Contacts of the helix formed by residues 548 - 564 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547C ASN* 1.3 77.5 - - - +
549C PRO* 1.3 75.1 - - + +
550C LYS* 3.0 12.9 + - - +
551C VAL* 2.8 41.4 + - + +
552C ILE* 3.3 11.6 + - - +
629C LYS* 4.4 2.0 - - - +
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Residues in contact with PRO 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ASP* 1.3 91.6 - - + +
550C LYS* 1.3 57.2 + - - +
552C ILE* 3.5 6.2 + - + +
553C ALA* 3.0 28.2 + - - +
629C LYS* 4.3 17.3 - - + +
632C GLN* 3.8 47.3 - - + +
633C VAL* 4.1 14.2 - - + +
636C GLU* 3.8 17.9 - - + +
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Residues in contact with LYS 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C ASP* 3.0 14.7 + - - +
549C PRO* 1.3 76.7 - - - +
551C VAL* 1.3 61.7 + - + +
553C ALA* 3.3 1.4 + - - +
554C GLN* 2.9 39.1 + - - +
636C GLU* 3.1 27.2 + - - +
640C SER* 3.4 25.5 + - - -
641C MET* 3.5 16.6 - - + -
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Residues in contact with VAL 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C ASN* 4.3 20.6 - - + +
548C ASP* 2.8 33.3 + - + +
550C LYS* 1.3 70.7 - - + +
552C ILE* 1.3 61.4 + - - +
554C GLN* 3.5 16.5 + - - +
555C HIS* 2.6 55.9 + - + +
768C PHE* 5.2 1.6 - - + -
774C MET* 4.3 2.0 - - + -
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Residues in contact with ILE 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C PHE* 3.8 39.7 - - + +
547C ASN* 3.8 26.7 - - + +
548C ASP 3.3 15.5 + - - +
549C PRO 3.6 5.4 - - - +
550C LYS 3.2 0.2 - - - -
551C VAL* 1.3 74.9 - - - +
553C ALA* 1.3 66.7 + - - +
555C HIS* 3.0 15.0 + - - +
556C VAL* 3.0 22.1 + - + +
629C LYS* 4.0 10.3 - - + -
633C VAL* 4.1 29.8 - - + -
774C MET* 4.1 14.8 - - + -
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Residues in contact with ALA 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PRO 3.0 18.9 + - - +
550C LYS 3.7 3.4 - - - +
552C ILE* 1.3 77.5 - - - +
554C GLN* 1.3 52.5 + - - +
556C VAL* 3.2 4.5 + - - +
557C LEU* 2.8 36.0 + - - +
633C VAL* 4.4 3.3 - - + +
636C GLU* 3.6 23.1 - - + -
637C LEU* 3.6 28.2 - - + +
641C MET* 3.7 12.1 - - + -
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Residues in contact with GLN 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C LYS* 2.9 24.4 + - - +
551C VAL* 3.6 23.4 - - - +
553C ALA* 1.3 77.9 - - - +
555C HIS* 1.3 57.1 + - - +
557C LEU* 3.4 2.6 + - - +
558C SER* 2.8 30.5 + - - -
641C MET* 3.5 25.9 - - + +
764C ILE 4.7 10.4 + - - +
765C LEU* 4.1 11.6 - - + +
768C PHE* 3.7 40.6 - - + +
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Residues in contact with HIS 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C VAL* 2.6 44.3 + - + -
552C ILE 3.0 8.0 + - - +
554C GLN* 1.3 78.0 - - - +
556C VAL* 1.3 58.5 + - - +
558C SER* 3.4 4.4 + - - -
559C MET* 2.9 29.8 + - - +
768C PHE* 3.6 21.9 - + - -
769C GLN 5.3 0.7 - - - -
770C PRO* 3.5 9.6 - - + +
771C ASP* 2.9 33.5 + - + -
774C MET* 3.4 32.3 - - + +
775C ASN* 3.9 15.9 + - + +
778C CYS* 3.8 20.0 - - - +
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Residues in contact with VAL 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C ILE* 3.0 26.2 + - + +
553C ALA* 3.5 7.6 - - - +
555C HIS* 1.3 74.7 - - - +
557C LEU* 1.3 60.6 + - - +
559C MET* 3.3 3.0 + - - +
560C ASP* 2.8 31.1 + - - +
601C ARG* 4.8 1.8 - - - +
605C MET* 4.7 12.1 - - + -
633C VAL* 5.6 1.3 - - + -
637C LEU* 4.1 13.7 - - + -
643C ASP* 4.0 2.0 - - - +
646C SER* 3.3 36.8 - - - +
778C CYS* 4.1 17.0 - - - -
