Contacts of the helix formed by residues 107 - 121 (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 TYR 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D PHE* 3.3 28.1 - + - -
74D TYR* 3.8 21.1 - + - -
75D LEU* 3.8 28.3 - - + -
105D GLN 3.5 2.8 - - - -
106D SER* 1.3 83.9 - - - +
108D LYS* 1.3 63.0 + - - +
109D THR 3.6 0.7 - - - -
110D TYR* 3.5 39.7 - + + -
111D LEU* 3.2 23.6 + - - +
275D MET* 3.6 2.8 - - - +
334D LEU* 4.1 2.8 - - + +
335D PRO* 4.0 21.9 - - + +
338D LYS* 2.9 28.3 + - - -
2001D AGS 3.2 34.6 + - - -
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Residues in contact with LYS 108 (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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100D LEU* 4.1 21.3 - - + +
102D GLY* 3.4 37.2 + - - +
103D PRO 3.4 8.7 + - - -
106D SER 4.4 1.8 - - - +
107D TYR* 1.3 75.8 - - - +
109D THR* 1.3 66.2 - - - +
111D LEU* 4.1 1.0 - - - +
112D LEU* 3.2 29.1 + - - +
250D CYS* 4.0 25.3 - - + +
251D THR 3.4 16.1 + - - +
275D MET* 3.6 27.6 - - + -
2001D AGS 2.7 60.7 + - - +
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Residues in contact with THR 109 (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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108D LYS* 1.3 76.6 - - - +
110D TYR* 1.3 58.9 + - - +
112D LEU* 4.1 8.2 - - + +
113D ASP* 2.9 53.6 + - - +
131D ARG* 5.1 4.9 - - - +
215D ILE* 6.3 2.2 - - + -
217D ASP* 4.0 14.4 + - - +
250D CYS* 5.0 2.0 - - - +
2001D AGS 2.9 17.5 + - - +
2002D MG 2.1 33.8 - - - -
154E GLU* 3.8 23.6 - - + +
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Residues in contact with TYR 110 (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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62D GLY* 4.8 11.4 - - - -
69D LYS* 4.1 18.9 + - + +
70D ILE* 2.9 31.0 + - - +
71D ILE* 3.9 22.3 - - + +
72D PHE* 6.3 1.1 - + - -
75D LEU* 5.5 1.6 - - + -
107D TYR* 3.5 36.6 - + + -
108D LYS 3.2 0.4 - - - -
109D THR* 1.3 74.9 - - - +
111D LEU* 1.3 66.8 + - + +
113D ASP* 3.8 2.2 - - - +
114D TYR* 2.9 29.5 + - + +
2001D AGS 2.7 72.4 + + + +
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Residues in contact with LEU 111 (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* 4.0 23.8 - - + -
75D LEU* 3.7 27.4 - - + +
78D CYS* 4.2 6.1 - - - -
79D GLN* 3.7 30.3 - - + +
82D ILE* 3.9 25.4 - - + -
107D TYR* 3.2 20.7 + - + +
108D LYS 4.2 1.1 - - - +
110D TYR* 1.3 84.5 - - + +
112D LEU* 1.3 61.3 + - - +
114D TYR* 3.4 5.0 + - + +
115D GLU* 3.0 34.2 + - + +
275D MET* 3.8 16.6 - - + -
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Residues in contact with LEU 112 (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* 3.8 16.6 - - + -
86D ILE* 5.4 2.5 - - + -
100D LEU* 3.7 8.7 - - + -
108D LYS 3.2 14.6 + - - +
109D THR* 4.1 6.5 - - + +
110D TYR 3.3 0.2 - - - -
111D LEU* 1.3 75.2 - - - +
113D ASP* 1.3 65.6 + - - +
115D GLU* 4.0 2.1 - - + +
116D LEU* 3.1 33.4 + - + +
215D ILE* 4.0 25.8 - - + -
217D ASP* 5.5 0.2 - - - +
248D PHE* 3.7 50.5 - - + -
250D CYS* 3.7 30.1 - - - -
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Residues in contact with ASP 113 (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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69D LYS* 5.0 5.1 + - - +
109D THR* 2.9 35.3 + - - +
110D TYR 4.0 1.6 - - - +
112D LEU* 1.3 78.2 - - - +
114D TYR* 1.3 59.7 + - - +
