Contacts of the helix formed by residues 616 - 622 (chain B) in PDB entry 3U1K
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 616 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612B VAL* 4.0 7.6 - - + -
613B PRO* 2.6 18.3 + - + +
615B SER* 1.3 89.3 + - - +
617B ARG* 1.3 56.5 + - - -
618B ALA 3.3 2.9 - - - -
619B LYS* 3.4 21.7 + - + +
620B PHE* 3.0 29.8 + - - +
667B ILE 4.5 4.6 + - - +
668B CYS* 3.8 43.5 - - + +
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Residues in contact with ARG 617 (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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612B VAL* 3.9 14.6 - - + +
613B PRO 2.9 6.4 + - - +
614B LEU* 3.4 32.6 - - + +
615B SER 3.6 2.4 - - - -
616B LYS* 1.3 77.7 - - - +
618B ALA* 1.3 66.8 + - + +
621B VAL* 3.1 45.8 + - - +
641B GLN* 2.8 45.1 + - - +
644B GLU* 3.0 31.8 + - - +
647B PHE* 4.5 6.5 - - + -
644C GLU* 5.1 12.6 + - - +
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Residues in contact with ALA 618 (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 SER 5.1 2.1 + - - +
616B LYS 3.3 0.6 - - - -
617B ARG* 1.3 84.1 - - + +
619B LYS* 1.3 61.4 + - - +
620B PHE 3.1 0.2 - - - -
621B VAL* 4.1 6.2 - - - +
622B GLY* 3.0 30.0 + - - -
623B PRO* 5.2 0.2 - - - +
642C VAL* 3.6 23.8 - - + +
643C ASP* 4.0 16.6 - - + +
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Residues in contact with LYS 619 (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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616B LYS* 3.4 26.1 + - + +
617B ARG 3.4 0.4 - - - -
618B ALA* 1.3 80.0 - - - +
620B PHE* 1.3 56.9 + - - +
622B GLY* 5.3 0.2 - - - -
627B ASN* 3.1 19.9 + - - -
666B GLU 4.9 1.2 + - - -
667B ILE* 2.4 56.3 + - + +
668B CYS* 4.7 0.2 - - - +
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Residues in contact with PHE 620 (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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610B VAL* 4.9 3.8 - - + -
612B VAL* 4.0 26.9 - - + -
616B LYS* 3.0 18.5 + - + +
617B ARG 3.6 2.7 - - - +
618B ALA 3.1 0.4 - - - -
619B LYS* 1.3 75.9 - - - +
621B VAL* 1.3 76.7 + - + +
627B ASN* 3.2 19.6 + - - +
628B LEU* 3.6 22.8 - - + +
631B LEU* 5.9 0.2 - - + -
639B ILE* 3.6 27.4 - - + -
647B PHE* 3.9 25.6 - + - -
664B ILE* 4.0 35.7 - - + -
667B ILE* 3.6 33.8 - - + +
668B CYS* 4.7 3.1 - - - -
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Residues in contact with VAL 621 (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 ARG* 3.1 29.8 + - - +
618B ALA* 4.1 6.3 - - - +
620B PHE* 1.3 81.9 - - + +
622B GLY* 1.3 73.1 + - - +
625B GLY* 2.9 35.3 - - - +
627B ASN* 3.0 8.1 + - - +
628B LEU* 3.6 23.1 + - + -
641B GLN* 5.4 1.1 - - - +
647B PHE* 3.7 30.3 - - + -
642C VAL 5.9 1.3 - - - +
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Residues in contact with GLY 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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618B ALA 3.0 18.7 + - - -
619B LYS* 5.3 0.4 - - - -
620B PHE 3.3 2.6 - - - -
621B VAL* 1.3 86.9 - - - +
623B PRO* 1.3 72.7 - - - +
624B GLY 3.1 0.7 + - - -
625B GLY 2.8 18.4 + - - -
626B TYR 4.0 0.9 - - - -
627B ASN* 3.1 18.6 - - - -
641C GLN 4.3 1.6 - - - +
642C VAL 5.3 3.0 - - - +
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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