Contacts of the helix formed by residues 685 - 695 (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 THR 685 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402D GLU* 5.7 3.4 - - - -
448D GLY 5.8 2.9 - - - +
650D LEU* 3.9 6.7 - - - -
683D VAL* 3.2 6.1 - - - +
684D ARG* 1.3 88.5 - - + +
686D THR* 1.3 64.6 + - - +
687D ALA* 3.8 9.8 + - - +
688D GLU* 3.0 38.3 + - - +
689D GLY 3.2 7.8 + - - -
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Residues in contact with THR 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D GLU* 4.5 21.9 + - - +
450D TYR* 5.6 1.6 + - - -
650D LEU* 3.4 22.8 - - - +
685D THR* 1.3 69.5 - - - +
687D ALA* 1.3 59.1 + - - +
689D GLY* 2.7 20.8 + - - -
690D VAL* 2.9 19.3 + - + +
702D TYR* 3.6 27.9 + - + +
704D LEU* 4.8 13.9 - - + -
708D MET* 5.2 11.6 - - + +
712D ILE* 6.4 1.3 - - + -
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Residues in contact with ALA 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D GLU* 5.6 1.2 + - - -
685D THR* 3.2 9.1 - - - +
686D THR* 1.3 79.1 - - - +
688D GLU* 1.3 61.7 + - - +
690D VAL* 3.1 11.4 + - - +
691D ALA* 2.9 24.5 + - - +
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Residues in contact with GLU 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682D PHE 5.2 0.2 - - - +
683D VAL* 3.5 22.4 - - + +
684D ARG* 3.1 26.7 + - - +
685D THR* 3.0 26.3 + - - +
687D ALA* 1.3 75.5 - - - +
689D GLY* 1.3 55.9 + - - +
691D ALA* 3.9 7.4 - - + +
692D ARG* 2.9 30.4 + - + +
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Residues in contact with GLY 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D VAL* 4.1 5.5 - - - +
685D THR 3.2 7.0 + - - -
686D THR 2.7 15.8 + - - -
688D GLU* 1.3 69.4 - - - +
690D VAL* 1.3 63.7 + - - -
692D ARG* 3.2 6.6 + - - +
693D VAL* 2.9 28.3 + - - +
702D TYR* 3.4 33.4 - - - -
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Residues in contact with VAL 690 (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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503D MET* 5.0 11.9 - - + -
686D THR* 2.9 23.4 + - + +
687D ALA* 3.1 11.0 + - - +
689D GLY* 1.3 73.9 - - - +
691D ALA* 1.3 64.6 + - - +
693D VAL* 3.1 8.6 + - - +
694D ARG* 2.9 59.6 + - + +
702D TYR* 5.6 1.5 - - + -
704D LEU* 6.4 0.7 - - + -
712D ILE* 4.5 33.4 - - + -
720D THR* 5.0 4.5 - - + -
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Residues in contact with ALA 691 (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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687D ALA 2.9 15.0 + - - +
688D GLU* 3.9 7.0 - - + +
690D VAL* 1.3 77.2 - - - +
692D ARG* 1.3 56.8 + - - +
694D ARG* 3.2 9.8 + - - +
695D LYS* 2.9 31.8 + - - +
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Residues in contact with ARG 692 (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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646D ALA* 5.5 1.4 - - - +
679D PRO* 6.0 1.4 - - - +
680D SER 3.3 21.1 + - - -
681D VAL* 3.3 36.2 + - - +
682D PHE 3.9 1.4 + - - +
683D VAL* 4.0 21.8 - - + +
688D GLU* 2.9 21.0 + - + +
689D GLY* 3.5 6.1 - - - +
691D ALA* 1.3 77.5 - - - +
693D VAL* 1.3 56.1 + - - +
695D LYS* 3.3 5.3 + - - -
696D SER* 2.3 41.6 + - - +
700D TYR* 3.3 49.2 + - + +
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Residues in contact with VAL 693 (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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503D MET* 5.2 9.9 - - + -
504D ILE* 4.3 7.0 - - - +
505D LYS* 4.1 34.3 - - + +
689D GLY 2.9 19.6 + - - +
690D VAL* 3.1 9.4 + - + +
692D ARG* 1.3 76.0 - - - +
694D ARG* 1.3 65.7 + - + +
695D LYS 3.2 0.7 + - - -
696D SER* 3.2 18.0 + - - -
697D LYS* 4.1 4.0 + - - -
698D GLY* 4.6 4.2 + - - -
700D TYR* 4.2 23.5 - - + +
702D TYR* 3.6 29.6 - - + +
720D THR* 5.5 5.8 - - + -
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Residues in contact with ARG 694 (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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505D LYS* 5.4 10.9 + - + +
690D VAL* 2.9 42.9 + - + +
691D ALA* 3.7 8.1 - - - +
693D VAL* 1.3 78.8 - - + +
695D LYS* 1.3 56.8 + - - +
696D SER 3.5 0.6 + - - -
697D LYS* 4.7 4.0 + - - +
712D ILE* 4.5 12.1 + - - +
715D ARG* 5.1 2.2 + - - +
716D LYS 3.3 10.3 + - - -
717D PRO* 3.3 33.6 - - - +
719D ASP* 2.8 34.2 + - - +
720D THR* 4.7 3.1 - - + +
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Residues in contact with LYS 695 (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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691D ALA 2.9 17.0 + - - +
692D ARG* 3.5 5.6 - - - +
693D VAL 3.1 0.2 - - - -
694D ARG* 1.3 78.1 - - - +
696D SER* 1.3 57.7 + - - +
697D LYS* 3.4 8.0 + - - +
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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