Contacts of the helix formed by residues 75 - 88 (chain D) in PDB entry 5ZR1
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 LEU 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ILE* 4.0 4.6 - - + +
72D PHE* 3.3 36.1 + - + +
73D THR 3.3 0.6 - - - -
74D TYR* 1.3 107.8 - - + +
76D GLN* 1.3 58.7 + - - +
77D ASP 3.6 1.3 - - - +
78D CYS* 4.0 7.0 - - + +
79D GLN* 3.3 23.9 + - - +
106D SER 5.1 2.0 - - - +
107D TYR* 3.8 28.3 - - + -
110D TYR* 5.5 1.6 - - + -
111D LEU* 3.7 29.8 - - + -
275D MET* 5.1 2.2 - - + -
276D PRO* 3.7 21.5 - - + -
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ILE* 3.9 26.0 + - + +
72D PHE 3.3 13.2 - - - +
73D THR* 3.6 30.0 + - - +
74D TYR 3.6 1.8 - - - -
75D LEU* 1.3 74.8 - - - +
77D ASP* 1.3 64.8 + - - +
78D CYS 3.2 1.3 - - - -
79D GLN* 3.3 10.9 + - + +
80D GLN* 2.8 37.8 + - + +
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Residues in contact with ASP 77 (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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73D THR 5.0 1.9 + - - -
74D TYR 5.2 2.3 + - - +
75D LEU* 4.4 0.4 - - - +
76D GLN* 1.3 80.6 - - - +
78D CYS* 1.3 59.1 + - - +
80D GLN* 4.1 9.1 - - - +
81D GLU* 3.6 21.3 + - - +
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Residues in contact with CYS 78 (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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74D TYR 5.5 0.4 + - - -
75D LEU* 4.0 8.3 - - + +
76D GLN 3.2 0.4 - - - -
77D ASP* 1.3 77.4 - - - +
79D GLN* 1.3 59.5 + - - +
80D GLN 3.3 0.4 - - - -
81D GLU* 3.2 9.1 + - - +
82D ILE* 3.0 35.6 + - - +
111D LEU* 4.2 1.6 - - + -
273D ILE* 5.1 7.6 - - - -
274D TYR 4.7 4.9 - - - +
275D MET* 3.6 37.7 - - - -
276D PRO* 3.6 32.1 - - + +
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Residues in contact with GLN 79 (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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71D ILE* 3.8 18.0 - - + +
75D LEU 3.3 20.2 + - - +
76D GLN* 3.4 15.8 + - - +
78D CYS* 1.3 76.0 - - - +
80D GLN* 1.3 94.0 + - - +
82D ILE* 3.7 5.1 - - - +
83D ASP* 2.8 29.1 + - - +
111D LEU* 3.7 27.4 - - + -
114D TYR* 3.9 14.5 - - - -
115D GLU* 2.8 27.4 - - + +
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Residues in contact with GLN 80 (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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76D GLN* 2.8 23.7 + - + +
77D ASP* 4.4 9.4 - - - +
79D GLN* 1.3 95.4 - - - +
81D GLU* 1.3 58.6 + - - +
83D ASP* 3.7 20.3 + - - +
84D ARG* 3.1 25.8 + - - +
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Residues in contact with GLU 81 (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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712A ARG* 4.4 4.7 + - - -
719A LYS* 6.5 0.9 - - - -
77D ASP 3.6 14.4 + - - +
78D CYS* 3.2 13.0 + - - +
80D GLN* 1.3 77.8 - - - +
82D ILE* 1.3 63.3 + - - +
84D ARG* 3.6 6.6 + - + +
85D ILE* 3.4 24.6 + - - +
271D ARG* 2.7 33.9 + - - +
273D ILE* 3.3 36.4 - - + +
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Residues in contact with ILE 82 (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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78D CYS* 3.0 23.5 + - - +
79D GLN* 3.9 4.7 - - - +
80D GLN 3.4 0.2 - - - -
81D GLU* 1.3 74.8 - - - +
83D ASP* 1.3 63.9 + - - +
85D ILE* 3.3 8.5 + - - +
86D ILE* 3.1 24.7 + - + +
