Contacts of the strand formed by residues 504 - 510 (chain B) in PDB entry 1NDM
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 THR 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B TRP* 3.4 8.2 - - - -
460B ASN* 2.6 45.9 + - - -
502B SER* 4.1 5.2 + - - -
503B ILE* 1.3 77.2 + - - +
506B CYS* 1.3 74.1 + - - +
507B ASN* 3.7 16.0 - - - +
518B ASP* 3.8 10.1 - - + -
519B LYS 3.6 21.8 - - - +
520B LYS* 3.9 16.2 - - + +
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Residues in contact with CYS 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B VAL* 4.5 1.6 - - - +
440B CYS* 2.0 53.2 - - + -
452B LEU* 3.9 10.5 - - - -
454B THR 3.7 3.6 - - - -
455B TRP* 3.8 15.0 - - + -
504B THR* 1.3 73.3 - - - +
507B ASN* 1.3 61.9 + - - +
508B VAL* 3.8 17.0 - - - -
517B VAL 3.7 0.7 - - - +
518B ASP* 3.2 5.0 - - - -
519B LYS* 2.8 43.6 + - + +
521B ILE* 4.6 2.2 - - + -
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Residues in contact with ASN 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B THR 3.7 0.7 - - - +
452B LEU* 3.2 4.7 - - - +
454B THR* 2.8 57.7 + - - +
460B ASN 3.5 1.7 + - - -
461B SER* 2.6 42.8 + - - +
504B THR* 3.7 12.9 + - - +
506B CYS* 1.3 77.4 + - - +
508B VAL* 1.3 63.0 + - - +
516B LYS* 3.9 16.8 - - - +
517B VAL 3.3 3.8 - - - -
518B ASP* 2.7 30.3 + - - +
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Residues in contact with VAL 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B PRO* 4.3 9.2 - - + -
421B VAL* 4.0 20.9 - - + -
442B VAL* 3.7 42.6 - - + -
450B VAL* 4.2 16.6 - - + -
451B THR 3.4 3.1 - - - +
452B LEU* 3.9 9.6 - - + -
506B CYS* 3.8 19.5 - - - -
507B ASN* 1.3 79.7 - - - +
509B ALA* 1.3 64.1 + - - +
515B THR 3.9 0.5 - - - +
516B LYS* 3.0 4.4 - - - +
517B VAL* 2.8 40.2 + - - +
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Residues in contact with ALA 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B VAL* 3.1 7.4 - - - +
451B THR* 2.9 47.2 + - + +
508B VAL* 1.3 75.0 - - - +
510B HIS* 1.3 61.2 + - - +
511B PRO* 3.9 4.9 - - + +
515B THR 3.3 6.5 - - - +
516B LYS* 3.5 31.6 - - + +
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Residues in contact with HIS 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B THR 3.4 17.6 + - - -
419B PRO* 3.8 22.1 - - + +
445B TYR* 4.0 3.9 - + - -
446B PHE 3.2 23.0 + - - -
447B PRO 2.7 23.8 + - - -
448B GLU 5.1 0.2 - - - -
449B PRO 3.3 19.5 - - - -
450B VAL* 3.6 15.0 - - + -
509B ALA* 1.3 75.3 - - - +
511B PRO* 1.4 68.8 - - + +
512B ALA* 3.6 18.0 - - + +
513B SER* 3.0 23.4 + - - -
514B SER 3.1 15.1 + - - -
515B THR* 2.8 21.5 + - - +
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Residues in contact with PRO 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B PRO* 3.3 32.5 - - + +
450B VAL* 4.7 0.4 - - - -
451B THR* 5.3 9.0 - - + -
509B ALA* 3.9 7.2 - - + +
510B HIS* 1.4 83.0 - - - +
512B ALA* 1.3 57.7 + - - +
514B SER* 2.7 32.0 + - - +
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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
------------------------------------------------------------
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