Contacts of the helix formed by residues 548 - 564 (chain B) in PDB entry 3T6A
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 ASP 548 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547B ASN* 1.3 74.7 + - - +
549B PRO* 1.3 78.8 - - - +
550B LYS* 2.8 39.3 + - - +
551B VAL* 2.9 29.5 + - + +
552B ILE* 2.9 12.2 + - - +
629B LYS* 4.7 0.2 - - - +
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Residues in contact with PRO 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ASN 3.7 0.4 - - - -
548B ASP* 1.3 94.3 - - - +
550B LYS* 1.3 55.8 + - - +
552B ILE* 3.4 5.9 + - + +
553B ALA* 3.0 29.3 + - - +
629B LYS* 4.1 18.4 - - + +
632B GLN* 3.9 41.1 - - + +
633B VAL* 3.8 28.0 - - + +
636B GLU* 4.0 8.5 - - + +
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Residues in contact with LYS 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ASP* 2.8 21.2 + - - +
549B PRO* 1.3 72.0 - - - +
551B VAL* 1.3 58.2 + - + +
553B ALA* 3.4 1.6 + - - +
554B GLN* 3.0 53.3 + - + +
636B GLU* 3.1 39.7 + - - +
640B SER* 3.2 23.2 + - - -
641B MET* 4.5 5.2 - - + +
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Residues in contact with VAL 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ASN* 4.3 17.5 - - + +
548B ASP* 2.9 28.4 + - + +
550B LYS* 1.3 74.8 - - + +
552B ILE* 1.3 62.9 + - - +
554B GLN* 3.4 16.4 + - - +
555B HIS* 2.7 53.2 + - + -
768B PHE* 5.2 1.6 - - + -
771B ASP* 6.4 0.2 - - + -
774B MET* 5.5 0.4 - - + -
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Residues in contact with ILE 552 (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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544B PHE* 3.5 49.4 - - + +
547B ASN* 3.7 24.9 - - + +
548B ASP 2.9 10.5 + - - +
549B PRO* 3.5 7.2 - - + +
551B VAL* 1.3 77.4 - - - +
553B ALA* 1.3 57.3 + - - +
555B HIS* 3.3 9.9 + - - +
556B VAL* 3.1 33.5 + - + +
629B LYS* 4.2 7.2 - - + -
633B VAL* 4.0 33.0 - - + -
774B MET* 4.1 14.8 - - + -
778B CYS* 4.9 0.8 - - - -
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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 PRO 3.0 17.7 + - - +
550B LYS* 3.9 3.4 - - - +
551B VAL 3.2 0.2 - - - -
552B ILE* 1.3 75.6 - - - +
554B GLN* 1.3 60.2 + - - +
556B VAL* 3.2 5.0 + - - +
557B LEU* 2.8 29.5 + - - +
633B VAL* 4.4 3.6 - - + +
636B GLU* 3.8 19.1 - - + -
637B LEU* 3.8 27.0 - - + +
641B MET* 3.8 15.4 - - + +
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Residues in contact with GLN 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 LYS* 3.0 37.1 + - - +
551B VAL* 3.8 14.8 - - - +
552B ILE 3.4 0.4 - - - -
553B ALA* 1.3 74.6 - - - +
555B HIS* 1.3 58.3 + - - +
557B LEU* 3.5 2.5 - - - +
558B SER* 2.8 30.8 + - - -
641B MET* 3.6 28.1 - - + +
764B ILE 5.1 7.0 + - - +
765B LEU* 4.0 11.4 - - + +
768B PHE* 3.3 38.2 - - + +
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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
----------------------------------------------------------
551B VAL* 2.7 43.9 + - + -
552B ILE 3.5 7.6 - - - +
553B ALA 3.2 0.4 - - - -
554B GLN* 1.3 76.3 - - - +
556B VAL* 1.3 64.9 + - - +
558B SER* 3.3 3.6 + - - -
559B MET* 3.0 25.1 + - - +
768B PHE* 3.6 24.1 - + - -
769B GLN 4.9 1.6 - - - -
770B PRO* 3.5 7.2 - - + +
771B ASP* 2.9 37.5 + - + -
774B MET* 3.6 26.0 - - + +
775B ASN* 3.9 18.9 + - + +
778B CYS* 3.9 17.7 - - + +
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Residues in contact with VAL 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B PHE* 6.5 0.2 - - + -
552B ILE* 3.1 27.5 + - + +
553B ALA* 3.2 7.8 + - - +
555B HIS* 1.3 74.7 - - - +
557B LEU* 1.3 57.9 + - - +
559B MET* 3.4 3.5 + - - +
560B ASP* 2.8 32.9 + - - +
601B ARG* 4.5 6.1 - - - +
605B MET* 4.7 7.2 - - - -
633B VAL* 5.6 1.1 - - + -
637B LEU* 4.1 12.8 - - + -
643B ASP* 4.1 1.6 - - - +
646B SER* 3.2 37.7 - - - +
650B LEU* 6.4 0.4 - - + -
778B CYS* 4.2 16.8 - - - -
