Contacts of the helix formed by residues 383 - 398 (chain K) in PDB entry 5A31
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 ASN 383 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547C LYS* 4.6 13.3 + - - +
551C ARG* 3.2 31.4 + - - +
378K TYR* 2.8 43.6 + - + +
379K GLY 4.3 0.4 + - - -
381K THR* 3.1 14.4 + - - +
382K ASN* 1.3 81.1 - - - +
384K SER* 1.3 57.9 - - - +
385K LYS 3.4 2.0 - - - -
386K LEU* 3.4 22.4 + - + +
387K ALA* 3.0 27.2 + - - +
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Residues in contact with SER 384 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C ARG* 3.9 13.6 + - - +
379K GLY* 5.3 1.3 - - - -
382K ASN 3.6 2.7 + - - -
383K ASN* 1.3 72.9 - - - +
385K LYS* 1.3 75.5 + - - +
387K ALA* 3.6 7.5 - - - +
388K GLU* 2.8 31.8 + - - +
411K VAL* 4.9 5.3 - - - +
415K ASN* 2.9 45.9 + - - -
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Residues in contact with LYS 385 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C ARG* 5.4 0.9 - - - +
554C LEU* 4.8 22.7 - - + +
555C GLN* 4.8 24.1 + - + +
557C ARG* 6.0 2.8 + - - +
383K ASN 3.4 0.4 - - - -
384K SER* 1.3 94.3 + - - +
386K LEU* 1.3 68.2 + - + +
388K GLU* 3.3 19.3 + - - +
389K ARG* 3.1 20.8 + - - +
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Residues in contact with LEU 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C LEU* 3.8 24.0 - - + -
551C ARG* 4.7 13.9 - - + +
554C LEU* 3.9 28.3 - - + -
378K TYR* 3.6 45.3 - - + +
383K ASN* 3.8 28.7 - - + +
384K SER 3.3 0.2 - - - -
385K LYS* 1.3 79.5 - - + +
387K ALA* 1.3 66.7 + - - +
389K ARG* 3.2 7.8 + - - +
390K PHE* 3.0 34.1 + - + -
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Residues in contact with ALA 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375K GLY* 3.3 28.2 - - - +
378K TYR* 3.8 5.1 - - + +
379K GLY* 3.6 12.3 - - - +
383K ASN 3.0 17.7 + - - +
384K SER 3.6 5.4 - - - +
386K LEU* 1.3 78.1 - - - +
388K GLU* 1.3 61.0 + - - +
389K ARG 3.3 0.2 + - - -
390K PHE* 3.3 2.3 + - - +
391K PHE* 3.0 30.6 + - + -
411K VAL* 3.8 16.8 - - + -
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Residues in contact with GLU 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K SER 2.8 21.5 + - - +
385K LYS* 3.5 20.6 - - + +
386K LEU 3.2 0.2 - - - -
387K ALA* 1.3 72.6 - - - +
389K ARG* 1.3 71.3 + - - +
391K PHE* 3.3 10.6 + - - +
392K SER* 2.9 35.7 + - - -
411K VAL* 5.4 1.1 - - - +
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Residues in contact with ARG 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C SER* 5.4 6.9 - - - -
534C GLN* 4.9 13.3 + - - +
554C LEU* 4.5 14.8 - - - +
557C ARG* 4.2 28.0 - - - +
385K LYS 3.1 10.2 + - - +
386K LEU* 3.2 10.6 + - - +
388K GLU* 1.3 88.4 - - - +
390K PHE* 1.3 82.8 + - - +
392K SER* 2.6 25.2 + - - +
393K GLN* 3.1 21.0 + - - +
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Residues in contact with PHE 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C GLN* 6.1 0.9 - - - -
358K PHE* 4.0 24.5 - + - -
371K MET* 3.6 34.8 - - + +
374K ILE* 3.7 20.4 - - + -
375K GLY* 4.0 6.1 - - - -
378K TYR* 3.6 26.7 - + - -
386K LEU* 3.0 29.9 + - + -
387K ALA 3.8 4.7 - - - +
389K ARG* 1.3 96.8 - - + +
391K PHE* 1.3 60.9 + - - +
