Contacts of the strand formed by residues 477 - 486 (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 GLY 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TRP* 3.7 16.8 - - - -
411A SER* 3.9 3.1 - - - -
414A ILE* 4.6 0.9 - - - -
476A ARG* 1.3 74.8 - - - +
478A ALA* 1.3 59.2 + - - -
500A ALA* 3.3 4.7 - - - -
501A ARG 2.6 33.5 + - - -
503A TRP* 3.4 29.6 - - - +
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Residues in contact with ALA 478 (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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24A TRP* 4.4 0.6 - - - -
73A LEU* 3.6 31.4 - - + -
86A ASN* 4.2 11.0 - - - +
87A PHE* 3.6 7.6 - - + -
410A THR* 3.3 4.2 - - - -
411A SER* 2.7 43.6 + - - +
414A ILE* 4.5 1.8 - - - +
476A ARG 5.2 1.6 - - - +
477A GLY* 1.3 75.1 - - - +
479A ILE* 1.3 66.7 + - - +
499A ILE 3.6 4.5 - - - +
500A ALA* 4.7 0.4 - - + -
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Residues in contact with ILE 479 (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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19A PHE* 3.6 25.6 - - + -
24A TRP* 3.8 19.1 - - + -
38A VAL* 6.1 0.2 - - + -
87A PHE* 4.1 2.9 - - - -
408A ILE* 3.1 33.7 - - + -
409A LYS 3.1 4.9 - - - +
410A THR* 4.5 5.8 - - + -
414A ILE* 4.9 7.4 - - + -
461A PHE* 3.4 39.0 - - + -
478A ALA* 1.3 82.4 - - - +
480A GLN* 1.3 58.8 + - - +
481A PHE* 3.8 16.4 + - + -
497A THR 3.9 0.9 - - - +
498A THR* 3.5 2.1 - - - +
499A ILE* 3.1 34.8 + - + +
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Residues in contact with GLN 480 (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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68A ALA* 3.6 13.6 - - - +
69A VAL* 2.8 60.7 + - - +
71A ASN* 3.3 8.3 - - - +
87A PHE* 3.6 15.7 - - + -
407A GLU 3.5 2.4 - - - +
408A ILE* 3.2 7.3 - - - -
409A LYS* 2.6 49.4 + - + +
479A ILE* 1.3 73.6 - - - +
481A PHE* 1.3 62.3 + - - +
482A VAL* 3.8 13.6 + - + +
496A VAL* 4.2 5.8 - - + +
497A THR 3.4 3.1 - - - +
498A THR* 3.1 25.5 + - - +
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Residues in contact with PHE 481 (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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17A VAL* 4.8 4.5 - - + -
19A PHE* 4.8 3.6 - + - -
40A ALA* 4.8 8.7 - - + -
42A PHE* 3.4 66.0 - + + -
406A LEU* 4.4 1.3 - - + -
407A GLU 3.9 2.5 - - - -
408A ILE* 3.6 32.5 - - + -
459A ILE* 4.3 5.4 - - + -
461A PHE* 4.0 20.4 - + - -
479A ILE* 3.8 18.6 - - + -
480A GLN* 1.3 73.2 - - - +
482A VAL* 1.3 64.2 + - - +
483A THR* 4.1 0.4 - - - -
495A ARG 3.6 1.0 - - - +
496A VAL* 3.4 5.0 - - - +
497A THR* 2.7 50.7 + - + +
499A ILE* 4.4 14.8 - - + -
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Residues in contact with VAL 482 (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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69A VAL* 4.1 18.4 - - + -
405A THR 3.1 5.5 - - - +
406A LEU* 3.6 2.0 - - - +
407A GLU* 2.9 51.1 + - + +
409A LYS* 5.4 5.4 - - + -
480A GLN* 3.9 26.0 - - + +
481A PHE* 1.3 77.2 - - - +
483A THR* 1.3 65.0 + - - +
484A GLN* 4.5 14.1 - - + +
494A ILE* 4.0 20.6 - - + -
495A ARG 3.5 2.2 - - - -
496A VAL* 4.4 5.6 - - + -
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Residues in contact with THR 483 (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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42A PHE* 4.2 6.1 - - - -
44A PRO* 3.7 29.3 - - + +
45A LEU* 4.9 1.1 - - + -
404A GLY* 5.0 1.6 - - - -
405A THR 3.4 10.5 - - - +
406A LEU* 3.9 14.5 - - + +
448A ILE* 5.9 2.0 - - + -
451A LEU* 4.4 13.9 - - + -
481A PHE 4.9 0.5 - - - -
482A VAL* 1.3 76.4 + - - +
484A GLN* 1.3 67.7 + - - +
485A TYR* 4.0 14.3 - - + -
493A ARG 3.5 1.7 - - - +
494A ILE* 3.2 2.9 - - - -
495A ARG* 2.7 52.4 + - + +
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Residues in contact with GLN 484 (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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403A GLY 3.6 1.7 - - - +
404A GLY* 2.9 3.8 - - - -
405A THR* 2.7 55.4 + - - +
407A GLU* 5.7 2.6 + - - -
445A GLN* 5.8 2.6 - - - +
482A VAL* 4.5 11.5 - - + +
483A THR* 1.3 72.9 - - - +
485A TYR* 1.3 61.1 + - - +
493A ARG 3.3 6.3 - - - +
494A ILE* 3.8 32.5 - - + +
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Residues in contact with TYR 485 (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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45A LEU* 3.5 32.0 - - + +
118A GLU* 2.6 30.7 + - - -
400A MET 5.4 0.2 - - - -
401A GLY* 3.9 14.6 - - - -
402A PHE 3.6 10.5 - - - +
403A GLY 3.8 3.8 - - - -
404A GLY* 3.7 9.4 - - - +
451A LEU* 4.5 11.2 - - + -
483A THR* 4.0 14.8 - - + -
484A GLN* 1.3 77.7 - - - +
486A GLN* 1.3 71.0 + - - +
487A HIS* 3.6 28.0 + + + -
492A ARG* 3.8 8.7 - - - +
493A ARG* 3.0 57.9 + - + -
495A ARG* 4.6 2.0 - - + -
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Residues in contact with GLN 486 (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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127A MET* 3.8 28.9 + - - +
129A LEU* 3.8 15.7 - - + +
282A THR* 3.3 9.5 - - - +
283A GLY* 2.8 41.5 - - - +
401A GLY* 3.3 6.6 - - - -
402A PHE* 2.7 47.5 + - + +
403A GLY* 4.4 0.8 + - - -
485A TYR* 1.3 71.3 - - - +
487A HIS* 1.3 72.5 + - - +
490A GLY* 4.2 12.2 - - - +
491A GLN 4.0 2.9 - - - -
492A ARG* 4.8 21.3 + - - +
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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