Contacts of the helix formed by residues 416 - 433 (chain D) in PDB entry 2W93
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 GLY 416 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 3.8 1.5 - - - -
387D GLU* 3.0 11.4 + - - -
415D ILE* 1.3 73.1 - - - +
417D PHE* 1.3 64.4 + - - +
418D THR 3.1 4.6 + - - -
419D THR* 3.3 5.6 + - - -
420D GLY 4.0 0.2 + - - -
446D SER* 3.6 18.1 - - - -
449D LEU* 4.4 1.8 - - - -
450D THR* 2.7 47.7 + - - +
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Residues in contact with PHE 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR* 3.5 38.6 - + + +
59D ASP* 3.6 39.9 - - + -
63D ARG* 4.0 10.1 - - - -
387D GLU* 4.2 2.5 - - - +
407D ILE* 3.7 22.2 - - + -
409D GLN* 3.4 46.0 - - + +
414D SER 3.0 20.1 + - - +
415D ILE 3.3 1.0 + - - -
416D GLY* 1.3 76.7 - - - +
418D THR* 1.3 71.8 + - + +
420D GLY 3.1 4.9 + - - -
421D ALA* 2.9 44.0 + - + -
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Residues in contact with THR 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D ILE* 3.6 18.6 - - + -
386D ALA 3.8 4.7 - - - +
387D GLU* 2.7 52.3 + - - +
407D ILE 5.5 0.2 - - - +
408D SER* 6.3 0.2 - - - -
409D GLN 6.2 0.4 - - - +
417D PHE* 1.3 86.1 - - + +
419D THR* 1.3 59.8 + - - +
421D ALA* 3.7 7.2 - - - -
422D THR* 2.6 37.4 + - - -
440D LEU* 3.4 17.6 - - - +
442D ILE* 3.3 14.6 - - - +
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Residues in contact with THR 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D GLY 3.3 1.8 + - - -
418D THR* 1.3 79.7 + - - +
420D GLY* 1.3 61.0 + - - +
422D THR* 3.5 2.4 + - - -
423D LEU* 3.3 7.1 + - - +
440D LEU* 4.6 7.2 - - + -
442D ILE* 3.1 20.6 - - - +
447D LEU* 4.0 10.5 - - + +
450D THR* 2.7 45.3 + - - +
451D VAL 4.5 0.4 - - - +
453D GLU* 4.2 6.4 - - + +
454D ILE* 4.2 17.3 - - + -
457D MET* 3.2 38.9 - - + +
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Residues in contact with GLY 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASN* 3.9 12.6 - - - -
56D TYR* 3.8 14.7 - - - +
57D ALA* 3.1 14.7 - - - +
416D GLY 4.0 1.8 + - - -
417D PHE 3.1 8.1 + - - -
419D THR* 1.3 76.2 - - - +
421D ALA* 1.3 65.3 - - - +
423D LEU* 3.0 11.4 + - - +
424D GLY 3.0 10.0 + - - -
450D THR* 4.8 0.8 + - - -
453D GLU* 4.4 13.2 - - - +
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Residues in contact with ALA 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR 3.5 11.7 + - - +
60D GLY* 3.8 12.7 - - - -
385D ILE* 4.1 11.2 - - + -
407D ILE* 4.9 3.4 - - + -
417D PHE* 2.9 46.2 + - + +
418D THR* 4.0 6.5 - - - +
419D THR 3.4 0.2 - - - -
420D GLY* 1.3 74.5 - - - +
422D THR* 1.3 53.9 + - - +
424D GLY* 3.2 0.7 + - - -
425D ALA* 2.7 36.4 + - - +
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Residues in contact with THR 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D ILE* 3.5 15.3 - - - +
418D THR 2.6 24.7 + - - -
419D THR 3.6 4.7 - - - -
421D ALA* 1.3 75.0 - - - +
423D LEU* 1.3 59.4 + - - +
425D ALA* 3.8 0.9 - - - +
426D ALA* 2.8 29.3 + - - +
438D VAL* 4.0 10.6 - - + +
440D LEU* 3.3 25.4 - - + +
457D MET* 4.1 12.8 - - + -
464D PRO* 3.8 28.5 - - + -
466D LEU* 4.1 9.2 - - + -
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Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 4.3 0.2 - - + -
48D ASN* 3.1 31.6 - - - +
57D ALA* 4.0 8.7 - - + -
419D THR 3.3 9.1 + - - +
420D GLY 3.0 9.9 + - - +
422D THR* 1.3 78.5 - - - +
424D GLY* 1.3 57.4 + - - +
426D ALA* 3.2 4.6 + - - +
427D PHE* 3.0 55.1 + - + -
453D GLU* 3.8 13.2 - - + +
456D THR* 3.7 15.3 - - + -
457D MET* 3.6 43.2 - - + +
462D LEU* 3.7 10.1 - - + -
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Residues in contact with GLY 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.9 15.3 - - - -
57D ALA* 3.2 24.4 - - - +
61D TYR* 3.4 19.4 - - - -
420D GLY 3.0 10.9 + - - -
421D ALA 3.7 0.9 - - - -
423D LEU* 1.3 76.6 - - - +
425D ALA* 1.3 57.1 + - - +
427D PHE 3.4 1.2 + - - -
428D ALA 3.0 22.5 + - - -
