Contacts of the helix formed by residues 782 - 787 (chain A) in PDB entry 4C3I
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 782 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A ILE* 4.2 5.8 - - - -
678A VAL* 3.4 13.0 - - - +
753A ASN* 3.0 16.3 + - - +
754A LYS* 2.8 36.4 + - + -
755A ILE* 3.3 28.7 + - - +
780A ILE* 3.8 4.5 - - - +
781A LEU* 1.3 74.2 - - - +
783A LYS* 1.4 59.6 + - - +
784A SER* 3.1 21.1 - - - +
785A GLN* 3.2 14.8 + - - +
786A TYR* 3.4 20.2 + - - -
931A SER* 3.4 10.9 - - - +
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Residues in contact with LYS 783 (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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669A LEU 5.5 0.2 - - - +
674A ILE* 3.7 28.5 - - + +
754A LYS* 3.8 23.3 - - - +
782A ASP* 1.4 71.7 - - - +
784A SER* 1.4 48.2 + - - +
785A GLN 3.2 3.1 - - - -
787A GLY* 3.2 23.5 + - - +
788A ALA 5.7 5.8 - - - +
789A SER* 2.7 30.3 + - - -
931A SER 3.3 19.7 + - - +
932A GLY* 3.7 22.1 + - - +
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Residues in contact with SER 784 (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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752A LYS 3.6 20.3 + - - -
753A ASN* 3.9 1.5 - - - -
754A LYS* 3.9 29.6 + - - +
782A ASP* 3.3 16.5 - - - +
783A LYS* 1.4 74.0 - - - +
785A GLN* 1.3 67.1 + - - +
789A SER* 3.2 23.5 + - - -
790A LYS 4.9 2.1 - - - +
792A GLY* 3.5 11.1 - - - -
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Residues in contact with GLN 785 (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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749A LEU* 4.3 1.2 - - - +
751A SER* 3.1 23.6 + - - -
752A LYS 2.9 27.5 + - - -
753A ASN* 4.5 0.4 - - - +
769A VAL* 3.7 18.1 - - + +
781A LEU* 3.8 24.5 - - + -
782A ASP 3.2 14.7 + - - +
783A LYS 3.2 1.0 - - - -
784A SER* 1.3 96.7 + - - +
786A TYR* 1.3 59.8 + - - +
787A GLY 3.5 5.5 + - - +
789A SER* 4.6 2.3 + - - +
792A GLY* 3.6 5.9 - - - -
793A ILE* 3.0 53.6 + - + +
794A VAL* 3.4 12.5 + - - +
795A HIS 4.9 0.3 + - - -
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Residues in contact with TYR 786 (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 GLY* 3.5 3.8 - - - -
669A LEU* 3.0 41.3 + - + -
673A HIS 2.7 36.2 + - - -
674A ILE* 3.1 22.2 + - + -
677A GLY* 3.0 17.9 - - - -
781A LEU* 3.2 43.5 + - + -
782A ASP 3.4 7.0 + - - -
785A GLN* 1.3 74.8 - - + +
787A GLY* 1.3 61.0 + - - +
793A ILE* 4.8 2.0 - - + -
794A VAL* 3.6 22.0 - - + -
810A LEU* 3.9 4.3 - - + +
813A LEU* 3.9 15.3 - - + -
817A PHE* 3.5 23.6 - + - -
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Residues in contact with GLY 787 (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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657A TYR* 4.5 6.6 + - - -
667A ARG 3.6 5.4 - - - +
668A GLY* 3.7 5.6 - - - -
669A LEU 3.8 16.4 - - - -
783A LYS* 3.2 27.3 + - - +
785A GLN 3.5 2.1 - - - +
786A TYR* 1.3 83.3 - - - +
788A ALA* 1.3 58.3 + - - -
789A SER* 2.9 16.5 + - - +
794A VAL* 5.3 1.0 - - - +
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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