Contacts of the helix formed by residues 605 - 618 (chain B) in PDB entry 6T8B
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 GLY 605 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600B MET 3.9 1.6 + - - -
601B MET* 3.4 38.2 + - - +
602B MET 5.7 0.2 - - - -
603B ILE 3.6 0.6 - - - -
604B VAL* 1.3 76.6 - - - +
606B LYS* 1.3 60.9 + - - -
607B LYS 3.2 6.5 + - - -
608B VAL* 3.5 9.7 + - - +
609B GLU 3.7 6.1 + - - -
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Residues in contact with LYS 606 (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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604B VAL 3.9 0.8 + - - -
605B GLY* 1.3 67.5 - - - -
607B LYS* 1.3 64.4 + - - +
608B VAL 3.2 2.1 + - - -
609B GLU* 3.8 31.1 + - + +
610B GLU* 3.8 31.4 - - + +
1H A 4.8 19.2 + - - -
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Residues in contact with LYS 607 (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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522B LYS* 5.5 10.4 - - + +
525B ALA* 4.8 14.8 - - + +
529B ARG* 5.4 10.7 + - - +
604B VAL* 3.7 33.1 + - + +
605B GLY 3.2 0.6 - - - -
606B LYS* 1.3 79.1 - - - +
608B VAL* 1.3 59.5 + - - +
610B GLU* 4.4 8.8 + - - +
611B LEU* 4.1 18.4 - - - +
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Residues in contact with VAL 608 (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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524B ALA* 4.5 5.2 - - + -
525B ALA* 4.2 22.7 - - - +
528B LEU* 3.5 17.9 - - + -
600B MET* 3.8 19.5 - - + -
601B MET* 4.6 7.4 - - - -
604B VAL* 3.5 29.2 - - + -
605B GLY 3.5 7.4 + - - +
606B LYS 3.2 0.2 - - - -
607B LYS* 1.3 76.7 - - - +
609B GLU* 1.3 67.9 + - - +
610B GLU 3.1 2.5 - - - -
611B LEU* 2.8 18.1 + - - +
612B ILE* 2.9 32.1 + - + -
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Residues in contact with GLU 609 (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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601B MET* 3.6 30.1 - - + +
605B GLY 3.7 3.6 + - - -
606B LYS* 4.0 32.8 - - + +
607B LYS 3.7 0.2 - - - -
608B VAL* 1.3 77.5 - - - +
610B GLU* 1.3 63.3 + - + +
612B ILE* 3.8 6.0 - - - +
613B ALA* 2.9 26.1 + - + +
639B THR* 2.2 39.8 + - - +
642B ILE* 3.9 10.7 - - + +
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Residues in contact with GLU 610 (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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606B LYS* 3.8 29.7 + - + +
607B LYS* 4.5 7.2 - - - +
608B VAL 3.1 0.6 - - - -
609B GLU* 1.3 79.4 - - + +
611B LEU* 1.3 64.4 + - + +
613B ALA* 3.3 5.7 + - - +
614B ARG* 2.9 28.7 + - - +
602C MET* 5.8 3.2 - - + +
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Residues in contact with LEU 611 (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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525B ALA* 3.6 13.7 - - + +
528B LEU* 3.6 21.3 - - + +
529B ARG* 3.4 40.6 - - + +
532B VAL* 3.8 24.2 - - + -
607B LYS 4.1 17.9 - - - +
608B VAL* 2.8 13.0 + - - +
610B GLU* 1.3 79.0 - - + +
612B ILE* 1.3 56.6 + - - +
614B ARG* 3.3 5.7 + - + +
615B ILE* 2.9 36.6 + - - +
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Residues in contact with ILE 612 (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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528B LEU* 3.6 29.6 - - + -
594B VAL* 4.6 7.4 - - + -
597B PHE* 3.8 22.7 - - + -
600B MET* 5.5 0.4 - - - -
608B VAL* 2.9 34.0 + - + +
609B GLU 3.9 4.0 - - - +
