Contacts of the helix formed by residues 606 - 619 (chain C) in PDB entry 6T8G
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 LYS 606 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601C MET* 6.0 0.8 - - - +
604C VAL* 4.5 0.6 - - - +
605C GLY* 1.3 102.8 + - - +
607C LYS* 1.3 70.9 + - + +
608C VAL 3.3 1.8 - - - -
609C GLU* 3.7 12.2 + - - +
610C GLU* 3.3 40.9 + - - +
641C LEU* 6.2 2.0 - - - +
15G A 4.6 18.6 + - - +
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Residues in contact with LYS 607 (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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525C ALA* 5.7 4.9 - - + -
529C ARG* 4.7 15.7 - - - +
604C VAL* 3.9 18.2 - - + +
606C LYS* 1.3 77.9 - - + +
608C VAL* 1.3 64.3 + - + +
610C GLU* 4.1 4.6 - - - +
611C LEU* 3.0 38.3 + - + +
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Residues in contact with VAL 608 (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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521C MET* 5.3 6.1 - - + +
524C ALA* 6.4 0.4 - - + -
525C ALA* 5.5 5.2 - - + +
528C LEU* 4.4 15.3 - - + -
597C PHE* 4.2 9.9 - - + -
600C MET* 3.7 43.1 - - + +
601C MET* 5.1 2.7 - - + -
604C VAL* 3.8 38.9 - - + +
605C GLY 5.4 0.2 - - - +
606C LYS 3.3 0.6 - - - -
607C LYS* 1.3 77.2 - - + +
609C GLU* 1.3 58.7 + - - +
611C LEU* 3.1 7.1 + - - +
612C ILE* 2.8 43.7 + - + +
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Residues in contact with GLU 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C PHE* 5.3 0.9 - - - -
601C MET* 3.3 29.5 - - + +
605C GLY 3.9 15.4 + - - +
606C LYS* 3.7 14.7 + - - +
607C LYS 3.4 0.4 - - - -
608C VAL* 1.3 80.6 - - - +
610C GLU* 1.3 60.2 + - + +
612C ILE* 3.4 6.8 + - - +
613C ALA* 3.0 27.7 + - - +
639C THR* 2.5 36.6 + - - +
641C LEU* 3.3 28.4 - - + +
642C ILE* 3.7 21.1 - - + +
602D MET* 4.4 0.6 - - - +
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Residues in contact with GLU 610 (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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606C LYS* 3.3 29.5 + - - +
607C LYS* 4.1 3.8 - - - +
608C VAL 3.3 0.4 - - - -
609C GLU* 1.3 77.9 - - + +
611C LEU* 1.3 59.9 + - + +
613C ALA* 3.4 2.4 + - - +
614C ARG* 2.9 27.7 + - - +
641C LEU* 5.8 2.7 - - + -
602D MET* 4.1 25.7 - - + +
603D ILE* 4.8 5.4 - - + +
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Residues in contact with LEU 611 (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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525C ALA* 4.7 3.4 - - + +
528C LEU* 4.2 27.1 - - + -
529C ARG* 4.0 37.2 - - + +
532C VAL* 3.9 26.0 - - + -
607C LYS* 3.0 30.7 + - + +
608C VAL* 3.6 4.9 - - + +
610C GLU* 1.3 73.6 - - + +
612C ILE* 1.3 61.7 + - - +
614C ARG* 3.2 9.8 + - + +
615C ILE* 2.9 34.5 + - + +
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Residues in contact with ILE 612 (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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528C LEU* 4.3 26.2 - - + -
594C VAL* 5.7 1.1 - - + -
597C PHE* 4.2 10.1 - - + -
600C MET* 5.5 3.4 - - - -
608C VAL* 2.8 33.0 + - + +
609C GLU 3.7 4.7 - - - +
611C LEU* 1.3 77.5 - - - +
613C ALA* 1.3 58.2 + - - +
615C ILE* 3.4 7.0 + - + +
616C ALA* 2.8 30.6 + - + +
626C LEU* 3.7 37.8 - - + +
628C LEU* 4.1 15.0 - - + -
641C LEU 5.7 0.2 - - - +
642C ILE* 3.8 22.2 - - + -
646C ILE* 4.9 5.2 - - + -
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Residues in contact with ALA 613 (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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609C GLU 3.0 14.7 + - - +
