Contacts of the strand formed by residues 693 - 701 (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 LEU 693 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688D LEU* 4.0 20.6 - - + -
689D LYS 3.5 15.5 + - - +
690D GLU* 2.8 18.1 + - - +
691D THR* 4.3 1.4 - - - -
692D GLU* 1.3 79.4 - - - +
694D LYS* 1.3 69.5 + - - +
695D ARG* 4.4 0.9 - - - -
711D ILE 3.5 2.5 - - - +
712D TRP* 3.7 33.0 - - + -
723D VAL* 4.5 1.6 - - + -
725D ILE* 4.2 25.1 - - + -
762D CYS* 3.8 27.1 - - + -
768D GLN* 5.2 6.3 - - - +
770D VAL* 4.1 19.7 - - + -
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Residues in contact with LYS 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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691D THR* 5.1 10.1 - - - +
692D GLU 5.6 0.7 - - - -
693D LEU* 1.3 80.8 - - - +
695D ARG* 1.3 64.6 + - - +
696D VAL* 3.7 1.9 + - - +
710D GLY* 3.3 2.0 - - - -
711D ILE* 2.8 50.3 + - + +
713D VAL* 6.0 5.4 - - + -
725D ILE* 4.6 1.3 - - - +
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Residues in contact with ARG 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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693D LEU 6.0 0.2 - - - -
694D LYS* 1.3 73.4 - - - +
696D VAL* 1.3 63.2 + - - +
708D TYR* 3.2 59.9 + - + -
709D LYS 3.7 4.5 - - - -
710D GLY* 4.3 0.9 - - - -
725D ILE* 4.1 19.7 - - + -
727D ILE* 3.4 25.4 - - - +
768D GLN* 4.4 7.6 - - - +
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Residues in contact with VAL 696 (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 4.2 0.9 - - - +
695D ARG* 1.3 78.3 - - - +
697D LYS* 1.3 68.8 + - + +
708D TYR* 5.7 0.2 - - - -
709D LYS* 2.7 40.7 + - + +
710D GLY* 4.1 5.2 - - - -
711D ILE* 3.9 35.4 - - + -
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Residues in contact with LYS 697 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696D VAL* 1.3 88.1 - - + +
698D VAL* 1.3 74.6 + - + +
699D LEU* 5.2 1.1 - - + -
708D TYR* 3.6 9.1 - - - -
709D LYS* 2.9 34.1 + - + +
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Residues in contact with VAL 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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697D LYS* 1.3 84.3 - - + +
699D LEU* 1.3 66.1 + - - +
700D GLY* 3.7 16.4 - - - +
701D SER* 4.8 2.9 - - - +
706D THR* 3.8 21.1 - - + -
707D VAL 4.0 2.9 - - - +
708D TYR* 3.7 26.9 - - + +
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Residues in contact with LEU 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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91D FMM 4.3 46.4 - - + +
697D LYS* 3.6 1.1 + - + +
698D VAL* 1.3 79.0 - - - +
700D GLY* 1.3 58.2 + - - +
707D VAL* 3.0 17.5 + - + +
708D TYR 4.1 4.5 - - - +
709D LYS* 3.8 47.1 - - + +
724D ALA* 5.1 1.1 - - + -
773D LEU* 4.1 17.0 - - + -
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Residues in contact with GLY 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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91D FMM 5.5 3.4 - - - -
698D VAL* 3.7 9.4 - - - +
699D LEU* 1.3 81.0 - - - +
701D SER* 1.3 57.0 + - - -
702D GLY 4.0 0.9 - - - -
706D THR* 3.6 1.4 - - - +
707D VAL* 2.6 42.0 + - - +
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Residues in contact with SER 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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698D VAL* 4.8 2.9 - - - +
700D GLY* 1.3 71.6 - - - -
702D GLY* 1.3 67.1 + - - +
705D GLY 3.5 5.6 - - - -
706D THR* 3.9 22.7 - - - +
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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