Contacts of the strand formed by residues 883 - 887 (chain D) in PDB entry 5TWV
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 883 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678D CYS* 6.2 0.2 - - - -
703D ILE* 5.6 6.5 - - - -
704D PRO 4.3 5.6 - - - -
705D ARG* 4.0 13.1 - - - +
706D GLY* 3.4 19.7 - - - +
707D GLN 4.5 1.6 - - - -
849D ASN 2.9 24.4 + - - +
850D VAL* 3.3 18.8 - - - +
851D VAL 3.5 1.4 + - - -
881D LYS 3.7 0.2 + - - -
882D ARG* 1.3 73.0 - - - +
884D VAL* 1.3 60.1 + - - +
885D VAL 4.2 0.2 - - - -
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Residues in contact with VAL 884 (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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707D GLN 3.2 22.0 + - - +
708D LEU* 4.0 5.3 - - + -
709D THR* 3.8 11.4 + - - -
851D VAL* 4.2 14.4 - - + +
876D LEU* 4.8 21.8 - - + -
882D ARG* 3.8 5.0 + - + +
883D THR* 1.3 74.1 - - - +
885D VAL* 1.3 59.1 + - - +
886D LEU* 4.1 2.6 + - + +
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Residues in contact with VAL 885 (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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709D THR* 4.0 11.9 - - + +
851D VAL* 2.9 28.2 + - - +
852D PHE* 3.6 4.9 - - + -
853D LEU* 3.2 17.2 + - - +
883D THR 4.2 1.0 + - - -
884D VAL* 1.3 72.1 - - - +
886D LEU* 1.3 59.5 + - - +
887D VAL 3.8 1.2 + - - -
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Residues in contact with LEU 886 (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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709D THR 3.2 13.1 + - - +
710D MET* 3.3 24.8 - - - +
711D ILE* 3.4 1.5 + - - -
853D LEU* 4.1 13.0 - - + -
856D PRO* 5.9 2.7 - - + -
884D VAL* 4.1 3.0 + - + +
885D VAL* 1.3 70.3 - - - +
887D VAL* 1.3 66.1 + - - +
888D THR* 3.6 4.9 + - + +
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Residues in contact with VAL 887 (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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711D ILE* 3.6 23.5 - - + +
719D LYS* 5.4 14.1 - - + +
723D LEU* 5.6 7.6 - - + -
853D LEU 3.0 27.8 + - - +
854D ASP* 4.4 7.2 - - + -
855D ASP* 3.2 12.8 + - - +
856D PRO* 3.8 5.5 - - - +
885D VAL 3.8 2.4 - - - -
886D LEU* 1.3 73.6 - - - +
888D THR* 1.3 62.7 + - - +
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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