Contacts of the helix formed by residues 683 - 687 (chain C) in PDB entry 4OIN
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 683 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677C MET 2.7 29.3 + - - -
678C PRO* 3.5 1.3 - - - +
679C PHE* 2.8 29.1 + - - +
681C GLY 4.5 0.3 - - - -
682C TYR* 1.3 78.7 + - - +
684C PHE* 1.3 65.9 + - - +
685C GLU 3.5 1.4 + - - -
686C ASP 3.6 3.5 + - - -
687C ALA 3.2 28.5 + - - +
689C VAL* 4.0 4.5 - - + +
870C ILE* 3.6 23.4 - - - +
872C ASN* 3.3 38.5 + - + +
784D ASP* 4.0 2.4 - - - +
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Residues in contact with PHE 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C GLY* 3.1 23.7 + - - +
682C TYR 3.4 0.6 - - - -
683C ASN* 1.3 80.1 + - - +
685C GLU* 1.3 91.1 + - + +
687C ALA* 3.3 8.5 + - - +
872C ASN* 4.2 0.2 - - - +
633D VAL* 3.8 18.1 - - + +
730D PRO* 3.5 36.1 - - + -
733D CYS* 4.1 9.4 - - + -
740D PHE* 3.3 15.2 - + - -
782D SER* 3.8 22.2 - - - -
783D ARG* 3.6 23.8 - - + -
784D ASP* 3.4 24.5 - - - +
785D ILE* 5.0 2.5 - - + -
939D PHE* 3.7 20.4 - + + -
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Residues in contact with GLU 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683C ASN 3.5 1.2 + - - -
684C PHE* 1.3 103.8 - - + +
686C ASP* 1.3 65.7 + - - +
687C ALA 3.1 3.5 + - - -
872C ASN* 5.1 1.0 - - - +
733D CYS* 4.9 7.3 - - + +
734D GLU* 5.7 1.7 + - - -
738D ALA 4.6 6.2 - - - +
739D ASP* 4.0 15.9 - - + +
740D PHE* 3.0 36.5 + - + -
782D SER* 5.3 1.0 + - - -
783D ARG* 3.3 39.7 + - - +
784D ASP* 4.6 2.2 + - - -
1029D ARG* 4.0 13.3 + - - -
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Residues in contact with ASP 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683C ASN 3.6 3.6 + - - -
684C PHE 3.4 0.6 - - - -
685C GLU* 1.3 77.2 - - - +
687C ALA* 1.3 67.4 + - - +
688C ILE* 3.6 3.8 - - - +
845C ASN* 5.1 5.2 - - - +
846C LYS* 3.7 19.0 + - - +
847C GLY* 3.2 21.6 - - - -
872C ASN* 5.6 3.9 - - - +
875C GLY* 4.3 6.9 - - - -
879C ARG* 2.5 47.4 + - - -
739D ASP* 4.3 8.3 - - - +
740D PHE 4.3 1.3 - - - -
741D ASP* 4.3 19.8 - - + +
1029D ARG* 4.9 2.9 + - - -
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Residues in contact with ALA 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682C TYR 3.3 20.2 - - - +
683C ASN* 3.2 21.9 - - - +
684C PHE 3.3 14.0 + - - +
685C GLU 3.1 5.1 + - - -
686C ASP* 1.3 81.5 - - - +
688C ILE* 1.3 61.5 + - - +
848C VAL 3.6 7.4 - - - +
850C ALA* 3.6 15.3 - - + -
870C ILE 4.9 0.2 - - - +
871C LEU* 5.7 0.3 - - - -
872C ASN* 5.2 2.6 + - - +
633D VAL* 3.9 5.4 - - + -
740D PHE* 3.6 17.7 - - + +
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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
------------------------------------------------------------
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