Contacts of the strand formed by residues 498 - 505 (chain B) in PDB entry 3N8E
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 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487B CYS* 3.2 4.2 - - - -
488B GLN* 2.7 61.5 + - + +
497B ASN* 1.3 68.4 - - - +
499B LEU* 1.3 68.7 + - - +
500B LEU* 3.3 14.5 + - + +
551B GLY 2.9 28.1 + - - -
552B GLY* 3.6 14.1 - - - -
553B LEU* 4.1 25.2 - - + +
561B MET* 4.7 22.0 - - + +
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Residues in contact with LEU 499 (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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485B LYS* 3.8 28.3 - - + -
486B VAL 3.5 8.5 - - - +
487B CYS* 4.1 10.5 - - - +
497B ASN 3.5 4.3 + - - +
498B LYS* 1.3 74.0 - - - +
500B LEU* 1.3 61.7 + - - +
501B GLY 3.4 27.1 - - - +
502B GLN* 3.6 24.0 - - + +
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Residues in contact with LEU 500 (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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445B LEU* 3.8 11.0 - - + -
486B VAL* 2.7 17.4 + - + +
487B CYS 4.7 0.4 - - - -
488B GLN* 3.6 49.8 - - + +
498B LYS* 3.8 32.5 - - + +
499B LEU* 1.3 72.8 - - - +
501B GLY* 1.3 53.7 + - - +
547B ILE* 3.3 48.1 - - + +
548B GLN 4.1 7.6 - - - +
549B SER* 4.1 8.1 - - - -
551B GLY 4.6 0.7 - - - +
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Residues in contact with GLY 501 (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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484B ILE 4.4 0.4 - - - -
486B VAL* 2.7 36.6 + - - +
499B LEU* 3.4 11.3 - - - +
500B LEU* 1.3 78.5 - - - +
502B GLN* 1.3 58.1 + - - -
545B ILE* 3.9 23.3 - - - -
547B ILE* 4.2 0.7 - - - -
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Residues in contact with GLN 502 (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 GLU* 2.7 32.5 + - - +
484B ILE 3.2 4.5 - - - +
485B LYS* 3.6 35.9 - - + +
499B LEU* 3.6 19.4 - - + +
501B GLY* 1.3 75.3 - - - +
503B PHE* 1.3 65.5 + - - +
545B ILE* 4.4 4.4 - - - +
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Residues in contact with PHE 503 (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 GLU* 3.6 3.5 - - - -
484B ILE* 2.7 81.2 + - + +
486B VAL* 4.4 1.1 - - + -
502B GLN* 1.3 76.2 - - - +
504B THR* 1.3 61.8 + - - +
505B LEU* 5.6 0.2 - - + -
532B VAL* 3.8 28.3 - - + -
534B ALA* 3.9 11.4 - - + -
543B GLN* 3.5 46.7 - - + -
544B GLN* 4.2 0.7 - - - -
545B ILE* 3.5 48.5 - - + -
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Residues in contact with THR 504 (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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481B GLN* 3.7 21.8 - - + +
482B VAL 3.5 11.7 - - - +
483B GLU* 3.6 22.9 + - + +
503B PHE* 1.3 73.1 - - - +
505B LEU* 1.4 60.9 + - - +
506B ILE* 3.7 29.4 + - + +
543B GLN* 3.7 19.3 - - - +
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Residues in contact with LEU 505 (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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481B GLN* 3.2 4.9 - - - -
482B VAL* 2.9 43.1 + - + +
484B ILE* 5.2 1.8 - - + +
503B PHE* 4.3 1.4 + - + -
504B THR* 1.4 69.4 - - - +
506B ILE* 1.4 66.7 - - - +
508B ILE* 4.1 8.2 - - + +
518B ILE* 3.7 40.8 - - + -
534B ALA* 3.3 35.4 - - + +
536B ASP* 4.3 7.2 - - + +
541B ARG* 3.9 22.2 - - + +
542B GLU 4.1 2.0 - - - -
543B GLN* 3.8 19.7 - - + +
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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