Contacts of the helix formed by residues 621 - 635 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A SER 5.9 0.7 - - - -
471A ILE* 3.7 5.8 - - - -
619A VAL* 3.8 2.8 - - - +
620A LYS* 1.3 84.5 - - + +
622A GLN* 1.3 66.9 + - - +
623A GLU* 3.8 29.6 - - + +
624A GLU* 2.7 39.1 + - - +
625A LEU 3.6 3.1 + - - -
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Residues in contact with GLN 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A GLU* 3.5 27.0 + - - +
466A THR 3.5 11.6 + - - +
467A PRO* 5.0 3.3 - - - +
468A GLY* 3.7 7.0 - - - +
469A SER* 2.6 50.0 + - - +
470A LYS 4.5 0.2 + - - -
471A ILE* 3.5 24.2 - - + +
479A LYS* 5.2 3.1 + - - -
621A LYS* 1.3 71.8 - - - +
623A GLU* 1.3 65.7 + - - +
624A GLU 3.0 5.4 + - - -
625A LEU* 3.3 17.5 + - + +
626A ASP* 4.7 5.7 + - - +
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Residues in contact with GLU 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A GLY* 5.2 11.6 + - - -
621A LYS* 3.8 30.9 - - + +
622A GLN* 1.3 86.6 + - - +
624A GLU* 1.3 58.6 + - + +
626A ASP 5.6 0.4 - - - -
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Residues in contact with GLU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A ARG 4.1 9.7 - - - +
619A VAL* 3.7 12.6 - - + -
620A LYS* 2.9 19.1 + - - +
621A LYS* 2.7 49.5 + - + +
623A GLU* 1.3 79.7 - - + +
625A LEU* 1.3 66.0 + - - +
626A ASP 3.5 1.8 - - - -
627A ALA* 3.6 9.2 + - - +
628A LYS* 3.2 35.7 + - + +
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Residues in contact with LEU 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ILE* 4.1 24.0 - - + -
475A THR* 4.6 4.3 - - + -
476A VAL* 4.4 13.7 - - + -
479A LYS* 3.9 29.6 - - + +
619A VAL* 4.0 24.9 - - + -
621A LYS 3.6 2.8 + - - -
622A GLN* 3.3 16.6 + - + +
624A GLU* 1.3 77.0 - - - +
626A ASP* 1.3 65.2 + - - +
628A LYS* 3.2 3.3 + - - +
629A LEU* 2.9 48.7 + - + +
643A VAL* 4.3 22.9 - - + -
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Residues in contact with ASP 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A LYS* 3.4 39.6 + - - +
483A VAL* 5.4 1.8 - - - +
622A GLN 4.7 4.2 + - - +
623A GLU 5.6 0.2 - - - -
624A GLU 3.5 0.6 - - - -
625A LEU* 1.3 78.1 - - - +
627A ALA* 1.3 61.7 + - - +
629A LEU* 3.4 8.6 + - - +
630A LYS* 3.2 42.0 + - - +
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Residues in contact with ALA 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A GLU* 3.6 11.0 + - + +
625A LEU 3.3 0.6 - - - -
626A ASP* 1.3 78.7 - - - +
628A LYS* 1.3 60.2 + - + +
630A LYS* 3.3 11.2 + - - +
631A GLU* 3.0 28.6 + - - +
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Residues in contact with LYS 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A LEU* 4.2 23.2 - - + +
618A ARG 3.6 17.6 - - - +
619A VAL* 3.3 32.3 - - + -
624A GLU* 3.2 28.6 + - + +
625A LEU 3.2 2.1 + - - +
627A ALA* 1.3 76.4 - - + +
629A LEU* 1.3 56.7 + - - +
631A GLU* 3.7 22.5 + - - +
632A PHE* 2.7 37.4 + - - +
641A LEU* 4.2 8.0 - - + +
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Residues in contact with LEU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A VAL* 4.2 12.6 - - + +
479A LYS* 3.6 34.3 - - + -
480A LEU* 3.9 34.8 - - + +
483A VAL* 4.3 14.6 - - + -
573A LEU* 5.3 0.9 - - + -
625A LEU* 2.9 44.0 + - + +
626A ASP* 3.7 8.1 - - - +
628A LYS* 1.3 75.6 - - - +
630A LYS* 1.3 62.4 + - - +
632A PHE* 3.3 5.6 - - + +
633A VAL* 3.1 28.9 + - - +
641A LEU* 4.0 19.1 - - + -
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Residues in contact with LYS 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A VAL* 4.2 29.2 - - + +
486A ASP* 5.7 2.4 + - - -
626A ASP* 3.2 30.1 + - - +
627A ALA* 3.6 10.1 - - - +
628A LYS 3.2 0.2 - - - -
629A LEU* 1.3 75.4 - - - +
631A GLU* 1.3 57.9 + - - +
633A VAL* 3.5 1.2 + - - +
634A SER* 2.6 38.8 + - - +
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Residues in contact with GLU 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LYS* 2.9 35.2 + - - +
617A LEU* 3.7 21.1 - - + +
627A ALA 3.0 16.3 + - - +
628A LYS* 3.8 20.9 + - - +
630A LYS* 1.3 73.6 - - - +
632A PHE* 1.3 56.8 + - - +
634A SER* 3.8 4.4 - - - -
635A THR* 2.8 41.9 + - - +
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Residues in contact with PHE 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 4.3 20.9 - - + -
545A ILE* 4.6 3.4 - - + -
571A LYS* 3.2 45.1 - - + +
572A ILE 3.6 24.9 - - - -
573A LEU* 3.8 16.6 - - + -
617A LEU* 3.9 9.8 - - + +
628A LYS 2.7 22.9 + - - +
629A LEU* 3.3 5.6 - - + +
631A GLU* 1.3 74.8 - - - +
633A VAL* 1.3 73.4 + - + +
635A THR* 3.5 6.7 + - - -
639A VAL* 3.5 42.6 - - + +
641A LEU* 3.4 33.2 - - + -
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Residues in contact with VAL 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 3.6 31.4 - - + -
483A VAL* 3.9 17.5 - - + +
484A ALA* 4.7 2.5 - - - +
487A THR* 3.6 30.7 - - + -
489A ARG* 5.0 3.9 + - - -
543A LEU* 3.8 25.1 - - + +
545A ILE* 4.7 5.4 - - + -
571A LYS* 4.0 18.9 - - + +
629A LEU 3.1 11.0 + - - +
630A LYS 4.1 1.6 - - - +
632A PHE* 1.3 84.1 - - + +
634A SER* 1.3 62.6 + - - +
635A THR 3.7 0.5 + - - +
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Residues in contact with SER 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A THR* 6.1 0.3 - - - +
630A LYS* 2.6 26.4 + - - +
631A GLU* 3.8 4.7 - - - -
633A VAL* 1.3 79.4 - - - +
635A THR* 1.3 65.4 + - - +
636A LYS* 3.4 3.6 + - - +
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Residues in contact with THR 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A LYS* 2.6 31.7 + - - -
615A LYS* 2.9 46.6 + - + +
631A GLU* 2.8 23.7 + - - +
632A PHE* 3.7 9.6 + - - -
633A VAL 3.4 1.3 - - - +
634A SER* 1.3 78.3 - - - +
636A LYS* 1.3 71.2 + - - +
637A GLY 4.2 2.7 - - - +
638A PRO 4.9 0.4 - - - +
639A VAL* 4.1 18.0 - - + +
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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