Contacts of the helix formed by residues 444 - 459 (chain D) in PDB entry 3ZXR
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 THR 444 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D SER* 3.9 15.7 + - - -
114D LYS* 4.0 9.8 - - - +
438D THR* 4.7 1.8 - - - -
441D GLY* 3.7 19.7 - - - +
443D PHE* 1.3 78.8 - - - +
445D ASN* 1.3 66.2 + - - +
446D ASP* 2.5 28.8 + - - +
447D LEU* 3.1 21.6 + - - +
448D ILE* 3.2 16.4 + - - +
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Residues in contact with ASN 445 (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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434D HIS* 3.4 25.3 + - - -
435D GLU* 5.5 0.3 - - - +
438D THR* 3.9 13.4 - - - +
444D THR* 1.3 73.4 - - - +
446D ASP* 1.3 57.7 + - - +
448D ILE* 3.4 5.1 + - - +
449D GLU* 2.8 47.8 + - + +
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Residues in contact with ASP 446 (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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105D SER* 2.6 27.5 + - - -
106D ARG* 2.8 27.5 + - - +
444D THR* 2.5 28.6 + - - -
445D ASN* 1.3 76.1 - - - +
447D LEU* 1.3 64.0 + - - +
449D GLU* 4.1 9.3 - - - +
450D THR* 2.8 31.7 + - - -
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Residues in contact with LEU 447 (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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28D LEU* 3.9 28.5 - - + -
105D SER 4.0 10.1 - - - +
106D ARG* 4.1 13.7 - - + +
111D ILE* 3.5 35.0 - - + -
319D PHE* 4.7 5.2 - - + -
378D LEU* 4.5 11.0 - - + -
443D PHE* 3.6 32.5 - - + -
444D THR* 3.1 16.9 + - - +
446D ASP* 1.3 83.2 - - - +
448D ILE* 1.3 57.4 + - - +
450D THR* 3.3 2.8 + - - -
451D TRP* 2.9 32.0 + - + +
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Residues in contact with ILE 448 (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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319D PHE* 4.6 9.2 - - + -
430D LEU* 4.1 12.8 - - + -
434D HIS* 3.8 47.3 - - + +
437D LEU* 4.3 7.0 - - + -
438D THR* 4.0 10.1 - - + -
443D PHE* 3.9 34.1 - - + -
444D THR 3.2 10.8 + - - +
445D ASN* 3.8 8.3 - - - +
447D LEU* 1.3 81.8 - - - +
449D GLU* 1.3 58.4 + - + +
451D TRP* 3.3 7.0 + - - +
452D ILE* 2.9 47.2 + - + +
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Residues in contact with GLU 449 (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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445D ASN* 2.8 37.3 + - - +
446D ASP* 4.1 7.2 - - - +
448D ILE* 1.3 71.8 - - + +
450D THR* 1.3 60.3 + - - +
452D ILE* 3.8 11.4 - - + +
453D SER* 2.9 32.2 + - - -
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Residues in contact with THR 450 (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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28D LEU* 3.7 21.3 - - + -
60D GLY* 3.8 23.1 - - - +
61D PHE 5.7 0.2 - - - +
106D ARG* 3.6 19.2 + - - +
446D ASP 2.8 22.9 + - - -
447D LEU 3.6 3.8 - - - -
449D GLU* 1.3 76.1 - - - +
451D TRP* 1.3 53.1 + - - +
453D SER* 3.6 5.0 - - - -
454D PHE* 2.7 36.0 + - + +
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Residues in contact with TRP 451 (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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28D LEU* 3.3 45.7 - - + +
29D PRO* 4.1 15.5 - - + -
318D ALA 3.0 28.9 + - - -
319D PHE* 3.5 35.4 - + + -
322D PRO* 3.7 12.6 - - + -
375D ASN* 4.7 5.2 - - + -
378D LEU* 3.6 19.1 - - + -
427D ILE* 4.2 9.2 - - + +
430D LEU* 3.9 15.9 - - + -
447D LEU* 2.9 18.9 + - + +
448D ILE* 3.5 5.8 - - - +
450D THR* 1.3 74.6 - - - +
452D ILE* 1.3 64.5 + - - +
