Contacts of the helix formed by residues 671 - 677 (chain A) in PDB entry 3DPK
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 LEU 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A GLY 4.0 0.4 + - - -
670A ASP* 1.3 71.2 - - - +
672A LEU* 1.3 61.2 + - - +
674A PHE* 3.2 5.0 + - + -
675A LEU* 2.8 48.2 + - + +
758A PHE* 3.9 35.7 - - + -
762A VAL* 5.4 1.3 - - + -
781A ALA* 3.4 11.9 - - + +
784A VAL* 2.8 37.0 + - + +
785A LEU* 4.6 0.4 - - - +
786A LEU* 4.1 20.8 - - + +
844A LEU* 4.3 10.3 - - + -
848A ILE* 4.0 29.8 - - + -
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Residues in contact with LEU 672 (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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2A SO4 4.4 5.8 - - - +
670A ASP* 3.3 9.3 - - - +
671A LEU* 1.3 79.1 - - - +
673A ASN* 1.3 59.9 + - - +
675A LEU* 3.3 3.9 + - + +
676A ARG* 3.0 72.3 + - - +
781A ALA* 3.4 11.2 + - + -
782A ARG* 3.8 33.0 - - + +
808A ASN* 6.2 0.7 - - - +
821A TRP* 6.3 0.9 - - + -
847A GLU* 4.1 20.0 - - - +
852A GLY* 3.9 18.8 - - - +
853A LEU 5.4 0.2 - - - +
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Residues in contact with ASN 673 (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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670A ASP* 2.9 40.0 + - - +
672A LEU* 1.3 74.9 - - - +
674A PHE* 1.3 65.9 + - - +
676A ARG* 3.3 13.2 + - - +
677A ARG* 3.1 39.8 + - - +
923A 8C5 6.2 2.2 - - - +
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Residues in contact with PHE 674 (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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668A TYR* 5.2 7.9 - - + +
670A ASP 3.2 14.6 + - - +
671A LEU* 3.5 9.2 - - + +
673A ASN* 1.3 72.7 - - - +
675A LEU* 1.3 69.2 + - - +
676A ARG 3.4 0.2 + - - -
677A ARG* 3.5 44.5 + - + +
697A LEU* 3.7 35.8 - - + +
758A PHE* 3.8 19.5 - + - -
786A LEU* 3.6 23.8 - - + -
790A HIS* 3.6 33.7 - + - -
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Residues in contact with LEU 675 (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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671A LEU* 2.8 44.3 + - + +
672A LEU* 3.5 8.1 - - - +
674A PHE* 1.3 77.5 - - + +
676A ARG* 1.3 61.8 + - - +
677A ARG 3.6 3.6 + - - +
697A LEU* 4.2 18.5 - - + +
755A LEU* 4.0 19.3 - - + -
758A PHE* 4.6 4.0 - - + -
781A ALA* 4.7 5.4 - - + -
847A GLU 3.6 24.0 - - - +
848A ILE* 3.7 28.0 - - + +
851A LEU* 3.5 31.2 - - + +
852A GLY* 4.0 5.6 - - - +
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Residues in contact with ARG 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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2A SO4 3.1 44.3 + - - -
672A LEU* 3.0 44.4 + - - +
673A ASN* 3.8 13.8 + - - +
674A PHE 3.2 0.6 - - - -
675A LEU* 1.3 78.0 - - - +
677A ARG* 1.3 64.7 + - - +
851A LEU 4.2 4.3 - - - +
852A GLY* 2.7 34.6 + - - +
853A LEU 4.2 0.8 - - - -
854A ASN* 4.0 13.5 - - - +
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Residues in contact with ARG 677 (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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668A TYR 4.3 13.3 + - - -
670A ASP 5.0 0.4 + - - -
673A ASN* 3.1 21.1 + - - +
674A PHE* 3.6 50.2 - - + +
675A LEU 3.4 6.8 - - - +
676A ARG* 1.3 82.0 - - - +
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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