Contacts of the strand formed by residues 683 - 689 (chain C) in PDB entry 2P5G
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 MSE 683 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C PHE* 3.4 38.1 - - + +
411C ASP 3.2 7.0 - - - +
412C LEU* 3.6 22.9 - - + +
594C LEU* 4.4 9.4 - - + -
597C ILE* 3.9 24.0 - - + -
623C ASP 3.4 27.8 - - - +
625C ILE* 4.5 6.5 - - + -
660C GLU* 4.3 15.8 - - - +
663C ILE* 3.8 29.5 - - + +
667C PHE* 4.2 12.6 - - + -
681C MSE 3.7 2.6 + - - -
682C PHE* 1.3 71.9 - - - +
684C ASP* 1.3 73.6 + - - +
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Residues in contact with ASP 684 (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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410C PHE* 3.3 6.4 - - - -
411C ASP* 2.7 40.9 + - - +
413C THR* 3.0 30.1 - - + +
660C GLU* 5.0 5.8 - - - +
682C PHE* 4.5 4.0 - - - +
683C MSE 1.3 84.2 + - - +
685C ARG* 1.3 65.7 + - - +
686C GLU* 3.3 14.0 + - - +
716C GLU* 5.3 5.5 - - + +
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Residues in contact with ARG 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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408C MSE 4.4 3.4 - - + -
409C SER 3.6 7.6 - - - +
410C PHE* 3.7 28.7 - - + -
652C ASP* 3.0 36.0 + - - +
655C ALA* 4.0 14.3 - - + +
660C GLU* 4.1 17.4 + - - +
684C ASP* 1.3 73.1 - - - +
686C GLU* 1.3 86.1 + - - +
687C ALA 4.0 2.5 - - - +
688C ILE* 3.4 29.6 - - - +
714C ASP* 2.7 42.2 + - - -
716C GLU* 3.7 23.1 - - - +
717C GLY* 3.8 13.3 - - - +
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Residues in contact with GLU 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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409C SER* 2.8 24.2 + - - +
411C ASP* 3.3 41.1 - - + +
684C ASP* 3.3 11.9 + - - +
685C ARG* 1.3 86.2 + - - +
687C ALA* 1.3 60.6 + - - +
714C ASP 3.3 1.0 - - - +
715C MSE 3.2 24.8 - - - +
716C GLU* 2.9 65.6 + - - +
726C LYS* 6.3 1.1 - - - -
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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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407C VAL* 5.5 0.9 - - + +
408C MSE 3.1 9.5 - - - +
409C SER* 2.9 37.7 + - - +
685C ARG* 4.0 2.1 - - - -
686C GLU* 1.3 79.4 - - - +
688C ILE* 1.3 63.9 + - - +
689C ALA* 4.1 1.6 - - + +
710C LEU* 5.1 6.5 - - + -
712C VAL* 3.7 27.8 - - + -
714C ASP 3.4 5.2 - - - -
715C MSE 4.0 11.9 - - + -
726C LYS* 4.7 7.0 - - + -
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Residues in contact with ILE 688 (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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407C VAL 3.5 3.4 - - - +
408C MSE 3.7 16.6 - - + -
647C TRP* 3.7 25.4 - - + -
648C VAL* 3.7 24.0 - - + +
651C LEU* 4.2 14.1 - - + -
652C ASP* 3.5 31.6 - - + +
685C ARG* 3.4 33.4 - - - +
687C ALA* 1.3 74.8 - - - +
689C ALA* 1.3 62.1 + - - +
712C VAL* 3.4 2.2 - - - -
713C TRP* 2.9 27.6 + - - +
714C ASP* 3.0 15.2 + - + +
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Residues in contact with ALA 689 (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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405C LYS 4.3 0.4 - - - -
406C TYR* 3.4 3.6 - - - +
407C VAL* 2.7 39.7 + - + +
647C TRP* 3.9 10.4 - - - -
651C LEU* 5.5 0.5 - - - +
687C ALA* 4.1 1.8 - - + -
688C ILE* 1.3 76.1 - - - +
690C GLY* 1.3 59.8 + - - +
699C GLY 5.0 1.1 - - - +
710C LEU* 3.9 27.1 - - + -
711C ASN 3.1 28.7 - - - +
712C VAL* 4.0 4.5 - - + +
713C TRP* 4.3 0.2 - - - -
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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