Contacts of the helix formed by residues 653 - 661 (chain B) in PDB entry 5VOT
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 GLY 653 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B TYR* 3.9 15.9 - - - -
452B ALA* 5.1 3.5 - - - +
485B ARG* 3.8 5.4 - - - -
650B LEU* 4.0 8.4 + - - -
651B ASP 3.0 6.8 - - - -
652B SER* 1.3 81.3 - - - +
654B SER* 1.3 66.2 + - - +
655B THR* 3.3 4.2 + - - -
656B LYS* 3.7 12.1 + - - +
657B GLU* 3.9 7.6 + - - +
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Residues in contact with SER 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B TYR* 4.5 3.7 - - - -
480B THR* 3.2 40.6 + - - +
482B THR* 4.2 10.6 - - - +
485B ARG* 3.2 26.0 - - - +
653B GLY* 1.3 69.9 - - - -
655B THR* 1.3 72.5 + - - +
657B GLU* 2.9 11.4 + - - +
658B PHE* 2.9 22.3 + - - +
705B GLU* 4.7 3.8 + - - +
730B LYS* 5.0 5.6 + - - +
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Residues in contact with THR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ILE* 5.2 15.4 - - + +
649B THR* 3.6 27.4 - - + -
650B LEU 5.2 3.8 - - - -
653B GLY* 3.3 2.1 - - - -
654B SER* 1.3 81.9 + - - +
656B LYS* 1.3 65.2 + - - +
658B PHE* 3.0 8.2 + - - +
659B PHE* 2.9 54.9 + - + -
703B LEU* 5.3 4.7 + - + +
704B LEU* 5.5 6.5 - - - -
705B GLU* 5.1 10.9 + - - +
730B LYS* 5.8 1.3 - - - +
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Residues in contact with LYS 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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649B THR* 4.6 12.4 + - - +
650B LEU 4.7 6.8 + - - +
651B ASP* 3.9 28.6 + - - +
652B SER 5.4 2.5 - - - +
653B GLY 3.7 10.0 + - - +
654B SER 3.3 0.4 - - - -
655B THR* 1.3 79.2 - - - +
657B GLU* 1.3 56.8 + - - +
659B PHE* 3.5 2.6 + - - +
660B ARG* 2.9 55.7 + - - +
671B TRP* 3.7 25.6 - - + -
682B PHE* 4.6 17.8 - - + -
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Residues in contact with GLU 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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482B THR* 5.8 8.3 - - + +
484B VAL* 5.1 22.3 - - + +
653B GLY 3.9 5.2 + - - +
654B SER* 2.9 15.4 + - - +
656B LYS* 1.3 76.9 - - - +
658B PHE* 1.3 65.5 + - - +
660B ARG* 2.3 38.4 + - - +
661B ARG* 2.9 61.3 + - + +
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Residues in contact with PHE 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ILE* 3.6 25.6 - - + -
654B SER 2.9 10.8 + - - +
655B THR* 3.3 10.3 - - - +
657B GLU* 1.3 78.0 - - - +
659B PHE* 1.3 73.2 + + - +
661B ARG* 3.3 3.6 + - - +
662B SER* 2.7 35.4 + - - -
667B PHE* 4.4 30.7 - + - -
727B LEU* 4.9 1.1 - - + -
728B ASP* 3.0 28.9 - - + -
730B LYS* 3.7 24.2 - - - +
754C ASN 5.5 5.4 - - - -
755C GLU* 5.2 16.8 - - + -
757C GLY* 6.6 0.4 - - - -
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Residues in contact with PHE 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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500B ILE* 4.3 8.5 - - + -
649B THR* 5.0 6.5 - - + -
655B THR* 2.9 49.7 + - + +
656B LYS* 4.2 2.5 - - - +
658B PHE* 1.3 89.2 - + - +
660B ARG* 1.3 66.2 + - - +
662B SER* 3.0 19.4 + - - +
667B PHE* 4.2 44.3 - + + +
668B ASP* 5.7 0.5 - - - -
670B MET* 4.6 17.3 - - + -
671B TRP* 4.0 28.7 - - + +
674B MET* 4.5 15.0 - - + -
703B LEU* 5.0 9.2 - - + -
727B LEU* 3.7 23.8 - - + -
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Residues in contact with ARG 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 LYS* 2.9 61.9 + - - +
657B GLU* 2.3 34.6 + - - +
659B PHE* 1.3 76.9 - - - +
661B ARG* 1.3 87.1 + - - +
662B SER 4.8 1.6 - - - +
671B TRP* 3.5 38.3 + - + +
675B ARG* 5.9 0.4 - - - +
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Residues in contact with ARG 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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657B GLU* 2.9 42.5 + - + +
658B PHE* 3.4 3.8 - - - +
660B ARG* 1.3 116.0 - - - +
662B SER* 1.3 65.6 + - - +
663B LYS* 3.6 8.7 + - - +
755C GLU 5.1 6.8 - - - +
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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