Contacts of the strand formed by residues 429 - 438 (chain A) in PDB entry 2PA5
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 LEU 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A ARG 4.7 2.2 - - - +
387A TRP* 3.6 18.8 - - + +
388A LEU* 3.5 38.1 - - + +
391A TRP* 4.3 10.8 - - + -
425A ARG* 3.8 0.3 - - - -
426A PHE* 2.7 49.2 + - + +
427A GLY 3.2 0.8 - - - +
428A PHE* 1.3 92.2 - - + +
430A THR* 1.3 59.1 + - - +
431A VAL* 5.3 0.7 - - + -
449A ILE* 4.0 19.5 - - + -
450A HIS 3.5 1.8 - - - -
451A ASN* 3.8 38.1 - - + +
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Residues in contact with THR 430 (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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423A ARG* 4.0 30.3 - - + +
424A ILE 3.5 12.1 - - - +
425A ARG* 3.5 25.9 + - + +
427A GLY 4.8 0.7 + - - -
428A PHE 4.1 0.2 - - - -
429A LEU* 1.3 72.7 - - - +
431A VAL* 1.3 64.0 + - - +
432A THR* 4.0 9.7 + - - +
448A GLU 3.5 1.4 - - - +
449A ILE* 3.4 2.1 - - - -
450A HIS* 2.8 53.2 + - + +
452A THR* 4.7 9.7 - - - +
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Residues in contact with VAL 431 (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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387A TRP* 3.9 37.5 - - + -
417A PRO* 3.4 24.4 - - + +
423A ARG* 3.1 4.2 - - - +
424A ILE 2.9 34.2 + - - +
426A PHE* 3.8 25.8 - - + -
429A LEU* 4.9 0.9 - - + +
430A THR* 1.3 77.9 - - - +
432A THR* 1.3 62.2 + - - +
447A LEU* 4.1 22.0 - - + -
448A GLU 3.2 9.2 - - - +
449A ILE* 4.4 11.0 - - + -
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Residues in contact with THR 432 (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 PRO* 4.1 2.7 - - - -
421A ASP* 4.5 10.1 - - - +
422A SER 3.5 10.5 - - - +
423A ARG* 3.5 20.7 + - + +
430A THR* 4.0 7.6 + - - +
431A VAL* 1.3 76.2 - - - +
433A ASN* 1.3 72.2 + - - +
434A LEU* 3.5 12.4 + - + +
447A LEU* 3.3 5.8 - - - -
448A GLU* 2.8 51.8 + - - -
450A HIS* 6.1 0.5 - - - +
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Residues in contact with ASN 433 (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 PRO* 2.9 30.5 + - + +
418A LEU 3.0 22.4 + - - -
419A GLU 3.2 21.1 - - - +
420A LYS* 3.4 5.4 - - - +
421A ASP* 2.8 31.0 + - - +
422A SER 2.9 12.3 + - - +
432A THR* 1.3 72.8 - - - +
434A LEU* 1.3 59.2 + - - +
435A GLY* 2.8 36.6 + - - +
436A VAL* 3.4 10.3 - - - +
445A THR* 3.5 12.7 - - - +
446A THR 3.7 3.6 - - - -
447A LEU* 3.9 3.6 - - + -
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Residues in contact with LEU 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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420A LYS* 3.7 19.8 - - - +
421A ASP* 5.5 1.8 - - - +
432A THR* 4.0 24.2 - - + +
433A ASN* 1.3 77.7 - - - +
435A GLY* 1.3 56.2 + - - +
446A THR* 2.8 27.4 + - + +
448A GLU* 3.9 28.0 - - + +
459A GLN* 3.6 35.4 - - + +
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Residues in contact with GLY 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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420A LYS* 4.1 15.2 - - - +
433A ASN* 2.8 9.0 + - - +
434A LEU* 1.3 80.7 - - - +
436A VAL* 1.3 63.4 + - - -
444A LYS 4.0 0.3 - - - +
445A THR* 3.3 3.5 - - - -
446A THR* 2.9 29.1 + - - -
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Residues in contact with VAL 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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418A LEU 3.4 13.0 - - - +
419A GLU* 4.8 0.7 - - - -
420A LYS* 4.5 9.1 - - + +
433A ASN* 3.4 29.8 - - - +
435A GLY* 1.3 74.2 - - - +
437A GLU* 1.3 64.0 + - - +
438A ASN* 4.1 8.7 - - - +
443A LYS* 3.3 38.1 - - + -
444A LYS 3.3 5.8 - - - +
445A THR* 3.9 7.0 - - - +
301B GLN* 4.3 13.8 + - - +
305B GLU* 5.8 0.9 - - - +
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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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436A VAL* 1.3 75.1 - - - +
438A ASN* 1.3 66.6 + - - +
439A MET* 3.4 33.6 - - + +
443A LYS* 3.3 2.6 - - - +
444A LYS* 2.8 50.6 + - + +
300B LYS* 5.1 7.9 - - - -
301B GLN* 3.6 9.2 - - - +
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Residues in contact with ASN 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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436A VAL* 4.1 2.8 - - - +
437A GLU* 1.3 75.1 - - - +
439A MET* 1.3 71.3 + - - +
442A TYR 4.1 2.7 - - - -
443A LYS* 3.8 27.7 - - - +
466A LEU* 4.7 3.4 - - - +
300B LYS* 4.2 9.0 - - - -
301B GLN* 2.8 40.3 + - - +
304B TYR* 3.7 36.4 - - + +
305B GLU* 4.1 11.0 - - - +
308B GLU* 3.8 29.1 + - - +
561B PRO* 6.1 0.2 - - - +
705B EDO 5.2 1.2 + - - -
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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