100D LEU* 3.8 34.1 - - + -
111D LEU* 3.9 32.8 - - + +
112D LEU* 3.8 24.9 - - + -
115D GLU* 4.0 16.8 - - + -
248D PHE* 4.1 9.4 - - + -
273D ILE* 4.0 8.3 - - + -
275D MET* 4.7 2.2 - - + -
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Residues in contact with ASP 83 (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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729A TYR* 5.8 1.0 - - - -
79D GLN* 2.8 21.4 + - - +
80D GLN* 3.7 23.8 + - - +
81D GLU 3.3 0.2 - - - -
82D ILE* 1.3 76.4 - - - +
84D ARG* 1.3 62.6 + - - +
86D ILE* 3.3 4.6 - - - +
87D LYS* 3.2 56.6 + - - +
115D GLU* 2.8 31.3 - - - +
118D LEU* 4.9 4.9 - - - +
119D LEU* 4.8 1.6 - - - +
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Residues in contact with ARG 84 (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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715A GLU* 3.9 9.7 + - - +
718A GLU* 2.7 45.1 + - - +
719A LYS* 3.7 37.2 - - - +
722A MET* 4.2 20.0 - - - +
729A TYR* 2.7 41.7 + - + +
80D GLN 3.1 16.7 + - - +
81D GLU* 3.9 7.6 - - + +
82D ILE 3.3 0.2 - - - -
83D ASP* 1.3 77.0 + - - +
85D ILE* 1.3 64.0 + - + +
87D LYS* 3.9 3.7 - - - -
88D GLN* 3.1 47.2 + - - +
271D ARG* 5.9 8.9 - - - +
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Residues in contact with ILE 85 (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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81D GLU 3.4 16.8 + - - +
82D ILE* 3.3 9.0 + - - +
84D ARG* 1.3 79.8 - - + +
86D ILE* 1.3 62.6 + - - +
88D GLN* 4.5 2.5 - - - +
89D SER* 3.4 16.5 + - - -
96D HIS* 3.4 36.4 + - + +
98D VAL* 3.9 32.5 - - + -
246D CYS* 4.3 6.9 - - - -
248D PHE* 3.7 22.7 - - + -
271D ARG* 3.6 35.2 - - - +
273D ILE* 4.6 8.5 - - + -
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Residues in contact with ILE 86 (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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82D ILE* 3.1 18.2 + - + +
83D ASP* 3.3 18.8 - - - +
85D ILE* 1.3 77.8 - - - +
87D LYS* 1.3 65.5 + - + +
89D SER* 3.4 3.6 + - - -
90D ILE* 2.9 41.2 + - + +
112D LEU* 5.4 2.0 - - + -
115D GLU* 3.6 32.5 - - + +
116D LEU* 4.6 17.7 - - + -
119D LEU* 3.6 31.9 - - + -
213D VAL* 5.5 1.8 - - + -
246D CYS* 5.0 3.1 - - - -
248D PHE* 3.6 33.0 - - + -
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Residues in contact with LYS 87 (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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729A TYR* 3.6 43.8 - - + -
83D ASP* 3.2 46.4 + - - +
84D ARG 4.3 0.9 - - - +
86D ILE* 1.3 80.6 - - + +
88D GLN* 1.3 59.6 + - - +
89D SER 3.4 0.9 - - - -
90D ILE* 4.2 3.4 - - - +
91D ILE* 3.3 44.2 - - + +
118D LEU* 4.9 7.5 - - - +
119D LEU* 4.0 20.7 - - + +
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Residues in contact with GLN 88 (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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427A LYS* 4.8 4.9 + - - +
715A GLU* 3.7 20.2 + - - +
718A GLU* 3.9 7.4 - - - +
729A TYR* 3.8 14.8 + - + -
84D ARG* 3.1 50.5 + - - +
85D ILE* 4.8 0.8 - - - +
87D LYS* 1.3 76.4 - - - +
89D SER* 1.3 56.7 + - - +
90D ILE 3.8 0.2 - - - -
92D GLN* 3.5 34.1 - - - +
94D GLU* 3.2 34.8 + - - +
96D HIS* 3.5 27.2 + - + -
271D ARG* 5.1 4.9 - - - +
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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