Contacts of the helix formed by residues 654 - 662 (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 SER 654 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652B PRO* 3.3 2.4 - - - +
653B ARG* 1.3 80.7 - - - +
655B LEU* 1.3 64.4 + - - +
656B GLU* 3.1 20.3 + - - +
657B ASN* 3.1 17.4 + - - +
658B VAL* 3.2 24.6 + - - +
674B PHE* 3.3 19.4 - - - -
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Residues in contact with LEU 655 (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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654B SER* 1.3 73.7 - - - +
656B GLU* 1.3 78.8 + - + +
658B VAL* 3.1 16.2 + - - +
659B LEU* 3.2 18.1 + - + +
667B GLU* 4.2 20.4 - - - +
670B ALA* 3.5 17.3 - - + +
671B ARG* 3.4 61.9 - - + +
674B PHE* 3.9 11.4 - - + -
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Residues in contact with GLU 656 (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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654B SER* 3.1 21.1 + - - +
655B LEU* 1.3 90.7 + - + +
657B ASN* 1.3 55.9 + - - +
659B LEU* 3.0 16.9 + - + +
660B GLU* 2.9 34.7 + - + +
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Residues in contact with ASN 657 (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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651B ARG 4.2 1.7 - - - +
652B PRO* 3.4 9.2 - - - +
653B ARG* 2.8 43.2 + - + +
654B SER* 3.1 21.0 + - - +
656B GLU* 1.3 77.0 - - - +
658B VAL* 1.3 60.7 + - - +
660B GLU* 3.0 32.9 + - - +
661B ILE* 3.0 22.4 + - - +
694B GLY 2.8 29.9 + - - +
695B ASP* 4.1 1.2 + - - +
700B ILE* 5.9 0.2 - - - +
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Residues in contact with VAL 658 (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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542B PRO* 4.7 12.6 - - + -
652B PRO* 3.4 23.6 - - + -
654B SER 3.2 14.8 + - - +
655B LEU 3.1 8.9 + - - +
657B ASN* 1.3 75.3 - - - +
659B LEU* 1.3 57.4 + - - +
661B ILE* 3.2 10.3 + - - +
662B ASN* 2.9 30.0 + - + +
665B ILE* 4.0 10.5 - - + -
670B ALA* 3.7 29.4 - - + +
673B ALA* 4.3 9.2 - - + -
674B PHE* 4.0 22.2 - - + +
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Residues in contact with LEU 659 (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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655B LEU* 3.2 24.4 + - + +
656B GLU* 3.0 15.3 + - + +
658B VAL* 1.3 74.4 - - - +
660B GLU* 1.3 66.5 + - - +
662B ASN 3.4 17.1 - - - +
663B LYS* 4.0 9.2 - - - +
665B ILE* 4.0 23.3 - - + +
666B THR 4.3 3.1 - - - +
667B GLU* 4.0 32.1 - - + +
670B ALA* 3.9 20.6 - - + -
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Residues in contact with GLU 660 (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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656B GLU* 2.9 15.1 + - + +
657B ASN* 3.0 36.6 + - - +
659B LEU* 1.3 79.4 - - - +
661B ILE* 1.3 61.1 + - - +
662B ASN 3.7 0.2 + - - -
663B LYS* 3.4 25.1 - - - +
695B ASP* 3.5 35.5 - - - +
696B SER* 4.5 4.0 - - - -
697B PHE 4.9 0.2 + - - -
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Residues in contact with ILE 661 (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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542B PRO* 4.2 20.2 - - + +
543B THR* 3.7 24.2 - - + +
546B ARG* 4.5 1.4 + - - -
650B ILE* 4.6 3.6 - - + -
652B PRO* 5.3 4.5 - - + -
657B ASN* 3.0 36.5 + - - +
658B VAL* 3.5 13.9 - - - +
660B GLU* 1.3 79.1 - - - +
662B ASN* 1.3 60.6 + - + +
663B LYS* 4.1 2.3 + - - +
664B ARG* 4.4 6.1 + - - -
694B GLY 3.7 11.0 - - - +
695B ASP 4.1 0.4 - - - -
696B SER 4.0 11.2 - - - +
697B PHE* 3.6 31.0 - - - +
700B ILE* 3.6 27.4 - - + -
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Residues in contact with ASN 662 (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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542B PRO* 6.0 1.9 - - + +
543B THR* 4.3 19.2 - - + +
658B VAL* 2.9 16.2 + - + +
659B LEU* 3.4 14.4 - - - +
661B ILE* 1.3 78.9 - - + +
663B LYS* 1.3 56.1 + - - +
664B ARG* 2.8 46.5 + - - +
665B ILE* 3.5 45.6 - - + +
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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