Contacts of the helix formed by residues 455 - 463 (chain C) in PDB entry 5MS0
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 SER 455 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C ILE 5.1 2.2 - - - -
34C SER* 3.7 24.0 - - - -
147C SER* 4.8 6.0 - - - -
453C ILE 4.0 2.4 + - - -
454C ARG* 1.3 78.8 - - - +
456C VAL* 1.3 62.6 + - - +
457C GLY 3.4 3.1 - - - -
458C GLU* 3.5 14.8 + - - +
459C MET* 3.0 25.8 + - - +
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Residues in contact with VAL 456 (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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30C ILE 5.3 4.2 + - - +
31C GLN* 5.9 4.9 - - + -
34C SER* 4.6 4.9 - - - -
35C PHE* 6.4 1.6 - - + -
145C ILE* 4.3 26.0 - - + +
146C VAL 5.9 0.4 - - - -
147C SER* 5.1 7.5 - - - +
455C SER* 1.3 72.9 - - - +
457C GLY* 1.3 61.1 + - - +
459C MET* 3.1 9.5 + - - +
460C ALA* 2.9 26.7 + - - +
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Residues in contact with GLY 457 (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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34C SER* 4.3 11.8 - - - -
35C PHE* 5.0 4.8 - - - +
38C PHE* 4.1 26.9 - - - +
48C GLY* 6.1 0.2 - - - -
455C SER* 3.4 2.6 - - - -
456C VAL* 1.3 81.2 - - - +
458C GLU* 1.3 55.9 + - - +
460C ALA* 3.1 9.1 + - - +
461C GLU* 2.9 26.9 + - - +
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Residues in contact with GLU 458 (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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454C ARG* 4.9 6.5 - - + -
455C SER* 3.5 25.6 + - - +
456C VAL 3.3 0.4 - - - -
457C GLY* 1.3 75.2 - - - +
459C MET* 1.3 57.8 + - - +
461C GLU* 3.4 9.5 + - - +
462C ASN* 2.9 28.4 + - - +
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Residues in contact with MET 459 (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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145C ILE* 5.8 6.5 - - + -
146C VAL 5.7 4.9 - - - +
147C SER* 6.5 0.4 - - - -
148C GLN* 6.5 1.8 - - + -
454C ARG* 5.9 3.3 - - + +
455C SER 3.0 14.9 + - - +
456C VAL* 3.1 12.7 + - - +
458C GLU* 1.3 74.9 - - - +
460C ALA* 1.3 59.3 + - - +
462C ASN* 3.2 8.4 + - - +
463C GLN* 2.9 28.2 + - - +
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Residues in contact with ALA 460 (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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456C VAL 2.9 12.4 + - - +
457C GLY* 3.1 11.4 + - - +
459C MET* 1.3 74.0 - - - +
461C GLU* 1.3 59.3 + - - +
463C GLN* 3.3 6.6 + - - +
464C PHE* 2.9 30.4 + - - +
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Residues in contact with GLU 461 (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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48C GLY* 4.7 22.9 - - - +
49C LEU* 5.1 2.9 - - - +
52C ALA* 5.1 9.5 - - + +
457C GLY 2.9 12.3 + - - +
458C GLU* 3.4 13.0 - - - +
460C ALA* 1.3 77.0 - - - +
462C ASN* 1.3 56.5 + - - +
464C PHE* 3.7 5.9 - - - +
465C ARG* 2.9 32.1 + - - +
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Residues in contact with ASN 462 (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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179C TYR* 6.5 0.9 - - + -
458C GLU 2.9 17.5 + - - +
459C MET* 3.2 8.7 + - - +
461C GLU* 1.3 75.3 - - - +
463C GLN* 1.3 56.9 + - - +
464C PHE 3.4 0.4 - - - -
465C ARG* 4.4 6.1 - - - +
466C VAL* 4.6 10.7 + - - +
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Residues in contact with GLN 463 (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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459C MET 2.9 15.1 + - - +
460C ALA* 3.3 8.0 + - - +
461C GLU 3.2 0.4 - - - -
462C ASN* 1.3 78.6 - - - +
464C PHE* 1.3 54.7 + - - +
465C ARG 3.8 0.4 - - - -
466C VAL* 4.5 6.9 - - - +
467C GLY 4.9 0.3 + - - -
498C ILE 5.2 0.7 - - - +
501C ALA* 4.1 24.0 - - - +
502C VAL* 4.1 17.5 - - + +
505C PHE* 4.4 23.3 - - + -
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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