Contacts of the helix formed by residues 621 - 635 (chain B) in PDB entry 1JSC
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 621 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B ILE* 3.8 4.7 - - - -
619B VAL* 3.7 2.6 - - - +
620B LYS* 1.3 86.6 - - + +
622B GLN* 1.3 66.1 + - - +
623B GLU* 3.0 30.1 - - + +
624B GLU* 2.7 39.0 + - - +
625B LEU 3.6 2.8 + - - -
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Residues in contact with GLN 622 (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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465B GLU* 3.1 32.6 - - - +
466B THR 2.8 30.9 + - - +
467B PRO* 4.0 5.3 - - + +
468B GLY 3.3 6.9 - - - +
469B SER* 2.6 36.8 + - - +
470B LYS 3.8 3.1 + - - -
471B ILE* 3.7 26.2 - - + +
621B LYS* 1.3 72.5 - - - +
623B GLU* 1.3 65.3 + - - +
624B GLU 3.0 5.6 + - - -
625B LEU* 3.3 19.5 + - + +
626B ASP* 4.7 5.5 + - - +
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Residues in contact with GLU 623 (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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467B PRO* 5.8 0.5 - - - +
468B GLY* 4.8 13.0 + - - -
621B LYS* 3.8 30.9 - - + +
622B GLN* 1.3 87.8 + - - +
624B GLU* 1.3 58.4 + - + +
626B ASP 5.6 0.4 - - - -
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Residues in contact with GLU 624 (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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618B ARG 4.1 9.2 - - - +
619B VAL* 3.7 12.6 - - + -
620B LYS* 2.9 20.1 + - - +
621B LYS* 2.7 48.5 + - + +
623B GLU* 1.3 79.2 - - + +
625B LEU* 1.3 67.0 + - - +
626B ASP 3.5 1.8 - - - -
627B ALA* 3.7 9.1 + - + +
628B LYS* 3.2 35.8 + - + +
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Residues in contact with LEU 625 (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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465B GLU* 5.0 3.1 - - - +
471B ILE* 4.2 13.2 - - + -
475B THR* 4.5 5.2 - - + -
476B VAL* 4.2 32.5 - - + -
479B LYS* 3.7 27.6 - - + -
619B VAL* 4.0 24.5 - - + -
621B LYS 3.6 2.8 + - - -
622B GLN* 3.3 18.0 + - + +
624B GLU* 1.3 77.9 - - - +
626B ASP* 1.3 65.5 + - - +
628B LYS* 3.2 3.3 + - - +
629B LEU* 2.9 50.1 + - + +
643B VAL* 4.4 11.4 - - + -
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Residues in contact with ASP 626 (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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479B LYS* 3.0 43.7 + - - +
483B VAL* 5.4 0.3 - - - +
622B GLN 4.7 5.4 + - - +
623B GLU 5.6 0.4 - - - -
624B GLU 3.5 0.2 - - - -
625B LEU* 1.3 76.1 - - - +
627B ALA* 1.3 62.1 + - - +
629B LEU* 3.4 6.9 + - - +
630B LYS* 3.2 43.5 + - - +
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Residues in contact with ALA 627 (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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624B GLU* 3.7 11.0 + - - +
625B LEU 3.3 0.6 - - - -
626B ASP* 1.3 78.8 - - - +
628B LYS* 1.3 60.2 + - + +
630B LYS* 3.3 11.2 + - - +
631B GLU* 3.0 29.1 + - - +
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Residues in contact with LYS 628 (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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617B LEU* 4.2 24.3 - - + +
618B ARG 3.6 18.1 - - - +
619B VAL* 3.4 30.5 - - + -
624B GLU* 3.2 28.6 + - + +
625B LEU 3.2 1.9 + - - +
627B ALA* 1.3 75.6 - - + +
629B LEU* 1.3 59.9 + - - +
631B GLU* 3.8 22.4 + - - +
632B PHE* 2.8 33.0 + - - +
641B LEU* 4.2 8.4 - - + +
