Contacts of the helix formed by residues 771 - 778 (chain D) in PDB entry 3T6A
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 ASP 771 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543D LEU* 4.5 6.2 - - - +
547D ASN* 5.6 3.3 + - - +
551D VAL* 6.1 1.1 - - + -
555D HIS* 2.9 17.9 + - + +
769D GLN 3.5 2.4 + - - +
770D PRO* 1.3 73.2 - - - +
772D GLU* 1.3 67.0 + - - +
773D GLU* 3.2 12.4 + - - +
774D MET* 3.1 30.1 + - + +
775D ASN* 3.0 22.7 + - - +
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Residues in contact with GLU 772 (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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523D LYS* 2.7 46.0 + - - +
524D PHE* 3.4 17.7 - - + -
770D PRO 3.7 4.2 + - - -
771D ASP* 1.3 74.8 + - - +
773D GLU* 1.3 62.2 + - - +
775D ASN* 3.2 7.3 + - - +
776D GLU* 3.0 28.3 + - + +
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Residues in contact with GLU 773 (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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524D PHE* 3.4 48.2 - - + -
539D ARG* 3.7 31.1 + - - +
543D LEU* 3.7 31.9 - - + +
771D ASP* 3.3 10.5 + - - +
772D GLU* 1.3 75.7 - - - +
774D MET* 1.3 66.8 + - - +
776D GLU* 3.1 11.8 + - + +
777D ILE* 3.2 10.7 + - - +
782D PHE* 5.8 0.2 - - - -
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Residues in contact with MET 774 (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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543D LEU* 3.7 22.4 - - + +
544D PHE* 3.9 24.7 - - + -
547D ASN* 3.1 45.5 - - + +
551D VAL* 4.9 2.5 - - + +
552D ILE* 4.1 17.9 - - + -
555D HIS* 3.2 43.1 - - + +
771D ASP* 3.1 16.6 + - + +
773D GLU* 1.3 76.8 - - - +
775D ASN* 1.3 61.4 + - - +
777D ILE* 3.3 6.1 - - - +
778D CYS* 3.3 24.5 + - - -
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Residues in contact with ASN 775 (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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555D HIS* 3.9 15.3 + - + -
558D SER* 4.9 12.9 + - - -
559D MET* 5.0 7.3 - - - +
562D ARG* 3.8 24.1 + - - +
770D PRO* 3.9 21.4 - - + +
771D ASP 3.0 19.7 + - - +
772D GLU* 3.4 7.2 - - - +
773D GLU 3.1 0.2 - - - -
774D MET* 1.3 78.4 - - - +
776D GLU* 1.3 63.5 + - - +
778D CYS* 3.8 12.2 + - - +
779D LYS* 3.7 22.3 - - - +
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Residues in contact with GLU 776 (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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520D PHE* 3.4 15.1 - - - -
521D GLU 4.5 0.9 - - - +
522D SER* 2.6 35.6 + - - +
523D LYS 5.5 0.7 - - - -
524D PHE* 3.7 17.7 - - + -
772D GLU* 3.0 22.0 + - + +
773D GLU* 3.1 8.5 + - + +
775D ASN* 1.3 78.2 - - - +
777D ILE* 1.3 60.5 + - - +
778D CYS 3.1 0.2 - - - -
779D LYS* 2.9 44.5 + - - +
782D PHE* 3.1 30.9 - - + +
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Residues in contact with ILE 777 (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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540D ALA* 3.7 26.0 - - + +
543D LEU* 4.1 15.0 - - + -
544D PHE* 3.2 49.4 - - + -
773D GLU 3.2 8.3 + - - +
774D MET* 3.3 13.9 - - - +
776D GLU* 1.3 80.5 - - - +
778D CYS* 1.3 63.6 + - - +
779D LYS 3.1 1.0 + - - +
782D PHE* 3.9 27.8 - - + -
783D GLN* 2.9 29.7 + - + +
786D LEU* 4.5 5.2 - - + -
840D UNX 4.3 7.9 - - - -
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Residues in contact with CYS 778 (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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544D PHE* 6.0 2.2 - - - -
552D ILE* 5.0 0.7 - - - -
555D HIS* 3.8 33.4 - - - +
556D VAL* 3.9 19.1 - - - -
559D MET* 3.2 21.9 - - + +
601D ARG* 3.0 27.8 + - - +
774D MET* 3.3 19.7 + - - +
775D ASN* 3.8 10.3 - - - +
776D GLU 3.1 0.6 - - - -
777D ILE* 1.3 84.3 - - - +
779D LYS* 1.3 57.3 + - - -
783D GLN* 3.6 7.8 + - - +
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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