Contacts of the strand formed by residues 705 - 712 (chain D) in PDB entry 3BBT
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 705 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701D SER* 3.3 1.2 - - - -
702D GLY* 2.7 38.0 + - - +
703D ALA 3.5 2.0 - - - -
704D PHE* 1.3 80.8 - - - +
706D THR* 1.3 59.8 + - - -
726D LYS* 4.4 11.5 + - - +
727D ILE 3.2 13.2 - - - -
728D LEU* 4.4 0.4 - - - -
729D ASN* 4.1 13.9 - - - -
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Residues in contact with THR 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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698D VAL* 3.8 22.4 - - + -
700D GLY 3.7 10.3 - - - +
701D SER* 3.9 14.8 - - - +
705D GLY* 1.3 73.5 - - - -
707D VAL* 1.3 64.5 + - - +
708D TYR* 3.7 32.8 + - + +
725D ILE 3.6 1.2 - - - +
726D LYS* 3.4 2.3 - - - -
727D ILE* 2.9 34.1 + - - -
729D ASN* 4.5 9.4 + - - +
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Residues in contact with VAL 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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91D FMM 3.6 50.7 - - + +
698D VAL* 4.0 4.0 - - - +
699D LEU* 3.0 30.9 + - + -
700D GLY* 2.6 25.1 + - - +
702D GLY 5.5 1.8 - - - +
705D GLY 5.1 0.9 - - - +
706D THR* 1.3 75.0 - - - +
708D TYR* 1.3 69.5 + - - +
724D ALA* 4.6 1.3 - - + -
725D ILE 3.5 4.3 - - - +
726D LYS* 3.8 32.1 - - + +
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Residues in contact with TYR 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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695D ARG* 3.2 53.4 + - + -
696D VAL 5.7 0.2 - - - -
697D LYS* 3.6 11.0 - - - -
698D VAL* 3.7 26.3 - - + +
699D LEU* 4.1 4.4 - - - +
706D THR* 3.7 33.3 + - + +
707D VAL* 1.3 76.9 - - - +
709D LYS* 1.3 66.5 + - - +
724D ALA* 3.3 8.8 - - - +
725D ILE* 2.7 46.7 + - + +
727D ILE* 3.6 23.4 - - + +
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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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695D ARG* 3.6 3.1 - - - -
696D VAL* 2.7 52.0 + - + +
697D LYS* 2.9 23.7 + - + +
699D LEU* 3.8 28.7 - - + +
708D TYR* 1.3 72.4 - - - +
710D GLY* 1.3 57.5 + - - +
722D PRO* 6.2 0.4 - - - -
723D VAL 4.0 2.5 - - - +
773D LEU* 4.2 30.7 - - + -
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Residues in contact with GLY 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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694D LYS 3.3 9.9 - - - -
696D VAL* 4.1 2.9 - - - +
708D TYR 3.8 0.8 + - - -
709D LYS* 1.3 79.0 - - - +
711D ILE* 1.3 65.9 + - - +
721D ILE 3.6 1.0 - - - +
722D PRO* 3.7 4.5 - - - +
723D VAL* 2.8 42.1 + - - +
725D ILE* 3.8 15.7 - - - -
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Residues in contact with ILE 711 (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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718B THR* 3.8 32.5 - - + +
719B VAL* 5.2 9.2 - - + -
692D GLU 3.9 1.0 - - - +
693D LEU* 3.5 3.6 - - - -
694D LYS* 2.8 49.2 + - + +
696D VAL* 3.9 20.6 - - + -
710D GLY* 1.3 78.2 - - - +
712D TRP* 1.3 62.4 + - - +
713D VAL* 4.3 9.8 - - + +
720D LYS* 3.9 30.5 - - + -
721D ILE 3.4 8.3 - - - +
722D PRO* 5.6 0.9 - - + -
723D VAL* 3.8 2.2 - - - +
725D ILE* 4.7 0.2 - - - +
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Residues in contact with TRP 712 (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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686D ARG* 3.3 39.5 - - - -
688D LEU* 3.5 25.5 - - + +
692D GLU* 2.8 40.2 + - + +
693D LEU* 3.7 18.4 - - + -
711D ILE* 1.3 73.0 - - - +
713D VAL* 1.3 70.9 + - - +
714D PRO* 3.5 31.2 - - + +
720D LYS* 3.3 5.7 - - - -
721D ILE* 2.9 64.2 + - + +
723D VAL* 3.4 23.9 - - + +
759D LEU* 5.0 14.8 - - + -
770D VAL* 6.0 0.4 - - + -
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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