Contacts of the strand formed by residues 401 - 410 (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 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 5.0 0.8 - - - +
285A ARG* 5.6 0.5 + - - -
400A MET* 1.3 75.1 - - - +
402A PHE* 1.3 68.6 + - - -
450A GLY* 3.6 2.9 - - - -
451A LEU* 2.7 50.4 + - - +
485A TYR* 3.9 10.1 - - - -
486A GLN 3.3 11.0 - - - -
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Residues in contact with PHE 402 (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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129A LEU* 4.0 35.4 - - + -
130A ILE 5.7 0.7 - - - -
131A PHE* 5.0 4.9 - + - -
283A GLY* 3.3 33.4 - - - +
284A ALA 3.9 16.4 - - - -
285A ARG* 3.5 29.8 - - + -
344A VAL* 4.4 7.0 - - + -
400A MET* 3.3 45.3 - - + -
401A GLY* 1.3 78.6 - - - -
403A GLY* 1.3 65.2 + - - +
404A GLY 3.4 2.8 + - - -
448A ILE 4.6 0.2 - - - -
449A CYS 3.2 4.7 - - - +
451A LEU* 4.3 0.2 - - - +
485A TYR* 3.6 1.7 - - - -
486A GLN* 2.7 56.3 + - + +
487A HIS 4.8 0.4 - - - -
488A SER* 4.9 2.2 - - - -
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Residues in contact with GLY 403 (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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283A GLY 5.7 2.7 - - - -
342A GLY* 4.7 10.5 + - - -
402A PHE* 1.3 75.2 - - - +
404A GLY* 1.3 60.7 + - - +
405A THR* 3.9 5.6 + - - -
447A LYS* 5.2 9.6 - - - -
448A ILE 3.9 1.6 - - - -
449A CYS* 2.7 23.1 + - - -
484A GLN 3.6 5.9 - - - +
485A TYR* 3.8 3.3 - - - -
486A GLN* 4.4 0.7 + - - +
492A ARG* 5.0 7.6 + - - -
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Residues in contact with GLY 404 (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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402A PHE 3.4 1.8 + - - -
403A GLY* 1.3 75.5 - - - +
405A THR* 1.3 61.1 + - - -
406A LEU 4.0 0.6 + - - -
446A TRP 3.8 0.2 - - - +
447A LYS* 3.3 6.6 - - - +
448A ILE* 2.7 51.1 + - - -
451A LEU* 5.1 3.1 - - - +
483A THR* 5.0 5.6 - - - -
484A GLN 2.9 10.8 - - - -
485A TYR* 3.7 11.2 - - - -
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Residues in contact with THR 405 (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 4.2 4.9 + - - -
404A GLY* 1.3 74.6 - - - -
406A LEU* 1.3 63.3 + - - +
407A GLU* 3.8 1.8 + - + +
426A LEU* 3.4 31.9 - - + +
445A GLN* 4.3 16.4 - - - +
446A TRP 3.5 1.6 - - - -
447A LYS* 4.7 5.8 - - - +
482A VAL 3.1 14.7 - - - +
483A THR* 3.4 2.9 - - - -
484A GLN* 2.7 44.8 + - - +
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Residues in contact with LEU 406 (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* 3.9 29.4 - - + -
44A PRO* 5.7 0.7 - - + -
404A GLY 4.0 1.0 - - - -
405A THR* 1.3 72.1 - - - +
407A GLU* 1.3 65.1 + - - +
408A ILE* 4.2 15.5 - - + -
445A GLN* 3.0 5.5 - - - -
446A TRP* 2.7 67.6 + - + +
448A ILE* 4.4 24.0 - - + -
457A LEU* 4.6 8.3 - - + -
459A ILE* 4.5 15.5 - - + -
481A PHE* 4.4 3.4 - - + -
482A VAL 3.6 5.8 - - - +
483A THR* 3.9 21.1 - - + +
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Residues in contact with GLU 407 (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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405A THR* 3.8 2.0 + - + +
406A LEU* 1.3 74.1 - - - +
408A ILE* 1.3 66.3 + - - +
409A LYS* 3.1 41.1 + - - +
444A CYS* 3.1 10.8 - - + +
445A GLN* 3.1 42.0 + - + +
480A GLN 3.5 1.4 - - - +
482A VAL* 2.9 47.7 + - + +
484A GLN* 5.7 2.9 + - - -
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Residues in contact with ILE 408 (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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406A LEU* 4.2 7.0 - - + -
407A GLU* 1.3 79.2 - - - +
409A LYS* 1.3 65.9 + - - +
410A THR* 4.1 0.7 + - + -
416A ILE* 3.6 26.0 - - + +
432A CYS* 4.3 10.0 - - - -
444A CYS* 3.1 16.6 + - - +
446A TRP* 3.7 22.2 - - + -
459A ILE* 3.7 29.6 - - + -
461A PHE* 4.3 1.6 - - + -
479A ILE* 3.1 35.2 - - + -
480A GLN 3.2 6.3 - - - +
481A PHE* 3.6 32.5 - - + -
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Residues in contact with LYS 409 (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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65A THR 3.8 7.7 + - - -
66A CYS* 2.4 35.3 + - - +
67A ARG* 4.1 14.8 + - - +
68A ALA* 4.2 8.3 - - + +
87A PHE* 3.4 15.7 - - + -
407A GLU* 3.1 31.8 + - - +
408A ILE* 1.3 74.9 - - - +
410A THR* 1.3 60.8 + - - +
432A CYS* 4.8 6.1 - - - -
479A ILE* 3.1 6.6 - - - +
480A GLN* 2.6 64.7 + - + +
482A VAL* 5.4 4.7 - - + -
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Residues in contact with THR 410 (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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87A PHE* 3.2 16.2 - - - +
408A ILE* 4.1 6.5 + - + +
409A LYS* 1.3 79.5 - - - +
411A SER* 1.3 66.8 + - - +
412A ARG* 3.8 1.0 + - - -
414A ILE* 2.6 42.9 + - + +
416A ILE* 4.2 30.7 - - + -
432A CYS* 3.7 22.1 - - + -
461A PHE* 4.7 1.1 - - + -
478A ALA 3.3 7.4 - - - -
479A ILE* 4.5 6.3 - - + -
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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