Contacts of the helix formed by residues 721 - 725 (chain D) in PDB entry 2BT4
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 TYR 721 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684D SER 2.9 9.4 + - - +
685D HIS 3.4 26.5 - - - -
686D THR* 3.9 7.6 - - - -
687D SER 3.9 28.3 - - - +
688D VAL* 3.7 29.6 - - + +
691D LEU* 3.4 25.0 - - + +
719D HIS 4.4 0.2 - - - -
720D SER* 1.3 69.5 - - - +
722D VAL* 1.3 66.8 + - + +
724D GLN* 3.1 37.6 + - - +
1086F THR* 5.4 2.4 - - + +
1116F PHE* 4.0 29.6 - + + +
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Residues in contact with VAL 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678D ILE* 4.3 4.9 - - + -
680D PRO* 3.8 26.0 - - + -
683D TYR 4.7 2.9 - - - +
684D SER* 4.3 9.9 - - - +
687D SER 5.1 0.7 - - - +
690D ILE* 4.0 24.9 - - + -
691D LEU* 4.9 7.2 - - - +
694D LEU* 3.8 22.7 - - + -
704D GLU* 3.6 28.9 - - + -
720D SER* 3.2 7.5 - - - +
721D TYR* 1.3 78.9 - - + +
723D SER* 1.3 57.5 + - - +
725D ARG* 3.1 6.8 + - - +
726D ALA* 2.9 25.7 + - + +
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Residues in contact with SER 723 (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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109A ASN* 2.9 27.0 + - - +
111A HIS* 3.8 25.9 + - - +
112A GLN* 3.1 8.1 + - - +
704D GLU* 2.5 29.0 + - - -
706D HIS* 5.1 0.2 + - - -
720D SER* 3.2 23.0 + - - -
721D TYR 3.1 0.8 - - - -
722D VAL* 1.3 76.2 - - - +
724D GLN* 1.3 57.9 + - - +
725D ARG 3.2 0.4 - - - -
726D ALA* 4.0 1.8 - - - +
729D VAL* 3.7 18.6 - - - +
2416D GOL 4.3 2.8 + - - -
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Residues in contact with GLN 724 (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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111A HIS* 4.7 11.9 - - + +
112A GLN* 3.2 23.8 + - - +
118A HIS* 6.5 0.7 - - - -
691D LEU* 4.0 12.0 - - + +
695D ASN* 5.3 0.9 - - - +
720D SER 3.8 10.2 - - - +
721D TYR* 3.2 36.6 + - - +
722D VAL 3.1 0.2 - - - -
723D SER* 1.3 78.7 - - - +
725D ARG* 1.3 55.6 + - - +
2416D GOL 5.2 8.3 - - - -
1114F GLU* 5.6 3.0 - - - +
1116F PHE* 3.3 32.4 - - - -
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Residues in contact with ARG 725 (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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112A GLN* 3.2 5.9 + - - +
691D LEU* 3.6 13.9 - - + +
694D LEU* 3.4 35.8 + - + -
695D ASN* 3.5 30.8 + - - +
697D CYS* 3.0 27.9 + - - +
698D ASP* 5.0 0.6 - - - +
699D GLY* 4.6 3.4 - - - +
700D LEU 3.0 19.4 + - - +
702D VAL* 3.7 15.2 - - + +
722D VAL 3.1 4.7 + - - +
724D GLN* 1.3 78.3 - - - +
726D ALA* 1.3 70.1 + - - +
727D ASP* 2.9 29.2 + - - +
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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