Contacts of the helix formed by residues 377 - 386 (chain D) in PDB entry 4O9U
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 377 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376D ALA* 1.3 73.8 - - - +
378D ASP* 1.3 75.6 + - - +
379D VAL 3.3 1.3 - - - -
380D VAL* 3.4 5.7 + - - +
381D ASN* 3.3 8.8 + - - -
409D LYS* 4.5 2.8 - - + +
413D GLY 4.0 15.6 + - - -
414D LYS* 4.4 6.3 - - - +
415D GLY 4.5 8.1 - - - +
419D VAL 4.0 8.0 + - - +
420D GLU* 5.6 0.8 - - - +
421D ASN* 2.6 46.7 + - - +
424D PHE* 3.3 28.8 - - - -
500D NAP 2.7 29.4 + - - +
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Residues in contact with ASP 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D ASN* 1.3 88.0 - - - +
379D VAL* 1.3 63.7 + - - +
380D VAL 3.1 3.4 + - - -
381D ASN* 3.2 18.3 + - - +
391D LEU* 3.9 15.1 - - + +
394D MET* 3.1 23.0 - - - +
415D GLY* 4.4 3.1 + - - -
416D PHE 3.4 6.1 + - - -
417D ALA* 3.0 34.3 + - - +
418D GLY 4.3 0.5 + - - -
419D VAL* 4.1 12.2 + - - +
500D NAP 3.0 40.1 + - + +
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Residues in contact with VAL 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D VAL* 4.7 4.9 - - + -
331D HIS* 3.1 49.1 - - + -
333D VAL* 3.9 9.0 - - + -
334D ALA* 3.8 14.8 - - + -
376D ALA* 3.8 18.2 - - + -
378D ASP* 1.3 76.2 - - - +
380D VAL* 1.3 69.3 + - + +
381D ASN 3.5 0.4 - - - -
394D MET* 3.3 14.6 - - - +
397D LEU* 3.2 9.5 - - - +
500D NAP 3.3 45.8 - - + +
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Residues in contact with VAL 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D VAL* 3.6 28.9 - - + -
373D VAL* 4.3 20.4 - - + -
376D ALA 4.3 1.6 - - - +
377D ASN* 3.5 17.9 - - - +
379D VAL* 1.3 87.9 - - + +
381D ASN* 1.3 59.5 + - - +
382D PRO* 3.4 11.8 - - - +
394D MET* 4.9 0.2 - - - -
396D ILE* 4.6 1.1 - - - +
397D LEU* 3.7 27.9 - - + +
399D VAL* 3.5 32.0 - - + +
400D ASP* 5.5 0.2 - - - +
421D ASN* 4.0 2.0 - - - +
423D LEU* 3.8 15.4 - - + +
424D PHE* 6.4 0.2 - - + -
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Residues in contact with ASN 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D ASN* 3.3 16.4 + - - +
378D ASP* 3.2 15.6 + - - +
379D VAL 3.5 0.8 + - - -
380D VAL* 1.3 75.0 - - - +
382D PRO* 1.4 68.3 - - - +
383D ALA* 2.9 21.9 + - - +
384D ALA* 3.2 13.9 + - - +
391D LEU* 3.6 11.4 - - + +
394D MET* 3.9 1.1 - - - +
396D ILE* 3.3 11.5 - - - +
419D VAL* 3.5 29.5 - - - +
420D GLU 3.5 14.0 + - - +
421D ASN* 3.3 17.6 - - - +
422D GLU* 4.0 7.3 + - - +
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Residues in contact with PRO 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D VAL 3.4 10.7 - - - +
381D ASN* 1.4 88.3 - - - +
383D ALA* 1.3 58.5 + - - -
384D ALA 3.2 1.2 + - - -
385D ARG* 3.5 39.3 + - - +
386D ARG* 3.1 13.6 + - - +
396D ILE* 4.0 10.5 - - + -
400D ASP* 4.3 17.0 - - + +
421D ASN* 3.4 10.3 - - - +
422D GLU* 3.6 27.4 - - + +
423D LEU* 4.0 12.1 - - + +
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Residues in contact with ALA 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ASN* 2.9 23.4 + - - +
382D PRO* 1.3 73.1 - - - +
384D ALA* 1.3 57.3 + - - +
385D ARG 3.0 11.2 + - - -
386D ARG* 3.4 30.3 + - - +
389D SER* 2.5 36.2 + - - +
391D LEU* 4.3 8.2 - - + -
419D VAL* 5.1 5.4 - - + -
420D GLU 5.7 1.1 - - - +
422D GLU* 3.9 3.0 + - + +
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Residues in contact with ALA 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ASN 3.2 5.4 + - - +
382D PRO 3.2 1.0 - - - -
383D ALA* 1.3 75.7 - - - +
385D ARG* 1.3 60.1 + - - +
386D ARG 3.6 0.2 - - - -
391D LEU* 3.3 30.3 - - + +
392D TYR* 3.5 20.4 - - - -
393D GLY 4.3 0.7 + - - -
394D MET* 3.3 51.7 - - + +
396D ILE* 4.3 6.4 - - + +
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Residues in contact with ARG 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D PRO* 3.5 36.8 - - - +
383D ALA 3.0 1.0 + - - -
384D ALA* 1.3 80.4 - - - +
386D ARG* 1.3 66.2 + - + +
387D PRO* 4.4 1.4 - - - +
392D TYR* 3.3 18.0 - - - -
396D ILE* 4.3 25.3 - - + +
398D ASP* 2.7 30.9 + - - -
400D ASP* 2.9 36.8 + - - -
401D LYS* 5.1 8.8 - - - +
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Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D PRO* 3.1 16.8 + - - +
383D ALA* 3.4 37.2 + - - +
385D ARG* 1.3 83.7 - - + +
387D PRO* 1.4 71.0 - - + +
388D GLY* 3.3 8.6 + - - +
389D SER* 3.8 16.0 + - - +
392D TYR* 3.3 20.3 - - - +
422D GLU* 3.0 27.7 + - - -
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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