Contacts of the helix formed by residues 697 - 710 (chain D) in PDB entry 6T8B
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 697 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D ASP* 3.7 19.0 + - - -
422D ARG* 5.8 1.8 - - - -
695D PHE* 4.0 21.3 - - - -
696D VAL* 1.3 77.3 - - - +
698D ASP* 1.3 55.8 + - - +
699D ASP* 3.0 12.2 + - - +
700D GLU* 2.6 41.4 + - - +
701D VAL* 3.2 7.3 + - - +
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Residues in contact with ASP 698 (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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548C ARG* 3.7 32.9 + - - +
506D ILE* 3.8 19.1 - - + +
696D VAL 4.1 1.2 + - - -
697D SER* 1.3 72.1 - - - +
699D ASP* 1.3 77.2 + - - +
700D GLU 3.1 3.3 + - - -
701D VAL* 4.1 6.7 - - - +
702D HIS* 3.6 21.1 + - - +
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Residues in contact with ASP 699 (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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322D ASP* 6.0 0.2 - - - -
697D SER* 2.9 10.7 + - - +
698D ASP* 1.3 91.3 + - - +
700D GLU* 1.3 56.8 + - - +
702D HIS* 4.6 5.8 - - - +
703D ARG* 3.2 30.3 + - - +
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Residues in contact with GLU 700 (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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320D LEU* 2.9 23.8 - - - +
321D LEU* 3.2 39.5 + - + +
322D ASP* 3.8 10.9 - - - +
481D LEU* 4.4 5.4 - - + -
485D PHE* 4.7 0.2 - - - -
696D VAL* 4.5 5.4 - - + -
697D SER* 2.6 26.7 + - - +
699D ASP* 1.3 73.2 - - - +
701D VAL* 1.3 65.7 + - - +
702D HIS 3.1 1.3 - - - -
703D ARG* 2.2 39.4 + - - +
704D VAL* 2.9 38.6 + - + +
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Residues in contact with VAL 701 (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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477D ASN* 4.0 21.5 - - + +
481D LEU* 3.7 24.2 - - + -
506D ILE* 3.8 30.3 - - + -
507D TYR* 3.5 34.3 - - + +
696D VAL* 4.0 13.9 - - + +
697D SER 3.2 6.9 + - - +
698D ASP* 4.5 4.9 - - - +
700D GLU* 1.3 76.8 - - - +
702D HIS* 1.3 58.8 + - - +
704D VAL* 3.3 2.9 + - - +
705D VAL* 2.9 34.7 + - + +
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Residues in contact with HIS 702 (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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546C GLY 5.8 3.6 + - - -
506D ILE* 4.2 13.4 + - + +
698D ASP 3.6 16.9 + - - +
699D ASP* 4.9 3.8 - - - -
700D GLU 3.1 0.6 - - - -
701D VAL* 1.3 80.0 - - - +
703D ARG* 1.3 58.8 + - - +
705D VAL* 3.3 11.8 + - + +
706D GLU* 2.5 70.6 + - + +
709D LYS* 5.8 5.6 - - - -
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Residues in contact with ARG 703 (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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320D LEU* 3.2 47.7 + - + +
322D ASP* 4.2 9.8 + - - -
699D ASP* 3.2 25.5 + - - +
700D GLU* 2.2 48.1 + - - +
702D HIS* 1.3 79.7 - - - +
704D VAL* 1.3 57.1 + - - +
706D GLU* 3.3 14.6 + - - +
707D ALA* 2.9 26.5 + - - +
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Residues in contact with VAL 704 (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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316D PRO* 4.7 2.2 - - + -
320D LEU* 5.5 3.4 - - + -
481D LEU* 3.9 13.5 - - + -
484D LEU* 3.6 30.1 - - + -
485D PHE* 3.4 36.8 - - + -
700D GLU* 2.9 27.9 + - - +
701D VAL 3.8 4.0 - - - +
703D ARG* 1.3 73.7 - - + +
705D VAL* 1.3 66.8 + - - +
707D ALA* 3.1 6.5 + - - +
708D TRP* 3.0 42.8 + - + +
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Residues in contact with VAL 705 (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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484D LEU* 5.8 1.3 - - + -
506D ILE 3.4 24.9 - - - +
507D TYR* 3.8 25.4 - - + -
508D GLU 3.8 22.7 - - - +
510D ILE* 3.9 18.0 - - + +
701D VAL* 2.9 23.5 + - + +
702D HIS* 3.6 11.2 - - - +
704D VAL* 1.3 76.2 - - - +
706D GLU* 1.3 60.1 + - + +
708D TRP* 3.9 4.0 - - - +
709D LYS* 2.8 43.3 + - + +
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Residues in contact with GLU 706 (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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702D HIS* 2.5 55.5 + - + +
703D ARG* 3.5 14.4 - - - +
705D VAL* 1.3 77.1 - - + +
707D ALA* 1.3 62.8 + - - +
709D LYS* 3.8 12.3 - - + +
710D LEU* 3.0 39.0 + - + +
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Residues in contact with ALA 707 (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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316D PRO* 3.8 15.5 - - + -
320D LEU* 3.7 27.1 - - + -
703D ARG 2.9 16.7 + - - +
704D VAL* 3.1 7.1 + - - +
706D GLU* 1.3 75.9 - - - +
708D TRP* 1.3 61.6 + - - +
710D LEU* 4.2 8.4 + - - +
711D ARG* 3.4 31.3 + - - +
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Residues in contact with TRP 708 (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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315D LEU* 4.1 15.0 - - + -
316D PRO* 3.4 33.6 - - + +
484D LEU* 3.0 59.7 - - + +
487D SER 3.5 17.5 - - - -
488D THR* 4.0 7.4 - - + -
489D PRO* 3.4 32.8 - - + -
510D ILE* 4.8 7.2 - - + -
511D PRO* 3.5 24.2 - - + +
512D HIS* 4.8 2.0 - + - -
704D VAL* 3.0 36.5 + - + +
705D VAL* 3.9 3.8 - - - +
707D ALA* 1.3 75.4 - - - +
709D LYS* 1.3 56.3 + - - +
710D LEU 3.1 1.8 - - - -
711D ARG* 2.6 38.1 + - + +
712D GLY 3.2 8.8 + - - -
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Residues in contact with LYS 709 (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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508D GLU 3.2 27.2 + - - -
509D GLY* 3.8 26.7 + - - +
510D ILE* 5.2 0.2 - - - +
511D PRO* 4.3 1.2 - - - +
702D HIS* 5.8 5.5 - - - -
705D VAL* 2.8 31.2 + - - +
706D GLU* 3.8 10.6 - - + +
708D TRP* 1.3 71.0 - - - +
710D LEU* 1.3 61.5 + - + +
712D GLY 2.9 25.6 - - - +
713D ALA* 6.3 0.4 - - - -
714D PRO* 6.2 1.6 - - + -
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Residues in contact with LEU 710 (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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706D GLU* 3.0 30.2 + - + +
707D ALA* 4.3 9.2 - - - +
709D LYS* 1.3 77.5 - - + +
711D ARG* 1.3 63.1 + - + +
712D GLY 3.5 0.7 - - - +
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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