Contacts of the strand formed by residues 426 - 439 (chain A) in PDB entry 5IG0
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 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A GLN 3.9 0.2 - - - +
422A MET* 3.5 6.7 - - - +
423A PHE* 2.8 46.5 + - + +
424A GLY 3.2 0.4 - - - -
425A ASP* 1.3 81.0 - - - +
427A ALA* 1.3 66.4 + - - +
428A ILE* 4.4 10.8 - - + -
453A VAL* 3.8 27.4 - - + -
454A TRP 3.5 4.5 - - - +
455A VAL* 4.3 10.8 - - + +
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Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 3.9 14.6 - - + -
420A VAL* 3.9 7.0 - - + -
421A GLN 3.5 4.0 - - - -
422A MET* 3.7 22.2 - - - -
425A ASP 4.2 0.4 + - - -
426A THR* 1.3 75.0 - - - +
428A ILE* 1.3 61.5 + - - +
429A VAL* 3.8 1.5 + - + -
452A ARG 3.6 3.1 - - - +
453A VAL* 3.6 2.4 - - - +
454A TRP* 2.8 43.6 + - + +
464A TRP* 3.8 18.2 - - + -
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Residues in contact with ILE 428 (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 3.6 0.9 - - - +
420A VAL* 3.3 3.3 - - - -
421A GLN* 2.9 49.3 + - + +
423A PHE* 3.6 30.5 - - + -
426A THR* 4.4 10.8 - - + -
427A ALA* 1.3 72.0 - - - +
429A VAL* 1.3 62.0 + - - +
430A THR* 3.9 14.5 + - + +
451A THR* 4.0 24.7 - - + -
452A ARG 3.7 2.9 - - - +
453A VAL* 4.8 9.6 - - + +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 4.3 10.5 - - + -
353A LEU* 4.0 15.7 - - + -
356A ASN* 3.8 27.8 - - + +
418A PRO* 5.2 0.9 - - + -
419A ALA 3.3 8.5 - - - +
420A VAL* 4.0 20.9 - - + -
427A ALA 4.7 1.3 - - - +
428A ILE* 1.3 75.4 - - - +
430A THR* 1.3 70.1 + - - +
431A ALA* 5.1 3.6 - - + -
450A GLU 3.7 1.0 - - - +
451A THR* 3.5 3.3 - - - +
452A ARG* 2.8 50.3 + - + +
454A TRP* 3.7 23.1 - - + +
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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
----------------------------------------------------------
417A ASP 3.7 2.3 + - - +
418A PRO* 3.2 1.6 - - - +
419A ALA* 2.9 47.6 + - - +
421A GLN* 4.8 11.5 + - - +
428A ILE* 4.3 17.2 + - + +
429A VAL* 1.3 82.0 - - - +
431A ALA* 1.3 65.0 + - - +
450A GLU 3.3 5.4 - - - +
451A THR* 4.3 14.6 - - - +
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASN* 5.5 1.3 - - - +
415A LEU* 4.2 26.2 - - + -
416A HIS 3.6 11.2 - - - +
417A ASP 4.0 4.5 - - - -
418A PRO* 4.0 12.8 - - + -
429A VAL* 5.1 5.2 - - + -
430A THR* 1.3 77.9 - - - +
432A LEU* 1.3 65.5 + - - +
449A GLU* 3.8 2.4 - - - +
450A GLU* 2.9 37.2 + - + +
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Residues in contact with LEU 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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414A THR 3.7 0.5 - - - +
415A LEU* 3.5 3.8 - - - -
416A HIS* 2.7 55.6 + - + +
417A ASP* 4.5 20.9 - - + +
431A ALA* 1.3 78.1 - - - +
433A ARG* 1.3 61.7 + - - +
434A VAL* 4.9 1.3 - - + -
447A ARG* 4.1 28.9 - - + -
448A TYR 3.3 9.6 - - - +
449A GLU* 4.1 20.9 - - + -
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Residues in contact with ARG 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 3.2 33.1 - - - +
363A VAL* 4.6 10.7 - - - +
413A THR* 3.6 24.9 + - + +
414A THR 3.5 3.6 - - - -
415A LEU* 4.0 14.9 - - + +
431A ALA 4.1 0.6 + - - -
432A LEU* 1.3 72.5 - - - +
434A VAL* 1.3 59.8 + - - +
435A VAL* 4.1 13.5 - - + +
446A THR 3.7 1.2 - - - +
447A ARG* 3.3 3.6 - - - -
448A TYR* 2.7 49.5 + - + +
450A GLU* 3.0 36.9 + - + -
452A ARG* 3.4 11.7 - - - +
471A ARG* 3.8 28.6 - - - +
501A SO4 3.8 12.3 + - - -
502A GOL 4.3 13.1 + - - -
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Residues in contact with VAL 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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412A LYS 3.7 1.4 - - - +
413A THR* 3.4 3.5 - - - +
414A THR* 2.9 46.1 + - - +
416A HIS* 3.5 25.8 - - + +
432A LEU* 4.7 2.0 - - + +
433A ARG* 1.3 76.3 - - - +
435A VAL* 1.3 64.5 + - - +
436A GLN* 5.1 4.4 - - + +
445A THR* 3.5 27.1 - - + -
446A THR 3.4 4.3 - - - +
447A ARG* 4.3 17.9 - - + -
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A MET* 4.3 16.6 - - + -
412A LYS 3.4 2.7 - - - +
413A THR* 3.9 27.1 - - + +
433A ARG* 4.1 4.7 - - + -
434A VAL* 1.3 76.7 - - - +
436A GLN* 1.3 75.1 + - - +
437A PHE* 3.8 11.8 - - + -
445A THR* 3.3 4.8 - - - -
446A THR* 2.9 36.2 + - - +
448A TYR* 3.9 29.2 - - + -
502A GOL 3.9 23.1 - - - +
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Residues in contact with GLN 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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410A LYS 4.4 1.2 - - - +
411A MET* 3.2 8.1 - - - +
412A LYS* 2.8 70.5 + - + +
434A VAL* 5.3 3.8 - - + +
435A VAL* 1.3 74.3 - - - +
437A PHE* 1.3 63.3 + - - +
444A LYS 3.5 6.1 - - - +
445A THR* 4.2 19.7 + - + +
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Residues in contact with PHE 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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410A LYS* 5.4 1.6 - - - -
411A MET* 3.9 37.0 - - + +
435A VAL* 3.8 16.4 - - + -
436A GLN* 1.3 75.2 - - - +
438A VAL* 1.3 68.3 + - - +
439A ALA* 4.1 15.5 - - + -
443A PRO* 3.4 3.9 - - - +
444A LYS* 2.7 71.3 + - + +
446A THR* 3.2 29.8 - - - -
448A TYR* 5.8 1.3 - - - -
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Residues in contact with VAL 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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407A ASN* 3.5 37.1 + - + +
410A LYS* 3.7 27.2 - - + +
411A MET* 5.6 0.4 - - - +
437A PHE* 1.3 81.8 - - - +
439A ALA* 1.3 72.6 + - - +
442A GLY* 3.6 15.5 - - - +
443A PRO* 4.2 4.5 - - + -
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Residues in contact with ALA 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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437A PHE* 4.1 19.4 + - + -
438A VAL* 1.3 84.8 - - - +
440A ASP* 1.3 70.5 + - - +
441A ASP 3.1 6.1 - - - +
442A GLY* 2.7 20.7 + - - +
444A LYS* 4.1 17.5 - - + -
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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