Contacts of the helix formed by residues 548 - 556 (chain B) in PDB entry 3NYN
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 548 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533B VAL* 5.0 3.8 - - - +
534B PRO* 3.5 46.9 + - - +
535B PRO 4.3 3.6 - - - -
536B ASP* 3.7 35.6 + - - +
544B PRO* 4.5 16.3 - - + +
546B PRO 3.7 1.9 + - - +
547B PRO* 1.3 71.7 - - - +
549B LYS* 1.3 66.9 + - - +
550B GLY 3.2 3.4 - - - +
551B LEU* 3.1 21.9 + - + +
552B LEU* 3.6 7.0 + - - +
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Residues in contact with LYS 549 (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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322A HIS* 5.0 17.0 + - - -
466A LYS* 5.7 4.0 - - - +
547B PRO 4.2 7.9 - - - +
548B LYS* 1.3 72.1 - - - +
550B GLY* 1.3 60.8 + - - +
551B LEU 3.2 0.2 - - - -
552B LEU* 3.5 12.3 + - + +
553B GLN* 3.3 43.9 + - - +
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Residues in contact with GLY 550 (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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536B ASP* 5.5 0.7 - - - -
548B LYS* 3.2 3.4 - - - +
549B LYS* 1.3 76.4 - - - +
551B LEU* 1.3 65.0 + - - +
553B GLN* 3.9 6.7 + - - +
554B ARG* 3.5 30.6 + - - +
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Residues in contact with LEU 551 (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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89A GLU* 4.2 13.9 - - + +
92A VAL* 6.0 0.2 - - + -
460A MET* 4.8 9.4 - - + -
536B ASP* 4.2 39.7 + - + +
537B LEU* 4.3 19.3 - - + -
543B PRO* 5.1 5.4 - - + -
547B PRO* 5.9 1.3 - - + -
548B LYS* 3.1 16.1 + - + +
550B GLY* 1.3 75.4 - - - +
552B LEU* 1.3 64.5 + - + +
554B ARG* 3.2 29.5 + - - +
555B LEU* 2.8 66.2 + - + +
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Residues in contact with LEU 552 (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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459A GLY 5.2 4.3 - - - +
460A MET* 4.1 40.2 - - + +
547B PRO* 4.4 25.8 - - + +
548B LYS 3.9 11.2 - - - +
549B LYS* 3.5 15.4 + - + +
551B LEU* 1.3 82.7 - - + +
553B GLN* 1.3 59.3 + - + +
555B LEU* 3.1 3.6 + - + -
556B PHE* 3.0 48.5 + - + +
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Residues in contact with GLN 553 (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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549B LYS* 3.3 33.3 + - - +
550B GLY* 4.3 6.1 - - - +
551B LEU 3.2 0.6 - - - -
552B LEU* 1.3 81.8 - - + +
554B ARG* 1.3 60.3 + - - +
556B PHE* 5.2 1.1 - - - -
557B SER* 3.1 35.5 + - - -
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Residues in contact with ARG 554 (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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89A GLU* 2.9 39.8 + - - +
97A LYS* 4.1 14.6 + - - +
536B ASP* 2.8 29.9 + - - -
550B GLY* 3.5 19.4 + - - +
551B LEU* 3.2 17.6 + - - +
553B GLN* 1.3 75.5 - - - +
555B LEU* 1.3 68.5 + - + +
556B PHE 3.3 0.4 - - - -
557B SER* 4.6 2.0 - - - +
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Residues in contact with LEU 555 (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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89A GLU* 4.4 12.8 - - + +
92A VAL* 4.2 17.3 - - + +
93A THR* 3.9 39.7 - - + +
94A PRO* 3.7 16.7 - - + +
97A LYS* 4.5 9.2 - - - +
460A MET* 4.2 22.7 - - + -
551B LEU* 2.8 48.9 + - + +
552B LEU* 3.6 5.6 - - - +
554B ARG* 1.3 82.5 - - + +
556B PHE* 1.3 80.7 + - + +
557B SER 3.9 0.7 - - - -
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Residues in contact with PHE 556 (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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92A VAL 5.4 1.8 - - - -
94A PRO* 4.1 20.9 - - + -
97A LYS* 5.0 2.5 - - - +
455A ARG* 4.1 33.4 - - + -
460A MET* 4.1 38.6 - - + -
552B LEU* 3.0 34.3 + - + +
553B GLN* 3.7 2.2 - - - -
554B ARG 3.3 0.2 - - - -
555B LEU* 1.3 107.0 - - + +
557B SER* 1.3 62.4 + - - +
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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