Contacts of the helix formed by residues 675 - 680 (chain B) in PDB entry 4D2Y
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 675 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B GLY 4.2 7.8 - - - +
413B SER* 3.0 19.8 + - - +
414B ARG* 2.9 44.2 + - + +
674B ALA* 1.3 70.2 - - - +
676B TRP* 1.3 63.7 + - - +
677B VAL* 3.2 22.0 + - - +
678B TRP* 3.0 11.0 + - + -
679B ILE* 2.9 23.6 + - - +
697B ASN* 3.8 24.9 + - - +
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Residues in contact with TRP 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A SER* 3.5 30.5 - - - +
676A TRP* 4.2 13.2 - + - -
677A VAL* 3.7 49.4 - - + -
680A VAL* 6.1 0.9 - - + -
760A H4B 3.6 12.4 - - - -
674B ALA 3.6 5.9 + - - -
675B ASP* 1.3 72.0 + - - +
677B VAL* 1.3 68.4 + - + +
679B ILE* 4.4 1.1 - - - +
680B VAL* 3.1 41.0 + - + +
690B VAL 3.3 11.3 + - - -
691B PHE* 3.2 59.7 + + - -
693B GLN 3.2 21.9 + - - -
695B MET* 3.7 18.1 - - + -
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Residues in contact with VAL 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A TRP* 3.6 38.1 - - + -
677A VAL* 4.1 16.2 - - + -
691A PHE* 5.0 0.5 - - - -
333B GLY* 3.7 25.4 - - - +
334B SER* 4.4 2.7 - - - -
675B ASP* 3.2 10.7 + - - +
676B TRP* 1.3 82.3 - - + +
678B TRP* 1.3 65.3 + - + +
680B VAL* 4.1 7.8 - - - +
760B H4B 3.0 54.2 + - - +
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Residues in contact with TRP 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLY 5.9 0.2 - - - -
336B MET* 3.3 26.3 - - + +
414B ARG* 3.3 69.8 - - + +
416B VAL* 5.8 0.7 - - - +
675B ASP* 3.0 13.9 + - - +
677B VAL* 1.3 89.5 - - + +
679B ILE* 1.3 65.6 + - - +
680B VAL 3.4 4.1 - - - +
706B TYR* 3.6 14.4 - - - -
750B HEM 3.2 53.4 - - + +
760B H4B 3.1 71.7 + + - -
800B L5Z 3.8 8.3 - + - -
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Residues in contact with ILE 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B SER 3.7 20.9 - - - +
414B ARG 4.0 4.3 - - - +
415B CYS 3.7 10.8 - - - +
416B VAL* 3.7 41.8 - - + +
589B MET* 5.4 3.5 - - - +
655B THR* 4.5 0.2 - - - +
658B PHE* 3.8 24.2 - - + -
674B ALA* 4.4 0.2 - - + -
675B ASP 2.9 25.1 + - - +
676B TRP 3.3 2.2 + - - +
678B TRP* 1.3 77.2 - - - +
680B VAL* 1.3 65.9 + - - +
681B PRO* 3.3 10.4 - - - +
690B VAL* 3.8 14.2 - - + +
695B MET* 3.8 30.5 - - + -
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Residues in contact with VAL 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A TRP* 6.2 0.9 - - + -
691A PHE* 5.3 3.8 - - - -
676B TRP* 3.1 60.4 + - + +
677B VAL 4.1 7.7 - - - +
678B TRP 3.8 8.9 - - - +
679B ILE* 1.3 76.0 - - + +
681B PRO* 1.3 84.6 - - + +
682B PRO* 3.8 1.0 - - - +
685B GLY* 3.9 20.4 - - - +
688B THR* 4.9 0.2 - - - +
690B VAL* 4.0 7.9 - - + -
691B PHE* 4.0 19.1 - - + -
760B H4B 4.9 3.6 + - - -
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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