Contacts of the strand formed by residues 424 - 433 (chain B) in PDB entry 1SOX
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 GLU 424 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B LEU 4.9 0.7 - - - +
422B GLY 5.2 2.8 - - - +
423B THR* 1.3 83.8 - - - +
425B LEU* 1.3 67.2 + - - +
426B GLU 4.4 0.2 + - - -
462B VAL 3.7 6.3 - - - +
463B SER* 3.2 28.5 - - - -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B VAL* 4.9 0.7 - - + -
365B LEU* 4.1 12.3 - - + -
386B LEU* 3.7 27.4 - - + +
419B VAL* 3.7 30.7 - - + -
420B GLU 5.9 0.4 - - - +
423B THR* 4.6 11.0 - - + -
424B GLU* 1.3 80.6 - - - +
426B GLU* 1.3 61.3 + - - +
427B ILE* 3.9 11.2 - - + -
461B ARG* 3.3 5.7 - - - +
462B VAL* 2.8 54.6 + - + +
464B VAL* 3.9 21.3 - - + -
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Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B SER 3.6 1.4 - - - +
386B LEU 3.2 14.0 + - - -
387B ASP* 3.6 1.8 + - - +
388B GLY* 2.9 38.1 + - - +
425B LEU* 1.3 75.3 - - - +
427B ILE* 1.3 60.8 + - - +
428B VAL* 3.7 1.0 - - + +
459B ARG* 2.6 53.5 + - + +
460B VAL 3.6 2.5 - - - +
461B ARG* 4.0 43.1 + - + +
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B VAL* 4.1 15.4 - - + +
354B PRO* 3.7 35.9 - - + -
365B LEU* 4.4 7.2 - - + -
367B VAL* 3.7 33.0 - - + -
384B VAL* 4.3 8.5 - - + -
385B SER 3.1 9.0 - - - +
386B LEU* 4.2 12.6 - - + -
425B LEU* 4.4 10.8 - - + -
426B GLU* 1.3 72.3 - - - +
428B VAL* 1.3 62.0 + - - +
458B HIS 3.7 0.7 - - - +
459B ARG* 3.3 5.0 - - - -
460B VAL* 2.7 51.0 + - + +
462B VAL* 4.1 13.9 - - + -
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 4.7 0.4 - - - -
384B VAL* 3.3 6.2 - - - +
385B SER* 2.8 39.7 + - - +
388B GLY* 3.7 26.5 - - - -
389B GLY 3.7 0.7 - - - +
392B TRP* 3.8 16.8 - - + -
426B GLU* 3.7 13.9 - - + +
427B ILE* 1.3 83.2 - - - +
429B CYS* 1.3 63.4 + - - +
457B TRP* 3.6 35.9 - - + -
458B HIS 3.3 7.4 - - - +
459B ARG* 4.0 16.8 - - + +
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Residues in contact with CYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B SER* 3.3 20.9 + - - +
350B ALA* 3.5 35.0 - - - -
351B VAL* 3.7 11.2 - - + +
382B VAL* 4.4 5.2 - - + -
383B ASP 3.3 10.5 - - - +
384B VAL* 4.8 1.1 - - + -
413B TRP* 3.8 23.8 - - + -
428B VAL* 1.3 76.9 - - - +
430B LYS* 1.3 65.7 + - - +
439B GLN* 4.4 0.2 - - - +
457B TRP* 3.7 20.6 - - - +
458B HIS* 3.4 8.9 + - - -
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Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A PRO* 4.4 1.4 - - - +
445A PRO* 3.0 31.8 + - - -
446A ILE* 5.3 4.0 - - + +
349B SER* 3.6 1.8 + - - -
381B ARG* 4.4 4.2 - - - +
382B VAL* 3.4 3.4 - - - +
383B ASP* 2.6 60.1 + - + +
392B TRP* 3.5 44.2 - - + -
429B CYS* 1.3 75.9 - - - +
431B ALA* 1.3 63.9 - - - +
432B VAL* 5.5 4.2 - - + +
438B VAL* 6.2 2.5 - - + +
439B GLN* 3.4 13.7 - - + +
457B TRP* 3.7 34.3 - - + +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B VAL* 3.7 24.1 - - + +
348B GLN 4.1 0.4 - - - +
349B SER* 3.8 15.0 - - - -
371B ALA* 3.9 17.5 - - + -
379B VAL* 4.3 4.0 - - + -
381B ARG 3.4 9.9 - - - +
382B VAL* 4.1 2.9 - - + -
430B LYS* 1.3 76.5 - - - +
432B VAL* 1.3 65.4 + - - +
438B VAL* 3.8 17.3 - - - +
439B GLN* 2.8 20.7 + - - +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B VAL* 4.5 2.7 - - - -
379B VAL* 3.5 4.7 - - - -
380B VAL* 2.8 35.2 + - + -
381B ARG* 2.9 47.4 + - + +
383B ASP* 5.0 2.9 - - - +
430B LYS* 5.5 3.8 - - - +
431B ALA* 1.3 79.4 - - - +
433B ASP* 1.3 75.1 + - - +
436B TYR* 3.7 30.1 - - + +
437B ASN 3.3 10.8 - - - +
438B VAL* 4.3 14.4 - - + -
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Residues in contact with ASP 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B VAL* 4.4 3.8 - - + +
373B SER* 2.6 37.1 + - - +
377B ARG* 3.3 15.1 + - + -
378B GLU 3.2 13.9 - - - +
379B VAL* 4.3 0.9 - - - +
380B VAL* 3.7 7.0 - - - +
432B VAL* 1.3 79.8 - - - +
434B SER* 1.3 60.1 + - - +
435B SER 2.9 16.1 + - - -
436B TYR* 2.9 19.8 + - - -
437B ASN* 2.9 52.7 + - - +
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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