454D PHE* 3.3 6.8 + + + +
455D LYS* 3.0 62.1 + - + +
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Residues in contact with ILE 452 (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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427D ILE* 3.7 20.6 - - + +
430D LEU* 4.0 16.4 - - + -
431D GLU* 3.6 38.1 - - + +
434D HIS* 5.4 0.4 - - + +
448D ILE* 2.9 38.1 + - + +
449D GLU* 3.8 10.5 - - + +
451D TRP* 1.3 77.2 - - - +
453D SER* 1.3 65.1 + - - +
455D LYS* 3.5 2.3 + - - +
456D ARG* 3.1 62.7 + - - +
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Residues in contact with SER 453 (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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449D GLU 2.9 19.6 + - - -
450D THR* 3.6 5.6 - - - -
452D ILE* 1.3 79.9 - - - +
454D PHE* 1.3 62.7 + - - +
456D ARG* 3.3 6.3 + - - +
457D GLU* 3.0 49.3 + - - +
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Residues in contact with PHE 454 (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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28D LEU* 5.8 3.6 - - + -
29D PRO* 3.9 20.9 - - + -
59D ARG* 3.9 47.3 - - + -
60D GLY* 4.9 9.2 - - - -
450D THR* 2.7 27.4 + - + +
451D TRP* 3.3 8.9 + + + +
453D SER* 1.3 72.9 - - - +
455D LYS* 1.3 67.8 + - + +
457D GLU* 5.2 0.2 - - - -
458D ASN* 2.9 69.8 + - + +
459D GLU* 3.3 26.5 - - + -
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Residues in contact with LYS 455 (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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29D PRO* 5.4 6.8 + - - +
322D PRO* 2.8 37.3 + - - +
323D THR* 4.4 5.1 - - - +
373D SER 5.3 1.2 + - - -
423D LEU* 4.3 3.1 - - + -
427D ILE* 4.0 29.6 - - + -
451D TRP* 3.0 50.4 + - - +
452D ILE 3.9 3.6 - - - +
454D PHE* 1.3 86.3 - - - +
456D ARG* 1.3 59.4 + - - +
459D GLU* 2.8 38.9 + - - +
460D ILE* 2.9 31.1 + - + +
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Residues in contact with ARG 456 (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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427D ILE* 3.7 8.5 + - + +
428D ASP* 2.9 36.7 + - - +
431D GLU* 2.9 42.0 + - - -
452D ILE* 3.1 37.3 + - - +
453D SER* 3.8 6.3 - - - +
455D LYS* 1.3 76.8 - - - +
457D GLU* 1.3 63.4 + - + +
460D ILE* 3.8 23.2 - - + +
461D GLU* 3.0 34.6 + - - +
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Residues in contact with GLU 457 (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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453D SER* 3.0 34.6 + - - +
454D PHE* 5.8 0.2 - - - -
456D ARG* 1.3 81.2 - - + +
458D ASN* 1.3 67.5 + - - +
461D GLU* 4.6 14.4 - - - +
462D PRO* 3.4 17.2 - - - +
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Residues in contact with ASN 458 (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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454D PHE* 2.9 63.8 + - + +
457D GLU* 1.3 85.3 + - - +
459D GLU* 1.3 64.5 + - + +
462D PRO* 3.4 16.7 - - - +
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Residues in contact with GLU 459 (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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29D PRO* 5.6 0.9 - - - +
322D PRO 3.5 9.7 - - - +
323D THR* 3.7 18.3 - - - +
324D VAL* 4.2 12.3 + - + -
423D LEU* 4.0 3.5 - - + +
454D PHE* 3.3 16.9 - - + -
455D LYS* 2.8 51.2 + - - +
458D ASN* 1.3 88.3 - - + +
460D ILE* 1.3 67.8 + - - +
461D GLU 3.5 0.7 - - - -
462D PRO* 3.4 2.7 - - - +
463D VAL* 3.1 30.6 + - - +
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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