Contacts of the helix formed by residues 513 - 517 (chain C) in PDB entry 1M7X
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 TYR 513 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462C ASP* 6.2 0.2 - - - -
482C ASN* 2.8 27.2 + - - -
484C GLY* 3.7 6.2 - - - -
485C TRP* 3.1 21.8 + - - +
488C ASP* 5.4 0.8 + - - -
509C PHE* 3.1 57.7 - + + -
510C GLY* 3.3 17.3 - - - -
512C LEU* 1.3 76.9 - - + +
514C ASN* 1.3 62.1 + - - +
515C TYR 3.3 2.9 - - - -
516C THR* 2.7 40.8 + - + +
519C PHE* 3.3 31.8 - + - -
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Residues in contact with ASN 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ASN* 5.0 1.6 - - - +
510C GLY 3.7 13.8 + - - +
511C ILE* 3.3 23.0 - - + +
512C LEU 3.3 1.2 - - - -
513C TYR* 1.3 79.9 - - - +
515C TYR* 1.3 83.2 + - + +
516C THR 3.0 5.8 + - - -
517C GLU 3.1 21.8 + - - +
519C PHE* 4.0 22.3 - - - +
560C PHE* 5.2 1.6 - - - -
561C PRO* 3.6 30.5 + - - +
562C GLY* 5.1 0.6 - - - +
620C ASP 3.5 12.0 + - - +
621C PHE* 5.3 8.2 - - - -
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Residues in contact with TYR 515 (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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468C ARG* 3.6 11.3 + - - +
511C ILE* 4.0 25.0 - - + +
512C LEU 5.0 4.9 + - - +
513C TYR 3.3 1.8 + - - -
514C ASN* 1.3 93.4 + - + +
516C THR* 1.3 61.0 + - + +
517C GLU 3.7 0.7 - - - -
561C PRO* 5.0 0.2 - - - +
620C ASP 3.8 4.2 + - - -
621C PHE* 3.4 27.8 - - - +
622C ASP 3.6 6.4 + - - -
623C PRO* 3.4 48.6 + - + +
626C PHE* 3.7 23.7 - - - +
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Residues in contact with THR 516 (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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465C GLY* 5.2 0.5 + - - -
468C ARG* 2.7 32.9 + - - +
512C LEU 5.4 0.7 - - - +
513C TYR* 2.7 34.8 + - + +
514C ASN 3.0 0.6 + - - -
515C TYR* 1.3 81.5 - - - +
517C GLU* 1.3 77.4 + - - +
519C PHE* 4.3 3.8 - - - -
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Residues in contact with GLU 517 (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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463C PHE 4.0 5.4 - - - +
464C PRO* 4.4 0.9 - - - +
465C GLY 3.2 13.5 + - - -
466C VAL* 3.0 24.7 + - - +
467C SER* 2.6 43.8 + - - +
468C ARG* 3.1 5.6 - - - +
480C LYS* 3.8 23.7 + - + +
513C TYR 4.4 0.2 + - - -
514C ASN* 3.1 16.0 + - - +
516C THR* 1.3 96.2 + - - +
518C ASN* 1.3 54.3 + - - +
519C PHE* 2.7 44.4 + - + -
621C PHE* 4.7 2.6 - - - -
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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