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Residues in contact with LEU 629 (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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476B VAL* 4.1 13.5 - - + +
479B LYS* 3.5 35.0 - - + +
480B LEU* 3.9 35.0 - - + +
483B VAL* 4.4 13.2 - - + -
573B LEU* 5.2 0.9 - - + -
625B LEU* 2.9 41.9 + - + +
626B ASP* 3.7 7.4 - - - +
628B LYS* 1.3 75.4 - - - +
630B LYS* 1.3 63.0 + - - +
632B PHE* 3.3 6.6 - - + +
633B VAL* 3.0 28.9 + - - +
641B LEU* 4.0 18.6 - - + -
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Residues in contact with LYS 630 (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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483B VAL* 4.2 30.6 - - + +
486B ASP* 5.8 1.8 + - - -
626B ASP* 3.2 29.5 + - - +
627B ALA* 3.6 9.0 - - - +
629B LEU* 1.3 75.1 - - - +
631B GLU* 1.3 61.2 + - - +
633B VAL* 3.5 1.4 + - - +
634B SER* 2.5 35.5 + - - +
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Residues in contact with GLU 631 (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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615B LYS* 2.9 35.8 + - - +
617B LEU* 3.7 22.1 - - + +
627B ALA 3.0 16.7 + - - +
628B LYS* 3.8 19.8 + - - +
630B LYS* 1.3 77.5 - - - +
632B PHE* 1.3 52.4 + - - +
634B SER* 3.6 4.9 - - - -
635B THR* 2.8 42.4 + - - +
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Residues in contact with PHE 632 (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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480B LEU* 4.3 20.0 - - + -
545B ILE* 4.6 3.4 - - + -
571B LYS* 3.3 40.6 - - + +
572B ILE 3.5 24.9 - - - -
573B LEU* 3.8 16.6 - - + -
617B LEU* 3.9 10.1 - - + +
628B LYS 2.8 19.6 + - - +
629B LEU* 3.3 5.2 - - + +
631B GLU* 1.3 79.2 - - - +
633B VAL* 1.3 74.2 + - + +
635B THR* 3.5 5.1 + - - -
639B VAL* 3.5 48.7 - - + +
641B LEU* 3.4 33.0 - - + -
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Residues in contact with VAL 633 (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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480B LEU* 3.6 31.2 - - + -
483B VAL* 3.9 17.5 - - + +
484B ALA* 4.7 2.2 - - - +
487B THR* 3.7 29.6 - - + -
489B ARG* 5.1 3.8 + - - -
543B LEU* 3.8 21.3 - - + +
545B ILE* 4.7 10.5 - - + -
571B LYS* 4.0 18.8 - - + +
629B LEU 3.0 12.0 + - - +
630B LYS 4.1 1.3 - - - +
632B PHE* 1.3 84.6 - - + +
634B SER* 1.3 61.2 + - - +
635B THR 4.3 0.5 - - - +
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Residues in contact with SER 634 (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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630B LYS* 2.5 26.2 + - - +
631B GLU* 3.8 5.2 - - - -
633B VAL* 1.3 78.4 - - - +
635B THR* 1.3 66.1 + - - +
636B LYS* 3.4 3.8 + - - +
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Residues in contact with THR 635 (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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571B LYS* 2.6 31.2 + - - -
615B LYS* 2.9 47.6 + - + +
617B LEU* 4.8 0.2 - - - +
631B GLU* 2.8 23.5 + - - +
632B PHE* 3.8 9.1 + - - -
633B VAL 3.4 1.7 - - - +
634B SER* 1.3 78.7 - - - +
636B LYS* 1.3 72.2 + - - +
637B GLY 4.2 2.0 - - - +
638B PRO 4.8 0.7 - - - +
639B VAL* 4.1 18.5 - - + +
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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
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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