611B LEU* 1.3 74.4 - - - +
613B ALA* 1.3 60.1 + - - +
615B ILE* 3.4 6.0 + - + +
616B ALA* 2.9 27.9 + - - +
626B LEU* 4.2 28.6 - - + +
628B LEU* 5.2 2.9 - - + -
642B ILE* 3.7 32.1 - - + -
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Residues in contact with ALA 613 (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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609B GLU* 2.9 20.9 + - + +
610B GLU* 3.7 5.2 - - - +
612B ILE* 1.3 77.1 - - - +
614B ARG* 1.3 56.6 + - - +
616B ALA* 3.4 3.8 + - - +
617B GLN* 2.9 47.2 + - - +
641B LEU* 4.9 12.3 - - + -
642B ILE* 3.7 21.5 - - + +
602C MET* 6.4 2.0 - - + -
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Residues in contact with ARG 614 (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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532B VAL* 4.2 14.5 - - + +
535B MET* 3.7 15.5 - - + -
536B GLU* 3.5 11.7 + - - -
610B GLU 2.9 17.2 + - - +
611B LEU* 3.5 10.1 - - + +
612B ILE 3.2 0.4 - - - -
613B ALA* 1.3 74.1 - - - +
615B ILE* 1.3 65.2 + - - +
617B GLN* 3.1 8.4 + - - +
618B LYS* 3.0 61.2 + - - +
599C ASP* 2.6 39.2 + - - +
602C MET* 4.3 22.8 - - + +
603C ILE* 5.8 6.5 - - - +
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Residues in contact with ILE 615 (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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461B HIS* 3.9 4.7 - - - -
528B LEU* 3.9 21.8 - - + +
531B SER* 3.8 28.9 - - - -
532B VAL* 4.0 16.6 - - + +
535B MET* 4.4 6.3 - - - -
592B VAL* 5.2 4.9 - - + -
611B LEU 2.9 23.4 + - - +
612B ILE* 3.9 7.6 - - + +
614B ARG* 1.3 75.6 - - - +
616B ALA* 1.3 54.8 + - - +
618B LYS 2.6 25.3 - - - +
619B ALA* 3.5 19.8 - - + +
624B ILE* 4.2 17.7 - - + +
626B LEU* 4.4 21.8 - - + -
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Residues in contact with ALA 616 (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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461B HIS* 4.0 11.9 + - - -
612B ILE 2.9 17.7 + - - +
613B ALA* 3.6 7.4 - - - +
615B ILE* 1.3 74.0 - - - +
617B GLN* 1.3 57.5 + - - +
618B LYS 2.9 15.5 + - - +
626B LEU* 4.9 6.5 - - + +
642B ILE* 4.4 17.5 - - + +
645B ASN* 3.8 26.0 - - + +
646B ILE* 5.2 2.9 - - + -
468C THR* 3.3 20.1 - - - +
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Residues in contact with GLN 617 (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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613B ALA* 2.9 29.4 + - - +
614B ARG* 3.1 9.9 + - - +
616B ALA* 1.3 70.9 - - - +
618B LYS* 1.3 54.4 + - + +
641B LEU* 3.7 31.8 - - - +
645B ASN* 3.5 15.5 - - - +
468C THR* 4.6 0.7 - - - -
500C LYS* 2.4 37.0 + - - +
598C ALA* 4.6 14.6 - - + +
599C ASP* 3.7 11.0 - - - +
602C MET* 3.4 31.1 - - - +
631C GLN* 2.9 23.8 + - + +
637C VAL* 5.6 2.0 - - - +
801C AGS 5.0 0.3 - - - -
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Residues in contact with LYS 618 (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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461B HIS* 4.1 3.8 + - - -
535B MET* 3.4 20.6 - - + -
536B GLU* 2.5 39.5 + - - -
539B TYR* 4.4 28.1 - - + -
614B ARG* 3.0 42.2 + - - +
615B ILE 2.6 19.0 - - - +
616B ALA 3.3 5.5 - - - +
617B GLN* 1.3 86.1 - - + +
619B ALA* 1.3 62.4 + - - +
620B ARG* 2.8 14.1 + - - +
468C THR* 5.3 0.2 - - - +
500C LYS* 3.5 33.7 - - + +
599C ASP* 4.3 1.1 - - - +
801C AGS 5.3 5.2 - - - -
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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