Contacts of the helix formed by residues 653 - 661 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450D TYR* 3.9 16.8 - - - -
451D GLY 5.7 0.2 - - - -
452D ALA* 5.1 3.4 - - - +
485D ARG* 3.7 4.7 - - - -
650D LEU* 4.0 9.5 + - - -
651D ASP 3.0 6.3 - - - -
652D SER* 1.3 79.9 - - - +
654D SER* 1.3 65.8 + - - +
655D THR* 3.3 2.6 + - - -
656D LYS* 3.7 13.2 + - - +
657D GLU* 3.9 7.8 + - - +
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Residues in contact with SER 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D TYR* 4.5 3.3 - - - -
480D THR* 3.2 39.7 + - - +
482D THR* 4.2 10.5 - - - +
485D ARG* 3.2 25.8 - - - +
653D GLY* 1.3 70.5 - - - -
655D THR* 1.3 71.4 + - - +
657D GLU* 2.9 11.2 + - - +
658D PHE* 2.9 22.8 + - - +
705D GLU* 4.7 3.6 + - - +
730D LYS* 5.0 6.1 + - - +
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Residues in contact with THR 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D ILE* 5.2 15.2 - - + +
649D THR* 3.6 27.6 - - + -
650D LEU 5.2 3.4 - - - -
653D GLY* 3.3 1.7 - - - -
654D SER* 1.3 82.0 + - - +
656D LYS* 1.3 64.5 + - - +
658D PHE* 3.0 8.6 + - - +
659D PHE* 2.9 53.8 + - + -
703D LEU* 5.3 4.7 + - + +
704D LEU* 5.5 6.3 - - - -
705D GLU* 5.1 11.3 + - - +
730D LYS* 5.8 1.3 - - - +
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Residues in contact with LYS 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649D THR* 4.6 11.6 + - - +
650D LEU 4.7 6.0 + - - +
651D ASP* 4.0 29.9 + - + +
652D SER 5.4 2.5 - - - +
653D GLY 3.7 11.0 + - - +
654D SER 3.3 0.6 - - - -
655D THR* 1.3 79.4 - - - +
657D GLU* 1.3 57.6 + - - +
659D PHE* 5.0 1.8 - - - -
660D ARG* 2.9 54.8 + - - +
671D TRP* 3.7 26.6 - - + -
682D PHE* 4.7 17.4 - - + -
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Residues in contact with GLU 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D THR* 5.8 8.1 - - + +
484D VAL* 5.1 22.8 - - + +
653D GLY 3.9 5.5 + - - +
654D SER* 2.9 14.5 + - - +
656D LYS* 1.3 76.5 - - - +
658D PHE* 1.3 66.4 + - - +
660D ARG* 2.3 38.7 + - - +
661D ARG* 2.9 62.1 + - + +
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Residues in contact with PHE 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A ASN 5.5 5.4 - - - -
755A GLU* 5.2 17.0 - - + -
757A GLY* 6.6 0.2 - - - -
500D ILE* 3.6 23.8 - - + -
654D SER 2.9 12.0 + - - +
655D THR* 3.0 10.1 + - - +
657D GLU* 1.3 77.5 - - - +
659D PHE* 1.3 75.3 + + - +
661D ARG* 3.4 3.6 - - - +
662D SER* 2.7 34.9 + - - -
667D PHE* 4.4 30.5 - + - -
727D LEU* 4.9 1.3 - - + -
728D ASP* 3.0 31.2 - - + -
730D LYS* 3.7 20.2 - - - +
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Residues in contact with PHE 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D ILE* 4.3 8.3 - - + -
649D THR* 5.0 6.3 - - + -
655D THR* 2.9 49.0 + - + +
656D LYS* 4.2 2.2 - - - +
658D PHE* 1.3 88.2 - + - +
660D ARG* 1.3 66.4 + - - +
662D SER* 3.0 19.8 + - - +
667D PHE* 4.2 43.5 - + + +
668D ASP* 5.7 0.7 - - - -
670D MET* 4.6 16.2 - - + -
671D TRP* 4.0 29.0 - - + +
674D MET* 4.5 15.9 - - + -
703D LEU* 5.0 9.4 - - + -
727D LEU* 3.7 24.0 - - + -
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Residues in contact with ARG 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656D LYS* 2.9 61.1 + - - +
657D GLU* 2.3 34.3 + - - +
659D PHE* 1.3 76.6 - - - +
661D ARG* 1.3 86.5 + - - +
662D SER 4.8 1.6 - - - +
671D TRP* 3.5 39.7 + - + +
675D ARG* 5.9 0.9 - - - +
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Residues in contact with ARG 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A GLU* 5.1 7.3 - - + +
657D GLU* 2.9 42.7 + - + +
658D PHE* 3.4 3.4 - - - +
660D ARG* 1.3 116.8 - - - +
662D SER* 1.3 67.8 + - - +
663D LYS* 3.6 8.7 + - - +
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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