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Residues in contact with ALA 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLY 3.9 5.0 - - - +
64D ILE* 3.8 28.0 - - + +
383D VAL* 4.1 11.2 - - + +
385D ILE* 4.0 18.6 - - + -
407D ILE* 4.6 2.7 - - + -
421D ALA 2.7 20.9 + - - +
422D THR 4.0 3.4 - - - +
424D GLY* 1.3 72.3 - - - +
426D ALA* 1.3 52.9 + - - +
428D ALA* 3.3 1.7 + - - +
429D ALA* 2.8 36.6 + - - +
438D VAL* 4.2 4.9 - - + -
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Residues in contact with ALA 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D THR 2.8 20.7 + - - +
423D LEU* 3.6 5.4 - - - +
425D ALA* 1.3 73.7 - - - +
427D PHE* 1.3 59.6 + - - +
429D ALA* 3.9 0.6 - - - +
430D GLU* 2.9 31.0 + - - +
438D VAL* 3.9 19.9 - - + +
457D MET* 5.8 0.2 - - + -
462D LEU* 3.9 26.9 - - + +
463D LYS 5.4 0.7 - - - +
464D PRO* 4.8 12.1 - - + -
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Residues in contact with PHE 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D THR* 3.9 8.3 - - + +
23D PHE* 3.5 26.0 - + - -
44D ARG* 3.3 37.0 + - - +
46D ALA* 3.9 13.0 - - + -
61D TYR* 3.9 12.8 - - + -
423D LEU* 3.0 47.8 + - + -
424D GLY 3.6 5.6 - - - +
426D ALA* 1.3 75.2 - - - +
428D ALA* 1.3 63.8 + - - +
430D GLU* 3.3 5.2 + - - +
431D GLU* 3.1 27.2 + - - +
456D THR* 4.6 0.4 - - + -
460D TRP* 3.5 44.6 - + + -
462D LEU* 3.8 13.7 - - + +
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Residues in contact with ALA 428 (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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61D TYR* 3.7 25.5 - - + +
64D ILE* 3.6 29.6 - - + -
65D LYS* 4.1 11.6 - - + +
424D GLY 3.0 15.1 + - - +
425D ALA 3.7 1.6 - - - +
427D PHE* 1.3 80.7 - - - +
429D ALA* 1.3 62.1 + - - +
431D GLU* 3.2 5.5 + - - +
432D ILE* 3.1 28.2 + - - +
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Residues in contact with ALA 429 (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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64D ILE* 4.5 1.7 - - + +
383D VAL* 4.8 4.5 - - + -
425D ALA 2.8 21.0 + - - +
426D ALA 3.9 2.2 - - - +
428D ALA* 1.3 72.2 - - - +
430D GLU* 1.3 54.3 + - - +
432D ILE* 3.2 4.9 + - - +
433D ASP 2.7 39.7 + - - +
436D LYS* 3.8 35.0 - - + +
438D VAL* 3.8 22.0 - - + -
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Residues in contact with GLU 430 (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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44D ARG* 2.9 39.1 + - - -
426D ALA 2.9 18.8 + - - +
427D PHE 3.5 3.8 - - - +
429D ALA* 1.3 78.2 - - - +
431D GLU* 1.3 60.3 + - - +
432D ILE 3.5 0.2 + - - -
433D ASP 3.6 0.2 + - - -
434D PRO* 3.5 41.0 - - + +
460D TRP 4.2 9.4 - - - +
461D GLY 4.9 3.1 - - - +
462D LEU* 3.6 21.7 - - + +
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Residues in contact with GLU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ASN* 3.8 14.8 - - + +
21D THR* 2.6 27.9 + - - -
44D ARG* 3.0 16.8 + - - +
61D TYR* 2.6 29.3 + - - -
65D LYS* 2.8 24.2 + - - +
427D PHE 3.1 14.3 + - - +
428D ALA 3.6 5.6 - - - +
430D GLU* 1.3 73.5 - - - +
432D ILE* 1.3 65.2 + - - +
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Residues in contact with ILE 432 (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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64D ILE* 3.6 33.2 - - + +
65D LYS* 4.4 18.2 - - + -
428D ALA 3.1 16.8 + - - +
429D ALA* 3.2 7.6 + - - +
430D GLU 4.2 0.2 - - - -
431D GLU* 1.3 80.9 - - - +
433D ASP* 1.3 68.0 + - + +
434D PRO* 4.7 0.8 - - - +
436D LYS* 4.4 19.3 - - + +
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Residues in contact with ASP 433 (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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429D ALA 2.7 20.4 + - - +
431D GLU 3.6 0.6 - - - -
432D ILE* 1.3 85.2 - - + +
434D PRO* 1.4 69.8 - - - +
435D LYS* 3.0 30.5 + - - +
436D LYS* 2.8 34.5 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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