Contacts of the helix formed by residues 456 - 468 (chain D) in PDB entry 1ZYR
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 MET 456 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D THR* 5.8 0.2 - - - +
127D LEU* 3.6 17.5 - - - +
130D SER 3.6 5.8 - - - +
131D LYS* 3.0 41.3 - - - +
132D TYR 4.5 1.3 - - - +
133D ILE* 3.4 27.4 - - + +
158D TYR* 5.2 2.9 - - + -
454D ALA 4.0 3.1 - - - +
455D ARG* 1.3 106.3 - - - +
457D GLY* 1.3 74.1 + - - +
459D GLU* 3.3 13.7 + - - +
460D ALA* 3.2 16.8 + - - -
568D ARG* 3.2 25.4 - - - +
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Residues in contact with GLY 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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97D THR* 5.9 4.3 - - - -
98D PRO 5.7 0.2 - - - -
127D LEU* 3.6 19.5 + - - +
128D TYR* 3.9 8.1 - - - -
456D MET* 1.3 93.4 - - - +
458D ALA* 1.3 54.0 + - - -
459D GLU* 2.7 10.9 + - - -
460D ALA* 3.0 10.0 + - - +
461D ILE 3.8 0.5 + - - -
568D ARG* 3.0 28.9 - - - +
575D GLN* 5.5 1.6 - - - -
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Residues in contact with ALA 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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97D THR* 5.6 0.2 - - - +
98D PRO* 3.8 9.0 + - + -
99D ALA* 3.8 33.7 - - - +
100D ALA* 4.0 8.7 - - + +
128D TYR* 5.0 7.8 - - + +
457D GLY* 1.3 70.9 - - - -
459D GLU* 1.3 56.1 + - - +
460D ALA 3.2 0.4 - - - -
461D ILE* 3.7 13.5 - - + -
462D GLN* 2.8 34.7 + - - +
513D ILE* 3.9 15.7 - - + -
575D GLN* 4.7 6.3 - - - +
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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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97D THR* 4.5 22.0 - - + +
98D PRO* 5.0 3.8 - - + +
455D ARG* 3.6 43.1 + - - +
456D MET* 3.3 10.4 + - - +
457D GLY 2.7 6.3 + - - -
458D ALA* 1.3 75.8 - - - +
460D ALA* 1.3 58.4 + - - +
462D GLN* 4.5 7.9 - - - +
463D GLN* 2.8 43.1 + - - +
140F ARG* 5.3 8.7 - - - +
144F ILE* 4.6 17.2 - - + +
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Residues in contact with ALA 460 (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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127D LEU* 4.7 0.2 - - + -
134D VAL* 4.1 17.7 - - + -
136D ASP* 4.1 8.9 - - - +
455D ARG* 4.1 11.4 - - + -
456D MET* 3.2 22.3 + - - +
457D GLY 3.0 10.1 + - - +
459D GLU* 1.3 81.6 - - - +
461D ILE* 1.3 72.4 + - + +
462D GLN 3.3 0.3 + - - -
463D GLN* 3.4 7.9 + - - +
464D LEU* 3.3 26.0 + - - +
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Residues in contact with ILE 461 (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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112D ILE* 3.8 17.7 - - + -
116D LEU* 3.4 21.3 - - + -
118D LEU* 4.3 12.6 - - + -
127D LEU* 3.3 40.2 - - + -
128D TYR* 3.5 28.7 - - + +
134D VAL* 4.8 0.7 - - + -
457D GLY 3.9 4.3 - - - +
458D ALA* 3.4 7.8 + - + +
460D ALA* 1.3 78.5 - - + +
462D GLN* 1.3 59.0 + - - +
464D LEU* 3.5 10.6 + - + +
465D LEU* 2.8 36.9 + - + +
513D ILE* 5.0 2.7 - - + -
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Residues in contact with GLN 462 (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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98D PRO* 3.1 36.8 - - - +
458D ALA 2.8 18.2 + - - +
459D GLU* 3.7 9.1 - - - +
460D ALA 3.3 0.2 - - - -