610C GLU 3.9 0.9 - - - +
612C ILE* 1.3 77.8 - - - +
614C ARG* 1.3 56.0 + - - +
616C ALA* 3.7 7.4 - - - +
617C GLN* 2.9 29.3 + - - +
641C LEU 3.6 23.3 - - - +
644C ALA* 4.8 5.8 - - + -
645C ASN* 4.1 4.4 - - - +
599D ASP* 4.9 2.4 - - - +
602D MET* 3.6 31.0 - - + -
603D ILE* 4.7 2.9 - - - +
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Residues in contact with ARG 614 (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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532C VAL* 4.4 30.7 - - + +
535C MET* 3.6 17.6 - - + +
536C GLU* 3.8 19.2 + - - +
610C GLU 2.9 15.4 + - - +
611C LEU* 3.3 17.0 - - + +
612C ILE 3.2 0.2 - - - -
613C ALA* 1.3 77.4 - - - +
615C ILE* 1.3 61.5 + - - +
617C GLN* 3.2 11.2 + - - +
618C LYS* 3.1 60.5 + - - +
520D ASP* 4.9 7.5 + - - -
521D MET* 5.0 10.4 - - - +
522D LYS* 5.6 4.2 - - - +
603D ILE* 4.2 24.1 - - + +
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Residues in contact with ILE 615 (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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528C LEU* 4.0 27.1 - - + +
531C SER* 4.2 13.5 - - - +
532C VAL* 3.7 29.6 - - + +
535C MET* 4.4 14.4 - - + -
611C LEU 2.9 18.4 + - - +
612C ILE* 4.0 7.9 - - + +
614C ARG* 1.3 75.1 - - - +
616C ALA* 1.3 55.1 + - - +
619C ALA* 2.6 52.6 + - + +
624C ILE* 4.7 15.0 - - + -
626C LEU* 5.0 19.5 - - + -
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Residues in contact with ALA 616 (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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461C HIS* 4.2 17.7 + - + -
612C ILE* 2.8 19.7 + - + +
613C ALA* 3.8 7.9 - - - +
615C ILE* 1.3 73.6 - - - +
617C GLN* 1.3 65.0 + - - +
619C ALA 4.5 0.7 + - - -
620C ARG* 5.5 0.9 + - - +
626C LEU* 5.6 2.6 - - + +
641C LEU 6.0 0.4 - - - +
642C ILE 5.8 0.2 - - - +
644C ALA* 6.0 0.2 - - + -
645C ASN* 3.3 35.5 - - + +
646C ILE* 4.2 24.5 - - + -
500D LYS* 5.8 0.2 - - - -
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Residues in contact with GLN 617 (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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613C ALA 2.9 12.5 + - - +
614C ARG* 3.3 11.0 - - - +
615C ILE 3.2 0.2 - - - -
616C ALA* 1.3 79.9 - - - +
618C LYS* 1.3 76.3 + - + +
619C ALA 3.5 0.7 + - - -
620C ARG* 4.8 4.0 + - - +
645C ASN* 3.7 8.4 + - - +
499D PRO* 2.7 43.3 + - - +
500D LYS* 4.4 16.5 - - + +
521D MET* 3.4 23.1 - - - +
599D ASP* 3.5 24.9 - - - +
603D ILE* 3.4 27.9 - - - +
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Residues in contact with LYS 618 (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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535C MET* 3.2 25.8 - - + +
536C GLU* 4.7 7.8 + - - +
539C TYR* 2.4 56.0 + - + -
614C ARG* 3.1 29.9 + - - +
617C GLN* 1.3 105.8 - - + +
619C ALA* 1.3 56.1 + - - +
620C ARG 3.6 0.9 - - - -
622C ALA* 4.0 0.2 - - - +
499D PRO 4.2 4.5 - - - +
500D LYS* 5.6 3.6 - - - +
519D THR* 3.8 26.8 - - + +
520D ASP* 3.5 36.7 + - - +
521D MET* 4.6 2.2 - - - +
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Residues in contact with ALA 619 (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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461C HIS* 3.4 18.8 - - + +
535C MET* 4.0 5.4 - - - -
615C ILE* 2.6 33.1 + - + +
616C ALA 4.5 0.4 + - - -
617C GLN 3.5 2.8 - - - -
618C LYS* 1.3 78.8 - - - +
620C ARG* 1.3 66.1 + - - +
621C ALA 3.4 0.7 - - - -
622C ALA* 3.2 12.9 + - - +
623C GLY 3.4 4.2 + - - -
624C ILE* 2.9 33.5 - - + +
625C HIS* 5.1 0.2 + - - -
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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