393K GLN* 3.0 10.7 + - + +
394K ALA* 2.8 29.0 + - - +
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Residues in contact with PHE 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372K LEU* 3.3 45.8 - - + -
375K GLY* 3.2 23.8 - - - -
376K LEU* 3.3 4.5 - - - -
387K ALA 3.0 26.0 + - - -
388K GLU* 3.7 9.0 - - - +
390K PHE* 1.3 76.3 - - - +
392K SER* 1.3 57.7 + - - +
394K ALA* 3.8 4.7 - - + +
395K LEU* 2.8 35.1 + - + +
404K VAL* 5.5 1.9 - - + +
407K GLU 4.1 5.8 - - - -
408K VAL* 4.0 39.9 - - + -
411K VAL* 3.3 37.0 - - + -
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Residues in contact with SER 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K GLU* 2.9 19.6 + - - -
389K ARG* 2.6 30.1 + - - +
391K PHE* 1.3 75.7 - - - +
393K GLN* 1.3 62.7 + - - +
395K LEU* 3.8 6.8 - - - +
396K SER* 3.1 24.4 + - - -
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Residues in contact with GLN 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371K MET* 4.0 21.8 - - + -
389K ARG* 3.1 23.9 + - - +
390K PHE* 3.0 17.8 + - + +
392K SER* 1.3 81.1 + - - +
394K ALA* 1.3 61.5 + - - +
396K SER* 3.5 17.4 - - - -
397K ILE* 3.6 13.1 + - + +
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Residues in contact with ALA 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K HIS* 3.9 34.0 - - + +
371K MET* 4.0 13.8 - - + -
372K LEU* 4.1 15.5 - - + +
390K PHE 2.8 16.8 + - - +
391K PHE* 3.8 6.1 - - + +
393K GLN* 1.3 71.0 - - - +
395K LEU* 1.3 65.2 + - - +
397K ILE* 3.2 5.7 + - - +
398K ALA* 3.1 21.2 + - - +
404K VAL* 5.3 7.9 - - + -
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Residues in contact with LEU 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391K PHE* 2.8 22.3 + - + +
392K SER* 3.8 7.0 - - - +
394K ALA* 1.3 70.3 - - - +
396K SER* 1.3 66.4 + - - +
398K ALA 3.1 24.8 - - - +
399K PRO* 3.5 23.9 - - + +
404K VAL* 4.3 22.4 - - + +
405K MET* 5.5 2.7 - - + -
408K VAL* 4.4 9.9 - - + -
424K TRP* 3.7 37.0 - - + -
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Residues in contact with SER 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392K SER 3.1 13.8 + - - -
393K GLN* 3.5 15.5 - - - -
395K LEU* 1.3 78.4 - - - +
397K ILE* 1.3 63.4 + - - +
398K ALA 5.0 0.2 - - - -
399K PRO* 5.1 2.9 - - - +
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Residues in contact with ILE 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177K THR 6.1 2.0 - - - +
178K ALA* 6.0 8.1 - - + -
212K TYR* 4.1 23.3 - - + +
365K LYS 4.0 9.2 - - - +
366K GLY* 3.7 22.4 - - - +
368K HIS* 4.0 16.6 - - + -
371K MET* 3.7 38.8 - - + -
393K GLN* 3.6 8.5 + - + +
394K ALA 3.2 9.3 + - - +
396K SER* 1.3 83.1 - - - +
398K ALA* 1.3 57.8 + - - +
399K PRO* 4.1 4.0 - - - +
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Residues in contact with ALA 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K TYR* 3.9 28.5 - - + -
368K HIS* 4.1 21.5 - - + +
394K ALA 3.1 9.8 + - - +
395K LEU* 3.1 13.7 - - - +
397K ILE* 1.3 76.6 - - - +
399K PRO* 1.3 68.4 - - + +
400K GLU 3.6 0.9 - - - +
401K ASP* 4.9 9.8 + - + -
404K VAL* 4.6 9.4 - - - +
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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