Contacts of the helix formed by residues 675 - 680 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A GLY 4.2 7.7 - - - +
413A SER* 2.9 18.5 + - - +
414A ARG* 2.9 46.8 + - + +
674A ALA* 1.3 70.0 - - - +
676A TRP* 1.3 64.1 + - - +
677A VAL* 3.3 22.7 + - - +
678A TRP* 2.9 8.9 + - - -
679A ILE* 2.9 23.5 + - - +
697A ASN* 3.8 26.1 + - - +
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Residues in contact with TRP 676 (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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674A ALA 3.6 5.7 + - - -
675A ASP* 1.3 72.5 + - - +
677A VAL* 1.3 66.5 + - + +
679A ILE* 4.3 0.9 - - - +
680A VAL* 3.0 45.2 + - + +
690A VAL 3.3 10.0 + - - -
691A PHE* 3.2 53.4 + + - -
693A GLN 3.2 22.4 + - - -
695A MET* 3.7 18.6 - - + -
697A ASN* 5.7 0.2 - - - +
334B SER* 3.5 33.2 - - - +
676B TRP* 4.2 13.9 - + - -
677B VAL* 3.6 42.6 - - + -
680B VAL* 6.2 0.7 - - + -
760B H4B 3.5 20.1 - - + -
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Residues in contact with VAL 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLY* 3.7 26.2 - - - +
334A SER* 4.5 3.4 - - - -
675A ASP* 3.2 10.5 + - - +
676A TRP* 1.3 83.5 - - + +
678A TRP* 1.3 66.4 + - + +
680A VAL* 4.1 7.6 - - - +
760A H4B 3.1 52.2 + - - +
676B TRP* 3.7 38.7 - - + -
677B VAL* 4.1 15.9 - - + -
691B PHE* 5.0 0.5 - - - -
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Residues in contact with TRP 678 (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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336A MET* 3.3 25.8 - - + +
414A ARG* 3.4 70.2 - - + +
416A VAL* 5.8 0.7 - - - +
675A ASP* 2.9 14.8 + - - +
677A VAL* 1.3 88.8 - - + +
679A ILE* 1.3 63.2 + - - +
680A VAL 3.5 4.6 - - - +
681A PRO* 5.5 0.7 - - - +
706A TYR* 3.7 4.0 - - - -
750A HEM 3.3 66.9 - - + +
760A H4B 3.0 75.3 + + - -
800A L5Z 3.9 7.2 - + - -
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Residues in contact with ILE 679 (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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413A SER 3.7 17.5 - - - +
414A ARG 4.0 4.3 - - - +
415A CYS 3.7 25.8 - - - +
416A VAL* 3.7 27.6 - - + +
589A MET* 5.5 2.8 - - - +
655A THR* 4.3 3.5 - - - +
658A PHE* 3.8 30.1 - - + -
675A ASP 2.9 24.5 + - - +
676A TRP 4.2 1.8 - - - +
678A TRP* 1.3 77.2 - - - +
680A VAL* 1.3 65.4 + - - +
681A PRO* 3.3 10.9 - - - +
690A VAL* 3.9 11.0 - - + +
695A MET* 3.8 28.0 - - + -
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Residues in contact with VAL 680 (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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676A TRP* 3.0 60.3 + - + +
677A VAL 4.1 8.9 - - - +
678A TRP 3.9 6.8 - - - +
679A ILE* 1.3 75.2 - - + +
681A PRO* 1.3 83.5 - - + +
682A PRO* 3.8 1.4 - - - +
685A GLY* 3.9 20.6 - - - +
690A VAL* 4.0 9.4 - - + +
691A PHE* 4.0 21.1 - - + -
760A H4B 5.1 2.9 + - - -
676B TRP* 6.1 1.1 - - + -
691B PHE* 5.3 4.2 - - - -
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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