Contacts of the strand formed by residues 501 - 507 (chain D) in PDB entry 1N2Q
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 ALA 501 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D PRO 3.5 4.1 + - - +
500D PRO* 1.3 73.2 - - - +
502D ASN* 1.3 76.9 + - - +
503D ILE 3.4 1.5 + - - -
519D TRP* 3.6 2.3 - - - +
520D GLN* 2.9 47.0 + - + +
521D ASP 4.4 2.9 - - - +
522D PRO* 4.6 4.3 - - + -
523D HIS* 4.3 15.3 - - + +
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Residues in contact with ASN 502 (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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501D ALA* 1.3 77.6 - - - +
503D ILE* 1.3 63.1 + - - +
504D THR* 3.2 12.9 + - + +
518D THR 3.0 15.4 - - - +
519D TRP* 3.5 4.4 - - - -
520D GLN* 3.5 33.9 - - + +
523D HIS* 5.2 1.2 + - - -
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Residues in contact with ILE 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D PRO* 3.4 35.4 - - + +
501D ALA 4.5 0.2 - - - -
502D ASN* 1.3 69.1 - - - +
504D THR* 1.3 67.1 + - - +
505D VAL* 5.1 0.4 - - + -
517D VAL* 4.7 7.0 - - + -
518D THR 3.7 2.7 - - - -
519D TRP* 3.6 21.5 - - + -
571D VAL 4.4 6.5 - - - +
573D LEU* 3.8 31.6 - - + -
588D SER* 3.7 17.3 - - - +
589D PRO* 5.1 4.5 - - + +
591D ALA* 3.6 32.2 - - + +
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Residues in contact with THR 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D ASN* 3.4 10.6 + - + +
503D ILE* 1.3 79.8 - - - +
505D VAL* 1.3 64.3 + - - +
506D THR* 4.0 7.4 - - - -
516D SER 3.6 0.7 - - - +
517D VAL* 3.1 6.6 - - - +
518D THR* 2.8 59.3 + - - -
591D ALA* 5.4 0.2 - - - -
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Residues in contact with VAL 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D ILE* 5.1 0.2 - - + -
504D THR* 1.3 77.4 - - - +
506D THR* 1.3 60.1 + - - +
507D ALA 3.9 1.0 + - - -
515D LEU* 3.9 33.6 - - + +
516D SER 3.4 2.7 - - - -
517D VAL* 4.1 15.5 - - + -
571D VAL* 3.8 32.1 - - + -
591D ALA* 4.2 12.5 - - + +
592D MET 3.9 20.5 + - - +
593D GLY* 3.9 22.4 - - - -
594D THR 5.1 1.0 + - - -
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Residues in contact with THR 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D THR* 4.9 7.4 - - - -
505D VAL* 1.3 74.8 + - - +
507D ALA* 1.3 73.7 + - - +
508D VAL 3.5 0.2 + - - -
515D LEU* 3.6 3.0 - - - -
516D SER* 2.7 49.6 + - - -
518D THR* 5.1 4.0 + - - -
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Residues in contact with ALA 507 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D VAL 3.9 2.2 + - - -
506D THR* 1.3 83.9 - - - +
508D VAL* 1.3 62.2 + - - +
509D ALA 3.5 2.3 + - - -
515D LEU* 3.8 9.6 - - + +
594D THR 3.2 25.1 + - - +
596D TRP* 3.7 28.8 - - + +
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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