Contacts of the strand formed by residues 869 - 873 (chain A) in PDB entry 3TJP
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 CYS 869 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A 13K 6.1 0.2 - - - -
787A TYR* 4.1 1.8 - - - +
838A LEU* 4.0 28.9 - - - -
841A ASP* 3.9 25.4 - - - -
842A MET* 3.4 18.1 - - - +
845A LEU* 3.3 24.4 - - + +
849A ARG* 4.6 3.0 - - - +
867A TYR* 3.5 5.6 + - + -
868A GLY* 1.3 74.6 - - - +
870A ILE* 1.3 76.7 + - - +
878A MET 3.6 11.7 - - - -
879A ILE* 4.2 7.2 - - + -
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Residues in contact with ILE 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694A PHE* 4.8 7.2 - - + -
697A TRP* 4.2 34.3 - - + +
698A PHE* 4.3 11.2 - - + -
786A PRO* 4.2 9.2 - - + +
787A TYR* 3.7 37.2 - - + +
838A LEU* 4.5 0.6 - - - +
842A MET* 3.5 18.2 - - + -
869A CYS* 1.3 88.2 - - - +
871A SER* 1.3 73.7 + - - +
872A THR* 3.4 6.7 + - + +
877A GLY* 3.4 0.5 - - - -
878A MET* 3.0 43.9 + - + +
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Residues in contact with SER 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A TRP* 4.4 1.7 - - - +
701A SER* 3.2 35.4 + - - -
705A GLN* 2.9 21.8 + - - -
838A LEU* 3.9 8.9 + - - +
839A ARG* 3.4 26.8 + - - +
842A MET* 3.3 17.0 - - - -
870A ILE* 1.3 77.3 - - - +
872A THR* 1.3 58.2 + - - +
873A GLY 3.4 8.7 + - - -
876A ILE 3.8 7.2 + - - -
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Residues in contact with THR 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A TRP* 4.1 21.4 - - + -
700A ARG* 5.0 12.9 + - - +
701A SER* 5.0 3.1 - - - +
704A ALA* 4.1 10.6 - - - +
739A ILE* 3.9 30.0 - - + +
743A GLN* 2.3 31.6 + - - +
832A PHE* 5.0 0.4 - - + -
870A ILE* 3.4 16.1 + - + +
871A SER* 1.3 74.1 - - - +
873A GLY* 1.3 56.7 + - - +
876A ILE 3.2 4.7 + - - -
877A GLY* 3.2 18.9 - - - -
878A MET* 4.6 6.7 - - + +
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Residues in contact with GLY 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A SER 5.1 0.2 + - - -
704A ALA* 3.9 17.3 - - - -
705A GLN* 2.9 27.8 + - - +
743A GLN* 5.8 0.4 - - - -
871A SER* 3.4 8.4 + - - -
872A THR* 1.3 80.0 - - - +
874A ASP* 1.3 64.1 + - - -
875A LYS 3.4 1.2 + - - -
876A ILE* 3.4 16.5 + - - +
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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