Contacts of the helix formed by residues 624 - 635 (chain L) in PDB entry 3OJ3
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 CYS 624 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ARG* 3.7 24.5 - - - -
58D ASP* 3.3 14.6 - - - +
607L CYS* 3.1 12.9 - - + -
612L CYS* 4.2 1.6 - - - -
614L TYR* 3.8 12.3 - - + -
615L PHE 3.7 13.9 - - - +
616L GLY* 3.8 0.6 - - - -
617L THR* 5.1 0.7 - - - -
623L PHE* 1.3 79.1 - - - +
625L THR* 1.3 62.2 + - - +
626L LEU 3.8 1.3 - - - -
627L CYS* 3.5 15.0 + - - -
628L PHE* 2.9 25.3 + - - +
904L ZN 2.6 32.1 - - - -
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Residues in contact with THR 625 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D SER* 6.1 0.9 - - - -
53D GLY 4.4 1.4 + - - -
54D ARG* 4.4 1.7 - - - -
55D THR* 3.0 43.9 + - + +
57D SER* 4.3 4.9 - - - +
58D ASP* 2.6 24.9 + - - +
47G GLY* 6.5 1.6 - - - -
617L THR* 5.6 0.2 - - + -
620L ASN* 4.2 18.4 - - - +
624L CYS* 1.3 72.5 - - - +
626L LEU* 1.3 71.8 + - - +
628L PHE* 3.4 4.8 + - - +
629L ILE* 3.1 31.9 + - - +
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Residues in contact with LEU 626 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLY 3.9 21.5 - - - +
54D ARG* 3.6 36.8 - - + +
8G LEU* 4.6 13.9 - - + +
44G ILE* 4.2 30.4 - - + +
47G GLY* 4.9 4.0 - - - +
68G HIS* 3.6 36.6 - - + +
70G VAL* 5.3 4.2 - - + +
624L CYS* 3.4 1.2 - - - -
625L THR* 1.3 81.8 + - - +
627L CYS* 1.3 66.3 + - - +
628L PHE 3.1 1.3 - - - -
629L ILE* 3.2 15.2 + - + +
630L GLU* 2.9 22.2 + - - +
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Residues in contact with CYS 627 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ARG* 5.9 0.2 - - - -
8G LEU* 5.2 5.2 - - - -
607L CYS* 3.7 12.6 - - - -
609L LYS* 3.3 36.8 - - + -
612L CYS* 3.9 4.3 - - - -
623L PHE* 3.9 13.9 - - + -
624L CYS* 3.5 4.8 + - - +
626L LEU* 1.3 77.5 - - - +
628L PHE* 1.3 58.0 + - - +
630L GLU* 3.2 10.3 + - - +
631L TYR* 2.8 29.5 + - - +
904L ZN 2.4 35.4 - - - -
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Residues in contact with PHE 628 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619L GLU 4.6 4.3 - - - -
620L ASN* 3.4 53.8 - - + -
621L LYS* 4.7 13.2 - - + -
623L PHE* 3.5 18.6 - + + +
624L CYS 2.9 19.3 + - - +
625L THR 3.5 6.3 - - - +
626L LEU 3.1 0.2 - - - -
627L CYS* 1.3 78.7 - - - +
629L ILE* 1.3 63.9 + - + +
631L TYR* 3.5 11.5 - + - +
632L ARG* 2.9 55.8 + - + +
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Residues in contact with ILE 629 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ILE* 3.7 27.1 - - + -
47G GLY* 3.2 38.8 - - - +
49G GLN* 5.3 3.8 - - + +
625L THR* 3.1 17.4 + - - +
626L LEU* 3.2 18.4 + - + +
628L PHE* 1.3 79.6 - - + +
630L GLU* 1.3 60.3 + - - +
632L ARG* 3.3 35.6 + - - +
633L GLU* 2.8 44.2 + - + +
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Residues in contact with GLU 630 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 3.9 12.5 - - + +
70G VAL* 4.0 29.8 - - + +
71G LEU 5.7 1.6 - - - +
609L LYS* 2.8 43.3 + - - +
626L LEU 2.9 12.8 + - - +
627L CYS* 3.3 10.8 - - - +
629L ILE* 1.3 78.4 - - - +
631L TYR* 1.3 63.4 + - - +
633L GLU* 3.3 6.5 + - - +
634L ASN* 3.3 32.4 + - - +
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Residues in contact with TYR 631 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608L ARG* 4.4 11.4 + - - -
621L LYS* 3.3 45.3 + - + +
623L PHE* 3.6 34.1 - + + -
627L CYS 2.8 16.3 + - - +
628L PHE* 3.5 17.7 - + - +
630L GLU* 1.3 73.0 - - - +
632L ARG* 1.3 65.8 + - + +
634L ASN* 3.0 5.3 + - - +
635L LYS* 2.9 57.0 + - + +
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Residues in contact with ARG 632 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G GLY 5.3 3.4 + - - -
49G GLN* 5.3 7.1 - - - +
628L PHE* 2.9 44.2 + - + +
629L ILE* 3.5 30.8 - - - +
631L TYR* 1.3 88.2 - - + +
633L GLU* 1.3 86.5 + - - +
634L ASN 3.3 0.9 + - - -
635L LYS* 3.4 37.8 + - - +
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Residues in contact with GLU 633 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ARG* 5.0 13.7 + - + +
44G ILE* 5.8 1.1 - - + -
49G GLN* 2.9 35.2 + - - +
70G VAL* 5.7 5.2 - - + -
629L ILE* 2.8 35.1 + - + +
630L GLU* 3.8 7.2 - - - +
631L TYR 3.2 0.2 - - - -
632L ARG* 1.3 102.3 + - - +
634L ASN* 1.3 66.9 + - - +
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Residues in contact with ASN 634 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G VAL* 5.6 1.4 - - - +
71G LEU 4.6 15.5 + - - +
630L GLU* 3.3 25.8 + - - +
631L TYR* 3.0 4.5 + - - +
633L GLU* 1.3 90.0 - - - +
635L LYS* 1.3 73.2 + - - +
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Residues in contact with LYS 635 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621L LYS* 5.6 3.8 - - - +
631L TYR* 2.9 48.4 + - + +
632L ARG* 3.4 35.9 + - - +
634L ASN* 1.3 82.7 - - - +
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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