Contacts of the strand formed by residues 439 - 444 (chain C) in PDB entry 1NYE
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 LYS 439 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430C HIS* 5.2 0.6 - - - -
431C TRP* 3.2 8.9 - - - -
432C GLU* 2.8 44.9 + - + +
437C ARG 4.3 12.4 + - - +
438C GLY* 1.3 79.3 - - - +
440C GLY* 1.3 59.2 + - - +
441C THR* 6.2 0.7 - - + -
454C TYR 4.4 2.9 - - - -
457C ASN* 5.9 1.0 + - - -
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Residues in contact with GLY 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C HIS* 2.9 17.9 - - - -
431C TRP* 3.9 3.6 - - - -
439C LYS* 1.3 78.5 - - - +
441C THR* 1.3 69.9 + - - +
453C PRO* 3.3 5.2 - - - +
454C TYR* 3.0 42.7 + - - +
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Residues in contact with THR 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ALA* 3.1 4.7 - - - -
430C HIS* 2.7 53.0 + - + +
439C LYS* 6.2 0.9 - - + -
440C GLY* 1.3 81.1 - - - +
442C VAL* 1.3 64.0 + - - +
443C SER* 4.5 1.9 + - - -
451C GLN* 3.1 55.3 + - + +
452C GLN 3.3 4.5 - - - -
453C PRO* 4.6 5.2 - - + -
454C TYR* 3.5 0.9 - - - -
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Residues in contact with VAL 442 (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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428C GLN 3.3 5.4 - - - +
429C ALA* 4.3 1.6 - - + -
441C THR* 1.3 75.2 - - - +
443C SER* 1.3 63.8 + - - +
449C LEU* 3.7 23.7 - - + +
452C GLN* 2.7 43.2 + - + +
454C TYR* 3.4 21.8 - - + -
466C THR* 4.4 18.8 - - + -
467C ASN* 6.6 0.2 - - - -
471C LEU* 4.6 6.1 - - + -
674D ALA* 4.7 5.2 - - + +
678D ALA* 3.3 35.4 - - + -
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Residues in contact with SER 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C GLN* 2.8 39.7 + - - +
441C THR* 4.5 2.1 + - - -
442C VAL* 1.3 75.5 - - - +
444C THR* 1.3 65.5 + - - +
449C LEU* 2.9 11.4 - - - -
450C ASN 2.4 28.6 + - - -
451C GLN* 3.6 10.6 - - - +
674D ALA* 3.5 16.8 - - - +
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Residues in contact with THR 444 (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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426C LYS 4.3 4.5 - - - -
427C GLY* 4.7 1.3 - - - -
428C GLN* 5.6 1.1 - - - -
443C SER* 1.3 81.1 + - - +
445C GLU* 1.3 58.8 + - - +
446C SER* 2.8 39.0 - - - +
447C GLY* 3.2 16.3 + - - +
448C VAL* 3.5 7.0 - - + +
449C LEU* 2.9 27.5 + - - +
670D GLU* 2.9 35.1 + - - +
671D LEU* 4.5 3.5 - - - +
674D ALA* 4.4 1.2 - - - +
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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