Contacts of the helix formed by residues 547 - 562 (chain B) in PDB entry 6G52
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 SER 547 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B ILE* 1.3 78.3 - - - +
548B PRO* 1.3 75.0 - - - +
549B GLN* 2.9 19.3 + - - +
550B LEU* 3.1 16.5 + - - +
551B LEU* 3.2 11.5 + - - +
633F THR* 6.3 3.6 - - - -
634F GLY 5.2 8.2 + - - -
635F ALA 4.2 8.8 + - - -
637F SER* 5.5 3.5 - - - -
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Residues in contact with PRO 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ILE 4.6 1.8 - - - +
547B SER* 1.3 86.7 - - - +
549B GLN* 1.3 55.8 + - - +
551B LEU* 3.6 11.8 - - + +
552B LEU* 2.9 31.2 + - - +
632E GLU* 5.3 11.0 - - - +
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Residues in contact with GLN 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B SER* 2.9 11.9 + - - +
548B PRO* 1.3 75.8 - - - +
550B LEU* 1.3 65.3 + - - +
552B LEU* 3.2 2.9 + - - -
553B ALA* 2.9 24.1 + - - +
557F PHE* 3.6 17.7 - - + -
636F PHE* 3.1 26.9 - - - +
637F SER* 5.0 3.1 - - - -
638F TYR* 6.0 1.8 - - + -
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Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ILE* 5.0 12.1 - - + -
547B SER* 3.1 15.3 + - - +
549B GLN* 1.3 78.7 - - - +
551B LEU* 1.3 58.0 + - - +
553B ALA* 3.5 2.1 + - - +
554B ALA* 2.9 28.8 + - - +
616B LEU* 5.5 4.9 - - + +
636B PHE* 4.8 3.3 - - + -
635F ALA* 3.7 22.7 - - + +
636F PHE* 4.0 19.7 - - + +
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Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ILE* 4.6 21.0 - - + +
547B SER 3.2 11.6 + - - +
548B PRO* 3.6 13.2 - - + +
549B GLN 3.2 0.4 - - - -
550B LEU* 1.3 78.6 - - - +
552B LEU* 1.3 62.8 + - + +
554B ALA* 3.2 10.8 + - + +
555B HIS* 2.9 25.2 + - + +
576B LEU* 5.2 9.0 - - + -
579B LEU* 3.6 41.5 - - + +
580B LYS* 5.1 18.2 - - + -
585B ILE* 5.4 7.4 - - + -
616B LEU* 6.1 2.9 - - + -
709B ILE* 5.7 7.2 - - + -
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Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B PRO 2.9 18.0 + - - +
549B GLN* 3.8 4.3 - - - +
551B LEU* 1.3 76.5 - - + +
553B ALA* 1.3 67.5 + - - +
555B HIS* 2.9 13.3 + - + +
556B ARG* 2.9 24.9 + - - +
557F PHE* 4.7 2.5 - - + -
561F GLU* 3.5 34.8 - - - +
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Residues in contact with ALA 553 (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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549B GLN 2.9 9.7 + - - +
550B LEU 3.6 1.8 - - - +
552B LEU* 1.3 77.0 - - - +
554B ALA* 1.3 62.6 + - - +
556B ARG* 3.4 2.2 + - - +
557B PHE* 2.9 25.8 + - - +
636B PHE* 4.9 1.3 - - - -
553F ALA 4.4 5.1 - - - +
557F PHE* 3.4 36.6 - - + +
636F PHE* 3.4 37.2 - - + -
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Residues in contact with ALA 554 (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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550B LEU 2.9 14.4 + - - +
551B LEU* 3.2 15.5 + - + +
553B ALA* 1.3 75.8 - - - +
555B HIS* 1.3 57.8 + - - +
557B PHE* 3.6 1.9 - - - +
558B LEU* 2.8 44.1 + - + +
579B LEU* 4.9 3.6 - - + -
614B LEU* 5.0 0.7 - - + -
616B LEU* 4.3 15.5 - - + -
636B PHE* 3.8 27.5 - - + -
709B ILE* 6.0 2.5 - - + -
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Residues in contact with HIS 555 (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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551B LEU* 2.9 15.6 + - + +
552B LEU* 2.9 15.4 + - + +
554B ALA* 1.3 75.9 - - - +
556B ARG* 1.3 66.5 + - + +