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Residues in contact with LEU 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 2.8 20.1 + - - +
554B GLN 3.5 4.7 - - - +
556B VAL* 1.3 71.4 - - - +
558B SER* 1.3 58.2 + - - +
560B ASP* 3.3 1.0 + - - +
561B CYS* 2.9 35.2 + - - -
641B MET* 3.7 39.9 - - + +
643B ASP* 3.6 15.9 + - + +
706B SER* 3.8 25.1 - - - +
707B VAL* 3.9 17.5 - - + -
761B ALA* 4.8 2.7 - - - +
764B ILE* 3.8 21.1 - - + -
765B LEU* 3.9 20.2 - - + -
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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
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554B GLN 2.8 17.1 + - - -
555B HIS* 3.5 6.1 - - - -
557B LEU* 1.3 78.4 - - - +
559B MET* 1.3 60.1 + - - +
561B CYS* 3.4 3.8 + - - +
562B ARG* 3.0 49.0 + - - +
567B LEU* 5.6 0.4 - - - +
765B LEU* 4.0 18.1 - - - +
768B PHE* 3.9 22.1 - - - -
770B PRO* 5.3 2.1 - - - +
775B ASN* 4.4 2.3 + - - -
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Residues in contact with MET 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B PHE* 6.4 1.3 - - + -
555B HIS 3.0 16.8 + - - +
556B VAL 3.8 0.9 - - - +
558B SER* 1.3 73.8 + - - +
560B ASP* 1.3 66.3 + - - +
562B ARG* 3.2 32.1 + - + +
563B VAL* 3.0 54.1 + - + +
601B ARG* 3.6 16.8 - - - +
775B ASN* 4.8 5.4 - - - +
778B CYS* 3.4 28.9 - - + +
779B LYS* 3.9 34.5 - - + -
780B THR 5.1 1.1 - - - +
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Residues in contact with ASP 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 VAL 2.8 17.7 + - - +
557B LEU 3.7 2.9 - - - +
559B MET* 1.3 76.6 - - - +
561B CYS* 1.3 57.9 + - - +
563B VAL* 4.1 1.5 - - - +
564B ALA* 3.0 32.6 + - - +
601B ARG* 2.7 36.6 + - - +
643B ASP* 2.6 29.0 - - - +
645B TYR* 3.6 15.4 - - + -
646B SER* 2.5 28.1 + - - -
707B VAL* 4.5 9.2 - - + +
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Residues in contact with CYS 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 LEU* 2.9 33.9 + - - +
558B SER* 3.7 5.2 - - - +
559B MET 3.2 0.2 - - - -
560B ASP* 1.3 75.4 - - - +
562B ARG* 1.3 62.0 + - - +
565B ARG 3.3 0.7 + - - -
566B ILE* 2.8 41.7 + - + -
567B LEU* 3.0 31.7 + - + -
707B VAL* 3.9 11.7 - - - -
761B ALA* 3.7 30.3 - - - -
765B LEU* 5.2 0.2 - - - -
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Residues in contact with ARG 562 (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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558B SER* 3.0 35.5 + - - +
559B MET* 3.2 29.5 + - + +
561B CYS* 1.3 78.4 - - - +
563B VAL* 1.3 59.1 + - + +
565B ARG* 3.0 23.9 + - - +
567B LEU* 3.7 22.0 - - + +
568B GLY* 5.2 4.0 - - - -
770B PRO* 5.7 1.8 - - - +
775B ASN* 3.0 42.8 + - - +
779B LYS* 5.1 5.3 - - - +
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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
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515B PHE* 4.6 22.2 - - + -
559B MET* 3.0 43.1 + - + +
560B ASP* 4.1 3.1 - - - +
562B ARG* 1.3 77.3 - - - +
564B ALA* 1.3 60.6 + - + +
565B ARG* 3.2 6.6 + - - +
594B LEU* 3.4 17.9 - - + +
597B ASP* 5.0 9.9 - - + -
598B ILE* 5.1 8.1 - - + -
601B ARG* 4.1 31.2 - - + +
645B TYR* 6.3 0.7 - - + -
780B THR* 6.1 0.2 - - - -
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Residues in contact with ALA 564 (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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560B ASP 3.0 19.2 + - - +
563B VAL* 1.3 75.6 - - - +
565B ARG* 1.3 71.2 + - - +
566B ILE* 3.4 19.5 + - + +
582B GLY* 3.1 20.4 - - - -
583B LEU* 4.0 5.3 + - + -
594B LEU* 4.1 9.7 - - - +
598B ILE* 4.7 14.8 - - + -
645B TYR* 6.5 1.1 - - + -
707B VAL* 5.1 2.2 - - + -
710B LEU* 4.7 13.5 - - + -
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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
------------------------------------------------------------
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