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Residues in contact with LEU 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C ALA 2.8 20.3 + - - +
554C GLN 3.7 3.4 - - - +
556C VAL* 1.3 73.4 - - - +
558C SER* 1.3 64.1 + - - +
560C ASP* 3.3 0.7 + - - +
561C CYS* 2.9 39.2 + - - -
637C LEU* 4.6 0.2 - - - +
641C MET* 3.7 38.8 - - + +
643C ASP* 3.7 16.5 + - + +
706C SER* 4.0 15.0 - - - +
707C VAL* 3.9 17.5 - - + -
761C ALA* 5.0 2.0 - - + -
764C ILE* 3.9 12.3 - - + -
765C LEU* 3.9 26.2 - - + -
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Residues in contact with SER 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C GLN 2.8 17.6 + - - -
555C HIS* 3.6 5.6 - - - -
556C VAL 3.3 0.2 - - - -
557C LEU* 1.3 79.1 - - - +
559C MET* 1.3 61.3 + - - +
561C CYS* 3.4 4.4 + - - +
562C ARG* 3.0 44.4 + - - +
567C LEU* 5.9 0.2 - - - -
765C LEU* 3.8 21.0 - - - +
768C PHE* 4.1 19.3 - - - -
770C PRO* 5.8 1.4 - - - +
775C ASN* 5.0 3.7 + - - -
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Residues in contact with MET 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C PHE* 6.5 0.7 - - + -
555C HIS 2.9 16.5 + - - +
556C VAL 3.8 1.1 - - - +
558C SER* 1.3 73.3 - - - +
560C ASP* 1.3 67.4 + - - +
562C ARG* 2.9 33.9 + - - +
563C VAL* 2.9 34.0 + - + +
601C ARG* 3.3 26.5 - - - +
775C ASN* 5.0 3.1 - - - +
778C CYS* 3.3 17.0 - - + +
779C LYS* 2.9 51.6 - - + -
780C THR 4.2 3.4 - - - +
781C GLU* 6.3 0.2 - - + -
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Residues in contact with ASP 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556C VAL 2.8 20.8 + - - +
557C LEU 3.7 2.7 - - - +
559C MET* 1.3 72.6 - - - +
561C CYS* 1.3 57.9 + - - +
563C VAL* 4.1 2.5 - - - +
564C ALA* 2.9 34.1 + - - +
601C ARG* 2.7 39.2 + - - +
643C ASP* 2.6 25.0 - - - +
645C TYR* 3.5 19.6 - - + -
646C SER* 2.4 27.7 + - - -
707C VAL* 4.3 11.0 - - + -
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Residues in contact with CYS 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C LEU* 2.9 40.2 + - - +
558C SER* 3.7 6.5 - - - +
559C MET 3.1 0.2 - - - -
560C ASP* 1.3 76.7 - - - +
562C ARG* 1.3 59.7 + - - +
565C ARG 3.2 1.4 + - - -
566C ILE* 2.8 44.3 + - - -
567C LEU* 3.2 30.2 + - + +
706C SER 4.8 0.2 - - - -
707C VAL* 4.2 10.1 - - - -
761C ALA* 3.7 24.5 - - - -
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Residues in contact with ARG 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558C SER* 3.0 36.3 + - - +
559C MET* 2.9 30.7 + - - +
561C CYS* 1.3 76.6 - - + +
563C VAL* 1.3 66.9 + - + +
565C ARG* 3.2 15.4 + - - +
567C LEU* 3.8 18.5 - - + +
568C GLY* 5.2 9.0 - - - +
775C ASN* 2.9 35.8 + - - +
779C LYS* 5.1 4.2 - - - +
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Residues in contact with VAL 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C PHE* 4.5 24.9 - - + -
559C MET* 2.9 36.2 + - + +
560C ASP* 4.1 3.1 - - - +
562C ARG* 1.3 78.0 - - + +
564C ALA* 1.3 59.0 + - - +
565C ARG* 3.1 9.9 + - - +
594C LEU* 3.6 15.5 - - + +
597C ASP* 4.9 10.3 - - + +
598C ILE* 4.9 14.6 - - + -
601C ARG* 4.0 33.7 - - - +
645C TYR* 6.2 0.7 - - + -
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Residues in contact with ALA 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C ASP 2.9 18.9 + - - +
563C VAL* 1.3 76.6 - - - +
565C ARG* 1.3 70.2 + - - +
566C ILE* 3.7 24.1 - - + +
582C GLY* 3.2 19.6 - - - -
583C LEU* 4.1 9.4 + - + -
594C LEU* 4.4 8.6 - - - +
598C ILE* 5.1 7.4 - - + -
645C TYR* 6.5 0.9 - - + -
707C VAL* 5.1 3.4 - - + -
710C LEU* 4.9 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
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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