Contacts of the strand formed by residues 589 - 594 (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 THR 589 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438D THR* 5.2 2.6 - - - +
439D VAL* 3.7 30.3 - - + +
491D GLU 3.5 12.4 + - - -
492D ALA* 3.5 1.9 - - - +
493D ARG* 2.7 34.7 + - - +
538D ARG* 5.3 0.2 - - - +
550D LEU* 3.8 17.2 - - - +
587D LEU 3.5 2.9 + - - -
588D PRO* 1.3 70.8 - - - +
590D ILE* 1.3 59.8 + - - +
591D VAL* 4.3 3.0 - - + +
623D GLY 3.2 20.6 - - - +
625D HIS* 3.4 23.7 - - + +
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Residues in contact with ILE 590 (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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493D ARG* 3.8 5.8 - - + +
494D LEU 5.1 0.2 - - - -
495D ILE* 4.0 7.2 - - + -
514D LEU* 3.7 35.7 - - + -
530D TRP* 4.6 7.6 - - + -
531D SER* 6.1 1.6 - - - -
534D GLU* 3.8 15.3 - - + -
538D ARG* 3.6 22.0 - - - +
588D PRO* 3.9 8.7 - - + +
589D THR* 1.3 76.0 - - - +
591D VAL* 1.3 61.1 + - - +
592D VAL* 3.8 24.2 - - + -
623D GLY 3.2 6.3 + - - +
624D ILE* 3.2 22.5 - - + -
625D HIS* 2.7 32.7 + - - -
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Residues in contact with VAL 591 (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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439D VAL* 3.8 28.7 - - + -
456D LEU* 3.8 11.0 - - + -
480D LEU* 5.7 0.2 - - + -
483D ILE* 5.2 9.2 - - + -
492D ALA* 6.1 1.8 - - + -
493D ARG 3.2 10.8 + - - +
494D LEU* 3.5 20.9 - - + +
495D ILE 3.3 17.0 + - - +
589D THR* 4.3 10.1 - - + +
590D ILE* 1.3 77.0 - - - +
592D VAL* 1.3 58.8 + - - +
593D VAL* 3.0 17.3 + - + -
625D HIS* 3.3 8.3 - - + +
627D ILE* 3.7 31.2 - - + -
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Residues in contact with VAL 592 (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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495D ILE* 3.5 33.2 - - + +
497D ILE* 4.4 1.8 - - + -
528D LEU* 4.0 17.3 - - + -
531D SER* 4.7 14.6 - - - -
590D ILE* 3.8 22.4 - - + -
591D VAL* 1.3 67.6 - - - +
593D VAL* 1.3 59.7 + - - +
594D VAL* 3.9 13.2 - - + -
615D ILE* 6.0 2.9 - - + -
624D ILE* 5.2 6.1 - - + -
625D HIS 2.7 14.3 + - - +
626D LEU* 3.3 26.3 - - + +
627D ILE 3.0 21.0 + - - +
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Residues in contact with VAL 593 (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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476D VAL* 5.4 8.1 - - + -
480D LEU* 4.0 27.1 - - + -
494D LEU* 4.8 2.0 - - + -
495D ILE 3.0 16.9 + - - +
496D MET* 3.5 32.3 - - + -
497D ILE 3.3 13.5 + - - -
504D LEU* 4.7 6.5 - - + +
591D VAL* 3.0 16.7 + - + +
592D VAL* 1.3 71.8 - - - +
594D VAL* 1.3 61.0 + - - +
595D ASP 4.0 1.5 + - - +
627D ILE* 3.6 39.5 - - + -
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Residues in contact with VAL 594 (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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497D ILE* 3.5 24.5 - - + +
528D LEU* 5.3 3.4 - - + -
592D VAL* 3.9 23.8 - - + +
593D VAL* 1.3 77.8 - - - +
595D ASP* 1.3 61.8 + - - +
596D GLU 3.5 0.5 + - - -
597D PHE* 3.5 28.0 + - + +
600D MET* 3.5 23.1 - - + -
612D ILE* 6.1 1.1 - - + -
626D LEU* 4.2 8.5 - - + -
627D ILE* 2.9 15.5 + - - +
628D LEU* 3.6 9.3 - - + -
629D ALA* 3.3 23.6 + - - +
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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