Contacts of the helix formed by residues 513 - 521 (chain D) in PDB entry 2NYM
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 GLY 513 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475D LYS* 4.5 12.7 - - - +
509D SER 4.6 1.6 + - - -
511D VAL* 3.7 1.4 - - - +
512D CYS* 1.3 91.2 - - - +
514D GLN* 1.3 66.5 + - - -
515D ASP* 3.1 3.5 + - - -
517D THR* 3.0 15.5 + - - -
550D ILE* 4.4 5.8 - - - -
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Residues in contact with GLN 514 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513D GLY* 1.3 70.9 - - - +
515D ASP* 1.3 61.1 + - - +
517D THR* 3.9 1.2 - - - -
518D THR* 2.8 35.1 + - - +
550D ILE* 3.3 32.3 + - + +
551D LEU 4.4 0.8 - - - -
552D ASP* 3.6 40.0 - - - +
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Residues in contact with ASP 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D GLY* 3.1 2.1 - - - -
514D GLN* 1.3 75.5 - - - +
516D ILE* 1.3 63.1 + - + +
517D THR 3.0 0.2 - - - -
518D THR* 2.6 30.7 + - - -
519D LYS* 3.0 43.2 + - - +
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Residues in contact with ILE 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D LYS* 3.3 46.9 - - + +
476D GLU* 4.7 1.3 - - - +
479D HIS* 4.1 27.6 - - + -
483D ILE* 4.6 16.2 - - + -
512D CYS* 3.2 26.4 + - + +
513D GLY* 5.5 0.2 - - - -
515D ASP* 1.3 77.6 - - + +
517D THR* 1.3 62.8 + - - +
519D LYS* 5.2 0.2 - - - -
520D HIS* 3.0 40.8 + - + +
521D MSE 3.7 3.5 + - + +
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Residues in contact with THR 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D SER* 3.7 22.1 + - - -
512D CYS* 3.9 3.6 + - - +
513D GLY 3.0 17.3 + - - -
514D GLN 3.9 2.7 - - - -
515D ASP 2.7 4.6 + - - -
516D ILE* 1.3 75.7 - - - +
518D THR* 1.3 59.1 + - - +
521D MSE 3.0 44.0 + - + +
522D LEU* 2.8 28.4 + - + +
547D ILE* 4.4 17.3 - - + -
550D ILE* 4.1 13.7 - - + +
551D LEU* 4.7 8.7 - - + -
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Residues in contact with THR 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D GLN* 2.8 23.3 + - - +
515D ASP* 2.6 9.9 + - - -
517D THR* 1.3 73.8 - - - +
519D LYS* 1.3 62.7 + - + +
522D LEU* 3.7 21.0 - - + +
523D PRO* 3.8 5.5 - - - +
551D LEU* 2.9 27.3 - - + +
552D ASP* 4.9 4.8 + - - +
555D THR* 4.2 24.2 - - + +
559D GLU* 5.7 0.4 - - - +
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Residues in contact with LYS 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D ASP* 3.0 36.0 + - - +
518D THR* 1.3 82.8 - - + +
520D HIS* 1.3 83.9 + - + +
521D MSE 3.9 0.2 - - - -
523D PRO* 3.7 12.9 - - - +
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Residues in contact with HIS 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D HIS* 3.2 46.2 + + - -
483D ILE* 4.1 16.4 - - + -
487D LEU* 3.1 28.1 - - + +
516D ILE* 3.0 25.9 + - + +
519D LYS* 1.3 98.4 + - + +
521D MSE 1.3 63.1 + - - +
523D PRO* 3.7 6.2 - - - +
524D THR* 3.8 3.5 + - - -
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Residues in contact with MSE 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D ILE* 3.9 26.2 - - + -
486D VAL* 6.5 0.4 - - - -
487D LEU* 5.1 0.9 - - + -
505D ILE* 4.1 35.1 - - + +
508D LEU* 3.8 22.7 - - - -
509D SER* 3.4 26.2 - - - +
512D CYS* 4.6 3.1 - - + -
516D ILE 3.9 6.5 - - - +
517D THR* 3.0 47.6 + - + +
520D HIS* 1.3 83.4 - - - +
522D LEU* 1.3 67.7 + - - +
523D PRO* 2.8 4.6 - - - +
524D THR* 2.9 16.4 + - - -
525D VAL* 3.2 15.0 + - - +
547D ILE* 5.9 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