Contacts of the helix formed by residues 391 - 406 (chain c) in PDB entry 4B2Q
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 SER 391 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390c GLY* 1.3 72.8 - - - +
392c LEU* 1.3 53.1 + - - +
393c LYS 3.3 2.7 - - - -
394c LEU* 2.9 29.3 + - - -
395c PHE* 2.6 37.8 + - - +
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Residues in contact with LEU 392 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157c ALA* 4.7 7.2 - - + +
158c LEU* 4.3 15.7 - - + -
389c ALA* 3.6 34.8 - - + -
390c GLY 3.3 2.8 - - - +
391c SER* 1.3 77.7 - - - +
393c LYS* 1.3 54.6 + - - +
395c PHE* 3.0 7.3 + - + +
396c LEU* 2.7 60.9 + - + +
426c LEU* 3.7 25.4 - - + -
430c LEU* 5.5 6.1 - - + -
447c ILE* 4.1 22.0 - - + -
451c VAL* 3.8 16.6 - - + -
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Residues in contact with LYS 393 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158c LEU* 4.0 33.5 - - + +
159c VAL* 5.1 4.7 - - - -
369c VAL* 3.6 35.8 + - + +
370c GLY* 5.3 2.4 + - - -
372c SER 3.4 22.9 + - - -
373c VAL* 4.2 17.0 - - - +
390c GLY 5.0 2.3 + - - +
391c SER 3.3 0.6 - - - -
392c LEU* 1.3 78.2 - - - +
394c LEU* 1.3 69.1 + - + +
396c LEU* 3.4 5.9 + - - +
397c ALA* 3.2 20.6 + - - +
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Residues in contact with LEU 394 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390c GLY 5.1 2.5 - - - +
391c SER* 2.9 32.6 + - - +
393c LYS* 1.3 83.4 - - + +
395c PHE* 1.3 59.9 + - - +
397c ALA* 3.2 10.6 - - + +
398c GLN* 3.1 27.3 + - + +
343d GLY* 5.0 13.5 - - - -
345d TYR* 6.4 0.9 - - + -
458d TYR* 4.7 22.4 - - + +
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Residues in contact with PHE 395 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391c SER* 2.6 17.4 + - - +
392c LEU* 3.0 13.7 + - + +
394c LEU* 1.3 71.5 - - - +
396c LEU* 1.3 61.6 + - + +
397c ALA 3.0 1.8 - - - -
398c GLN* 3.0 26.3 + - + +
399c TYR* 2.9 25.1 + - + +
419c THR* 4.0 36.8 - - + -
422c ARG* 3.3 40.4 - - - -
423c GLY* 3.9 16.6 - - - -
426c LEU* 3.5 34.3 - - + -
451c VAL* 6.4 0.7 - - - -
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Residues in contact with LEU 396 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158c LEU* 4.3 9.9 - - + -
369c VAL* 4.2 24.5 - - + -
392c LEU* 2.7 55.7 + - + +
393c LYS* 3.8 6.1 - - - +
394c LEU 3.4 0.2 - - - -
395c PHE* 1.3 77.3 - - + +
397c ALA* 1.3 61.1 + - - +
399c TYR* 3.6 12.1 - - + +
400c ARG* 3.4 31.6 + - - +
423c GLY* 5.6 1.8 - - - +
426c LEU* 4.3 18.2 - - + -
427c THR* 5.2 10.1 - - + +
430c LEU* 3.8 29.8 - - + -
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Residues in contact with ALA 397 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369c VAL* 6.1 0.2 - - - +
393c LYS 3.2 12.7 + - - +
394c LEU* 3.2 15.9 - - + +
395c PHE 3.0 0.2 - - - -
396c LEU* 1.3 76.2 - - - +
398c GLN* 1.3 64.7 + - + +
400c ARG* 3.1 30.6 + - - +
401c GLU* 3.2 19.9 + - - +
341d GLU 4.5 13.0 - - - +
342d LEU 5.8 2.7 - - - +
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Residues in contact with GLN 398 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394c LEU* 3.1 14.3 + - - +
395c PHE* 3.0 33.8 + - + +
397c ALA* 1.3 74.2 - - + +
399c TYR* 1.3 60.6 + - - +
401c GLU* 3.0 20.6 + - - +
402c VAL* 2.8 38.5 + - + +
419c THR* 5.7 6.2 - - + +
455d HIS* 6.1 2.2 + - - -
