Contacts of the strand formed by residues 433 - 439 (chain A) in PDB entry 2NUP
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 VAL 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A LYS* 3.6 14.6 - - - +
416A ILE* 3.9 4.7 - - - +
428A SER 3.7 19.7 - - - +
429A LYS* 4.4 7.4 - - + +
430A GLY 2.8 21.8 + - - +
431A PRO* 3.7 4.3 - - - +
432A CYS* 1.3 79.1 - - - +
434A SER* 1.3 73.4 + - - +
435A GLU* 4.2 0.5 + - - +
442A GLY* 3.5 26.5 - - - +
443A THR 3.8 12.3 - - - +
444A CYS* 3.6 18.4 - - - -
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A LYS* 3.9 21.8 - - - -
416A ILE 3.0 25.9 + - - +
417A SER* 4.0 4.0 - - - -
432A CYS 3.7 0.6 + - - -
433A VAL* 1.3 86.8 - - - +
435A GLU* 1.3 69.2 + - - +
436A ASN 3.2 24.5 + - - +
437A GLU* 4.5 4.7 + - - +
442A GLY* 4.9 1.4 + - - -
462A GLU* 3.5 22.4 + - - -
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Residues in contact with GLU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A LYS* 5.4 0.4 - - - +
433A VAL 4.2 0.8 + - - +
434A SER* 1.3 77.3 + - - +
436A ASN* 1.3 61.3 + - - +
437A GLU* 3.2 9.4 + - - +
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Residues in contact with ASN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A SER* 3.2 28.0 + - - -
434A SER* 3.2 7.9 + - - +
435A GLU* 1.3 76.9 - - - +
437A GLU* 1.3 71.4 + - - +
438A ILE* 4.6 11.1 - - - +
462A GLU* 3.6 25.1 - - - +
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A SER 3.0 10.1 - - - +
434A SER 4.9 1.6 - - - +
435A GLU 3.2 8.8 + - - +
436A ASN* 1.3 84.4 + - - +
438A ILE* 1.3 62.4 + - - +
439A GLY 4.4 5.0 - - - +
441A GLY* 3.5 25.8 + - - +
442A GLY* 4.0 14.5 - - - +
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Residues in contact with ILE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO* 5.5 6.1 - - + -
417A SER* 2.7 33.8 + - - +
418A GLY* 3.0 25.5 - - - +
419A ALA 3.3 1.7 + - - -
420A ILE* 4.1 7.2 - - + -
436A ASN* 4.6 12.6 - - - +
437A GLU* 1.3 79.6 - - - +
439A GLY* 1.3 72.5 + - - +
440A THR 3.2 0.3 + - - -
441A GLY 3.6 0.7 + - - -
460A TYR* 3.8 27.8 - - + -
461A PHE 6.0 0.2 - - - +
529A LEU* 3.2 33.4 - - + -
532A TYR* 5.6 0.9 - - + -
533A ARG* 6.3 1.3 - - - +
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Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ALA 3.5 8.3 - - - -
420A ILE* 3.9 6.7 - - - -
437A GLU* 4.4 6.1 - - - +
438A ILE* 1.3 77.5 + - - +
440A THR* 1.3 57.7 + - - -
441A GLY 3.1 6.8 + - - -
532A TYR* 3.3 48.0 + - - -
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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
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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