461D ILE* 1.3 70.9 - - - +
463D GLN* 1.3 79.4 + - - +
465D LEU* 2.8 12.1 + - - +
466D LYS* 2.8 31.3 + - + +
513D ILE* 3.6 33.1 - - + +
514D LEU 6.1 0.2 - - - -
515D GLU* 4.1 22.5 - - - +
144F ILE* 5.6 5.3 - - - +
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Residues in contact with GLN 463 (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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136D ASP* 3.8 24.5 - - - +
137D PRO* 6.1 0.7 - - + -
455D ARG* 3.7 19.3 + - - +
459D GLU* 2.8 31.6 + - - +
460D ALA 3.5 7.0 - - - +
462D GLN* 1.3 84.9 - - - +
464D LEU* 1.3 58.6 + - + +
466D LYS* 2.7 30.5 + - - +
467D GLU* 3.1 32.1 + - - +
144F ILE* 5.4 7.3 - - - +
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Residues in contact with LEU 464 (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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116D LEU* 4.0 26.2 - - + -
118D LEU* 5.1 3.4 - - + -
134D VAL* 4.3 23.8 - - + -
135D LEU 6.0 0.7 - - - +
136D ASP* 4.4 16.2 - - - +
137D PRO* 6.3 0.9 - - + -
149D LYS 6.0 1.3 - - - +
150D ARG* 4.5 33.0 - - + +
460D ALA 3.3 15.9 + - - +
461D ILE* 3.7 12.8 - - + +
462D GLN 3.2 0.4 - - - -
463D GLN* 1.3 82.0 - - + +
465D LEU* 1.3 58.5 + - - +
467D GLU* 3.4 11.8 + - + +
468D LEU* 3.0 33.3 + - - +
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Residues in contact with LEU 465 (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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112D ILE* 5.0 7.6 - - + -
115D LEU* 4.5 7.6 - - + -
116D LEU* 4.8 12.6 - - + -
461D ILE* 2.8 24.2 + - + +
462D GLN 2.8 8.8 + - - +
464D LEU* 1.3 74.5 - - - +
466D LYS* 1.3 60.1 + - - +
467D GLU 3.2 1.5 + - - -
468D LEU* 3.9 22.3 + - + +
509D PRO* 2.9 48.5 - - + +
510D GLU* 4.0 13.6 - - - +
512D MET* 4.0 23.1 - - + -
513D ILE* 3.8 29.8 - - + -
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Residues in contact with LYS 466 (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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462D GLN* 2.8 29.5 + - + +
463D GLN* 2.7 18.9 + - - +
465D LEU* 1.3 71.6 - - - +
467D GLU* 1.3 62.3 + - + +
468D LEU 3.7 0.7 - - - -
510D GLU* 3.6 34.4 - - + +
511D TRP* 5.8 3.4 - - - -
513D ILE* 5.8 0.4 - - + -
515D GLU* 5.6 3.4 + - - -
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Residues in contact with GLU 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D PRO* 4.8 18.2 - - - +
463D GLN* 3.1 32.1 + - - +
464D LEU* 3.4 13.1 + - + +
465D LEU 3.2 0.2 - - - -
466D LYS* 1.3 83.4 - - + +
468D LEU* 1.3 65.0 + - + +
469D ASP* 3.2 5.9 + - - +
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Residues in contact with LEU 468 (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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115D LEU* 3.2 41.3 - - + +
116D LEU* 3.4 16.4 - - + -
150D ARG* 3.2 36.6 - - - +
464D LEU* 3.0 24.2 + - - +
465D LEU* 3.9 16.8 + - + +
466D LYS 3.7 1.5 - - - -
467D GLU* 1.3 77.2 - - + +
469D ASP* 1.3 60.3 + - - +
470D LEU* 3.0 22.6 + - + +
473D LEU* 5.4 6.7 - - + -
508D ARG* 5.0 1.7 + - - -
509D PRO* 5.7 1.5 - - + +
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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
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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