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Residues in contact with TYR 399 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395c PHE* 2.9 13.8 + - + +
396c LEU* 3.6 14.1 - - + +
397c ALA 3.2 0.2 - - - -
398c GLN* 1.3 76.1 - - - +
400c ARG* 1.3 63.8 + - + +
402c VAL* 3.1 5.5 + - - +
403c ALA* 2.6 49.3 + - + +
419c THR* 4.3 7.4 - - - +
420c LEU* 3.7 30.7 - - + +
423c GLY* 3.4 31.6 - - - -
424c GLU* 3.4 41.1 + - + +
427c THR* 3.8 16.1 - - + -
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Residues in contact with ARG 400 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368c ASN* 5.2 7.0 - - - -
369c VAL* 5.3 6.7 - - - +
370c GLY* 4.1 31.3 - - - +
396c LEU* 3.4 16.2 + - - +
397c ALA* 3.1 33.9 + - - +
398c GLN 3.3 0.2 - - - -
399c TYR* 1.3 86.6 - - + +
401c GLU* 1.3 60.7 + - - +
403c ALA* 4.0 7.7 - - - +
404c ALA* 3.2 24.9 + - - +
341d GLU* 4.7 9.7 + - - +
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Residues in contact with GLU 401 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397c ALA 3.2 13.4 + - - +
398c GLN* 3.0 25.5 + - - +
400c ARG* 1.3 80.0 - - - +
402c VAL* 1.3 62.8 + - + +
404c ALA* 3.8 3.9 + - - +
405c PHE* 3.5 21.1 + - - +
342d LEU* 5.6 5.7 - - - +
408d ARG* 5.3 6.2 + - - -
412d ARG* 5.0 10.2 + - - -
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Residues in contact with VAL 402 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398c GLN* 2.8 23.4 + - + +
399c TYR* 3.8 5.4 - - - +
401c GLU* 1.3 80.0 - - + +
403c ALA* 1.3 65.6 + - - +
404c ALA 3.2 0.7 - - - -
405c PHE* 3.3 8.2 + - + +
406c ALA* 3.0 23.4 + - - +
412c LEU* 4.8 4.7 - - + -
416c THR* 3.3 41.1 - - + +
419c THR* 4.0 16.4 - - - +
420c LEU* 4.3 16.6 - - + -
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Residues in contact with ALA 403 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399c TYR* 2.6 43.2 + - + +
400c ARG* 4.0 9.0 - - - +
402c VAL* 1.3 74.2 - - - +
404c ALA* 1.3 54.9 + - - +
406c ALA* 3.8 6.7 + - - +
407c GLN* 2.8 32.1 + - - +
420c LEU* 4.3 10.1 - - + +
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Residues in contact with ALA 404 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400c ARG 3.2 18.9 + - - +
401c GLU* 4.2 4.5 - - - +
403c ALA* 1.3 77.8 - - - +
405c PHE* 1.3 58.3 + - - +
407c GLN* 2.9 29.8 - - - +
408c PHE 4.6 0.3 + - - -
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Residues in contact with PHE 405 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401c GLU 3.5 16.5 + - - +
402c VAL* 3.3 10.2 + - + +
404c ALA* 1.3 76.7 - - - +
406c ALA* 1.3 58.5 + - - +
407c GLN 3.1 6.1 + - - -
408c PHE* 3.6 25.0 + + + +
410c SER* 6.0 2.2 - - - -
412c LEU* 5.0 16.0 - - + +
416c THR* 6.0 6.5 - - + -
388d ILE* 3.2 34.3 - - + -
389d ALA* 4.4 14.6 - - + -
392d GLY* 5.2 7.6 - - - -
393d MET* 5.7 2.7 - - + -
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Residues in contact with ALA 406 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402c VAL 3.0 16.5 + - - +
403c ALA* 4.3 5.6 - - - +
404c ALA 3.4 0.4 - - - -
405c PHE* 1.3 72.9 - - - +
407c GLN* 1.3 64.9 + - - +
408c PHE* 3.2 2.6 + - - -
409c GLY* 3.5 12.0 + - - +
410c SER 4.8 5.7 + - - +
412c LEU* 3.7 38.1 - - + +
420c LEU* 4.5 8.3 - - + -
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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