Contacts of the helix formed by residues 684 - 692 (chain D) in PDB entry 3DXE
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 ASN 684 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C VAL* 2.8 24.0 + - - +
609C LEU* 2.8 35.8 + - + +
610C SER 3.1 10.8 + - - +
654C CYS* 3.3 33.4 - - - +
682D TYR* 3.7 8.2 + - + -
683D GLU* 1.3 69.8 - - - +
685D PRO* 1.4 68.1 - - - +
686D THR* 2.9 36.0 + - - -
687D TYR* 3.3 13.3 + - - +
688D LYS* 3.5 14.1 + - - +
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Residues in contact with PRO 685 (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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654C CYS 4.6 1.1 - - - +
655C MET* 5.3 1.3 - - + -
658C TYR* 3.7 42.8 - - + -
682D TYR* 3.0 28.9 - - + +
683D GLU 3.2 8.5 - - - +
684D ASN* 1.4 85.0 - - - +
686D THR* 1.3 65.1 + - - +
688D LYS* 3.4 16.7 + - + +
689D PHE* 2.9 26.3 + - - +
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Residues in contact with THR 686 (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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606C VAL* 4.6 0.7 - - - -
607C ARG* 3.9 22.4 - - + -
654C CYS 2.9 24.3 + - - -
657C ARG* 3.6 25.1 - - + +
658C TYR* 3.1 18.3 + - - +
661C CYS* 4.2 7.6 - - + -
684D ASN* 2.9 15.9 + - - -
685D PRO* 1.3 78.8 - - - +
687D TYR* 1.3 60.6 + - - +
689D PHE* 3.4 2.8 + - - +
690D PHE* 3.3 36.0 + - + -
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Residues in contact with TYR 687 (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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556C PRO* 4.5 8.4 - - + +
557C VAL* 6.2 1.3 - - + -
607C ARG 3.5 20.8 + - - +
608C PHE* 4.2 16.4 - + - -
609C LEU 3.5 18.8 - - - +
610C SER* 3.7 28.9 - - - -
626C ALA* 3.7 23.0 - - + +
629C PRO 5.2 2.8 + - - -
632C PHE* 3.7 22.9 - + - -
684D ASN* 3.3 10.8 + - - +
685D PRO 3.2 0.8 - - - -
686D THR* 1.3 76.5 - - - +
688D LYS* 1.3 70.2 + - + +
690D PHE* 3.5 2.5 + - - +
691D GLU* 2.8 63.2 + - + +
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Residues in contact with LYS 688 (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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683D GLU* 3.1 39.7 + - + +
684D ASN 3.5 6.4 + - - +
685D PRO* 3.4 23.0 + - + +
687D TYR* 1.3 83.4 - - + +
689D PHE* 1.3 55.1 + - - +
691D GLU* 3.0 7.6 + - + -
692D GLN* 2.7 56.8 + - + +
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Residues in contact with PHE 689 (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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658C TYR* 3.6 17.3 - + + -
661C CYS* 3.4 46.9 - - + -
662C LEU* 3.6 25.1 - - + -
665C ARG* 3.4 37.5 - - + -
685D PRO 2.9 21.3 + - - +
686D THR* 3.5 4.5 - - - +
687D TYR 3.3 0.2 - - - -
688D LYS* 1.3 73.1 - - - +
690D PHE* 1.3 87.7 + + - +
692D GLN* 3.6 14.6 + - - +
693D MET* 3.9 26.5 + - + +
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Residues in contact with PHE 690 (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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607C ARG* 3.4 71.1 - - + +
608C PHE* 6.0 3.1 - - + -
657C ARG* 4.4 3.6 - - - -
661C CYS* 3.7 31.9 - - + -
686D THR* 3.3 23.6 + - + +
687D TYR 4.2 2.5 - - - +
689D PHE* 1.3 93.3 - + - +
691D GLU* 1.3 64.0 + - - +
693D MET* 3.4 37.2 + - + +
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Residues in contact with GLU 691 (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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629C PRO 5.3 4.3 - - - +
687D TYR* 2.8 54.0 + - + +
688D LYS* 3.0 11.2 + - + +
690D PHE* 1.3 74.0 - - - +
692D GLN* 1.3 58.6 + - + +
693D MET 3.0 15.6 + - - +
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Residues in contact with GLN 692 (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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688D LYS* 2.7 41.8 + - - +
689D PHE* 4.0 8.2 - - - +
690D PHE 3.4 0.2 - - - -
691D GLU* 1.3 70.9 - - + +
693D MET* 1.3 63.5 + - + +
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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