558B LEU* 3.0 5.8 + - - +
559B ALA* 3.0 27.3 + - + +
572B GLU* 3.6 34.0 + - + +
575B LEU* 3.4 41.2 - - + +
576B LEU* 4.3 19.8 + - + +
579B LEU* 4.1 16.6 - - + +
561F GLU* 5.8 2.9 - - - -
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Residues in contact with ARG 556 (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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552B LEU 2.9 15.9 + - - +
553B ALA* 4.1 3.6 - - - +
555B HIS* 1.3 78.0 - - + +
557B PHE* 1.3 64.4 + - - +
559B ALA* 3.5 5.3 + - - +
560B THR* 2.9 27.2 + - - -
556F ARG* 4.3 15.2 + - + +
560F THR* 3.9 34.5 - - + +
561F GLU* 6.1 0.9 - - - +
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Residues in contact with PHE 557 (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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553B ALA 2.9 18.6 + - - +
554B ALA 3.6 0.9 - - - +
556B ARG* 1.3 76.8 - - - +
558B LEU* 1.3 65.9 + - + +
560B THR* 3.2 1.9 + - - -
561B GLU* 2.9 54.4 + - + +
562B VAL* 4.2 4.7 + - + -
614B LEU* 3.9 13.9 - - + -
636B PHE* 3.5 60.3 - + + -
638B TYR* 4.3 12.3 - + - -
549F GLN* 4.2 18.6 - - - -
552F LEU* 4.1 11.0 - - + -
553F ALA* 3.5 23.1 - - + -
556F ARG* 4.4 9.7 - - - +
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Residues in contact with LEU 558 (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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554B ALA* 2.8 35.0 + - + +
555B HIS 3.0 5.1 + - - +
557B PHE* 1.3 80.9 - - + +
559B ALA* 1.3 63.9 + - - +
562B VAL* 3.4 32.6 + - + +
565B PHE* 3.7 32.5 - - + +
575B LEU* 4.3 14.8 - - + -
579B LEU* 4.4 19.1 - - + -
612B PHE* 5.0 1.3 - - + -
614B LEU* 3.4 39.0 - - + -
709B ILE* 4.3 19.7 - - + -
711B ILE* 4.8 1.8 - - + -
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Residues in contact with ALA 559 (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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555B HIS* 3.0 20.3 + - + +
556B ARG* 4.0 5.2 - - - +
558B LEU* 1.3 77.9 - - - +
560B THR* 1.3 64.5 + - - +
562B VAL 3.7 9.0 - - - +
565B PHE 4.3 9.9 - - - +
566B SER* 4.1 1.7 - - - -
567B PRO* 3.7 36.8 - - + +
572B GLU* 6.5 0.7 - - - -
575B LEU* 4.2 14.3 - - + +
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Residues in contact with THR 560 (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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556B ARG 2.9 18.6 + - - -
557B PHE* 3.2 2.2 + - - -
559B ALA* 1.3 80.9 - - - +
561B GLU* 1.3 62.4 + - - +
562B VAL 3.6 1.6 + - - +
552F LEU* 4.8 1.6 - - - -
556F ARG* 3.3 46.7 - - - +
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Residues in contact with GLU 561 (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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557B PHE* 2.9 37.9 + - + +
560B THR* 1.3 72.3 - - - +
562B VAL* 1.3 62.3 + - - +
563B SER 4.2 0.7 + - - -
638B TYR* 4.7 11.5 + - + -
552F LEU* 3.7 22.7 - - + -
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Residues in contact with VAL 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B PHE* 4.6 5.4 - - + +
558B LEU* 3.4 32.6 + - + +
559B ALA 3.7 6.6 - - - +
560B THR 3.4 2.0 - - - -
561B GLU* 1.3 84.1 - - + +
563B SER* 1.3 64.4 - - - +
564B GLN* 4.0 17.9 - - + +
565B PHE* 3.4 36.8 + - + -
566B SER* 3.4 7.6 + - - -
612B PHE* 5.8 1.1 - - + -
614B LEU* 5.7 0.9 - - + -
638B TYR* 4.2 32.1 - - + -
641B THR* 4.4 7.2 - - - +
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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