Contacts of the helix formed by residues 613 - 622 (chain B) in PDB entry 5YPO
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 VAL 613 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596B HIS 3.8 11.2 - - - +
597B LYS* 2.7 32.9 + - + +
598B PHE 4.1 1.8 - - - +
599B ILE* 3.8 25.1 - - + +
611B THR 3.9 0.8 + - - -
612B SER* 1.3 71.6 - - - +
614B GLN* 1.3 58.4 + - - +
616B VAL* 3.1 8.2 + - - +
617B ARG* 2.9 54.4 + - - +
637B ARG 5.5 0.7 - - - +
641B ALA* 4.0 25.8 - - + -
643B LEU* 3.9 8.8 - - + +
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Residues in contact with GLN 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B LYS 4.5 0.6 + - - -
612B SER* 3.2 7.0 + - - +
613B VAL* 1.3 80.4 - - - +
615B SER* 1.4 56.5 + - - +
617B ARG* 2.7 47.7 + - - +
618B GLU* 2.9 68.3 + - - +
621B GLU* 5.2 3.4 + - - -
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Residues in contact with SER 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B CYS* 3.4 22.4 - - - +
563B VAL 3.6 17.8 + - - -
565B HIS* 3.8 10.7 - - - -
581B HIS* 3.9 9.2 + - - -
612B SER* 3.0 29.6 + - - -
614B GLN* 1.4 76.6 - - - +
616B VAL* 1.3 62.6 + - - +
618B GLU* 3.7 13.4 + - - +
619B VAL* 3.4 24.8 + - - +
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Residues in contact with VAL 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PRO* 3.7 35.4 - - + -
562B CYS* 4.2 0.9 - - - -
599B ILE* 4.0 17.3 - - + -
611B THR* 4.1 5.2 - - + -
612B SER 3.4 13.9 - - - +
613B VAL* 3.1 7.1 + - - +
615B SER* 1.3 75.9 - - - +
617B ARG* 1.3 65.7 + - - +
619B VAL* 3.1 6.6 + - - +
620B ALA* 3.0 21.4 + - + +
626B CYS* 4.4 11.2 - - + +
628B LEU* 4.0 26.7 - - + -
638B LEU* 4.0 6.1 - - + -
643B LEU* 4.0 13.7 - - + -
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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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533B TYR* 5.3 3.8 - - + -
613B VAL* 2.9 36.2 + - - +
614B GLN* 2.7 55.5 + - - +
616B VAL* 1.3 75.3 - - - +
618B GLU* 1.3 52.7 + - - +
620B ALA* 3.2 6.8 + - - +
621B GLU* 2.7 66.2 + - + +
641B ALA* 4.4 12.7 + - - +
643B LEU* 4.2 20.6 - - + +
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Residues in contact with GLU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B HIS* 5.7 3.1 + - - -
614B GLN* 2.9 50.6 + - - +
615B SER* 4.0 13.0 + - - +
616B VAL 3.2 0.4 - - - -
617B ARG* 1.3 75.4 - - - +
619B VAL* 1.3 64.0 + - + +
621B GLU* 3.5 11.2 + - - +
622B GLN* 3.2 40.2 + - - +
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Residues in contact with VAL 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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560B GLY* 4.4 10.8 - - - -
561B SER 3.6 20.6 - - - +
562B CYS* 3.9 9.0 - - + -
615B SER 3.4 16.4 - - - +
616B VAL 3.1 5.9 + - - +
618B GLU* 1.3 76.3 - - + +
620B ALA* 1.3 66.2 + - - +
622B GLN* 3.1 20.3 + - - +
624B LYS* 3.3 39.4 + - + +
626B CYS* 3.7 24.5 - - + +
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Residues in contact with ALA 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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533B TYR* 3.5 30.0 - - + +
534B ALA 3.1 40.5 + - - +
536B PRO* 4.7 7.6 - - + -
616B VAL* 3.0 14.8 + - + +
617B ARG* 3.6 8.3 - - - +
619B VAL* 1.3 77.3 - - - +
621B GLU* 1.3 57.3 + - - +
623B GLY* 2.9 16.8 + - - -
624B LYS 3.7 5.8 - - - -
626B CYS* 5.1 1.0 - - + +
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Residues in contact with GLU 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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531B VAL* 3.6 17.5 - - - +
532B HIS 4.6 1.9 - - - +
533B TYR* 4.8 14.3 + - + +
614B GLN* 5.2 2.8 + - - -
617B ARG* 2.7 53.9 + - + +
618B GLU* 3.9 13.2 - - - +
620B ALA* 1.3 72.3 - - - +
622B GLN* 1.3 59.0 + - + +
623B GLY 3.1 4.1 + - - -
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Residues in contact with GLN 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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531B VAL* 3.5 13.8 - - - +
618B GLU* 3.2 28.0 + - - +
619B VAL* 3.1 12.7 + - - +
621B GLU* 1.3 77.4 - - + +
623B GLY* 1.3 60.9 + - - +
624B LYS* 3.3 10.1 + - + +
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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