
568B LEU* 3.7 7.4 + - - +
569B ILE* 3.4 30.9 + - + +
598B LYS* 4.8 4.3 - - + +
601B ASP* 3.6 34.7 - - + +
602B VAL* 3.6 30.4 - - + +
605B SER* 4.9 8.1 + - - -
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Residues in contact with CYS 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ALA* 4.7 3.6 - - + +
530B ILE* 4.8 9.9 - - + +
531B ARG* 3.5 60.8 - - - +
532B GLY 5.1 0.2 - - - -
537B CYS* 5.4 0.3 - - - +
562B GLU 2.9 16.8 + - - +
563B VAL* 3.8 5.4 - - - +
565B TYR* 1.3 83.0 - - + +
567B VAL* 1.3 61.7 + - - +
569B ILE* 3.3 22.9 + - - +
570B GLU* 3.8 11.6 + - - +
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Residues in contact with VAL 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ILE* 5.0 8.9 - - + +
537B CYS* 4.2 26.0 - - + +
540B PHE* 4.1 23.1 - - + -
544B LEU* 5.5 1.3 - - + -
547B LEU* 4.4 9.2 - - + -
563B VAL* 2.9 19.7 + - + +
564B LEU* 3.3 33.7 - - + +
566B CYS* 1.3 77.7 - - - +
568B LEU* 1.3 67.3 + - + +
569B ILE 3.4 0.7 + - - -
570B GLU 4.6 0.7 - - - -
571B SER* 3.7 19.1 + - - +
574B VAL* 4.3 19.4 - - + +
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Residues in contact with LEU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 6.0 0.7 - - + -
564B LEU* 3.2 37.5 + - + +
565B TYR 3.7 2.0 + - - +
566B CYS 3.3 0.6 - - - -
567B VAL* 1.3 81.7 - - + +
569B ILE* 1.3 57.7 + - - +
571B SER 4.7 7.3 - - - +
572B PRO* 5.4 4.0 - - - +
574B VAL* 3.7 35.9 - - + -
575B LEU* 4.9 4.3 - - + +
578B ILE* 5.4 1.8 - - + -
602B VAL* 4.0 20.4 - - + -
605B SER* 3.7 28.8 + - - +
606B LEU* 3.7 36.1 - - + +
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Residues in contact with ILE 569 (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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565B TYR* 3.4 30.9 + - + +
566B CYS* 3.3 25.1 - - - +
568B LEU* 1.3 81.0 - - - +
570B GLU* 1.3 69.5 + - + +
571B SER 3.7 1.3 - - - -
572B PRO* 5.4 0.9 - - - +
605B SER* 4.9 13.7 - - - -
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Residues in contact with GLU 570 (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 ILE 5.9 0.7 - - - +
532B GLY 5.9 4.9 - - - +
533B ASN 4.7 5.6 - - - +
534B ARG* 5.2 16.5 + - + +
537B CYS* 3.7 23.1 - - + -
566B CYS* 3.8 11.9 + - - +
567B VAL 4.5 0.6 + - - +
569B ILE* 1.3 86.7 - - + +
571B SER* 1.3 59.4 + - - +
572B PRO* 3.9 6.3 - - - +
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Residues in contact with SER 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ARG* 5.0 12.8 - - - +
537B CYS* 4.0 32.1 + - - +
538B ALA* 4.6 4.7 + - - -
541B SER* 5.9 0.2 - - - -
567B VAL 3.7 14.9 + - - +
568B LEU* 4.7 3.5 - - - -
569B ILE 5.0 2.0 - - - -
570B GLU* 1.3 79.6 - - - +
572B PRO* 1.3 60.6 - - - +
573B GLU* 3.2 29.7 + - - +
574B VAL* 3.9 12.3 + - - +
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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