116D LEU* 4.2 3.9 - - - +
117D SER* 2.8 30.4 + - - +
131D ARG* 3.0 34.8 + - - -
215D ILE* 5.4 0.2 - - - +
2001D AGS 3.1 32.5 + - + +
154E GLU* 5.6 2.1 - - - +
158E LYS* 4.7 9.6 - - - -
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Residues in contact with TYR 114 (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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66D THR* 4.0 16.3 + - - -
67D ASP* 5.3 6.9 + - - -
69D LYS* 3.7 49.6 + - + +
71D ILE* 4.1 31.6 - - + +
79D GLN* 3.9 16.4 - - - -
110D TYR* 2.9 22.1 + - + +
111D LEU* 3.7 9.0 - - + +
112D LEU 3.2 0.2 - - - -
113D ASP* 1.3 78.3 - - - +
115D GLU* 1.3 79.6 + - + +
117D SER* 3.5 3.5 + - - -
118D LEU* 3.1 49.5 + - + +
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Residues in contact with GLU 115 (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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79D GLN* 2.8 32.7 - - + +
82D ILE* 4.0 22.0 - - + -
83D ASP* 2.8 39.3 - - - +
86D ILE* 3.6 22.1 - - + +
111D LEU* 3.0 22.3 + - + +
112D LEU* 3.4 4.2 + - - +
114D TYR* 1.3 83.7 - - + +
116D LEU* 1.3 64.9 + - - +
118D LEU* 3.5 7.2 + - - +
119D LEU* 3.2 30.0 + - - +
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Residues in contact with LEU 116 (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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86D ILE* 4.6 18.8 - - + -
90D ILE* 4.6 8.5 - - + -
112D LEU* 3.1 19.2 + - + +
113D ASP* 4.6 2.7 - - - +
115D GLU* 1.3 78.6 - - + +
117D SER* 1.3 53.6 + - - +
119D LEU* 3.2 3.1 + - + +
120D GLN* 2.6 35.4 + - - +
127D PHE* 4.1 26.2 - - + -
129D THR* 4.0 14.8 - - + +
131D ARG* 3.9 15.5 - - - +
213D VAL* 4.5 14.6 - - + -
215D ILE* 3.6 30.3 - - + -
248D PHE* 6.2 0.4 - - + -
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Residues in contact with SER 117 (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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66D THR* 4.0 30.2 - - - +
69D LYS* 5.3 4.5 + - - -
113D ASP* 2.8 23.1 + - - +
114D TYR* 3.9 4.3 - - - -
115D GLU 3.3 0.4 - - - -
116D LEU* 1.3 78.7 - - - +
118D LEU* 1.3 60.4 + - - +
120D GLN* 3.3 23.5 + - - +
121D GLN* 3.7 9.9 + - - +
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Residues in contact with LEU 118 (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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66D THR* 4.1 8.9 + - - +
67D ASP* 6.2 1.1 - - - -
83D ASP* 4.9 6.3 - - - +
87D LYS* 4.9 10.5 - - - +
114D TYR* 3.1 51.8 + - + +
115D GLU* 4.0 7.6 - - - +
116D LEU 3.2 0.4 - - - -
117D SER* 1.3 77.2 - - - +
119D LEU* 1.3 71.5 + - + +
121D GLN* 3.4 35.4 + - - +
122D SER* 4.0 8.6 + - - +
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Residues in contact with LEU 119 (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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83D ASP* 4.8 0.4 - - - +
86D ILE* 3.6 30.3 - - + -
87D LYS* 4.0 28.9 - - + +
90D ILE* 4.2 25.1 - - + -
91D ILE* 4.6 1.8 - - + -
115D GLU* 3.2 13.6 + - - +
116D LEU* 3.5 5.6 - - + +
118D LEU* 1.3 87.8 - - + +
120D GLN* 1.3 59.8 + - - +
121D GLN 3.3 2.0 - - - -
122D SER* 4.6 2.7 - - - +
123D TYR* 2.9 68.1 + - + +
127D PHE* 4.1 10.5 - - + -
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Residues in contact with GLN 120 (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 2.6 20.7 + - - +
117D SER* 3.3 18.4 - - - +
119D LEU* 1.3 73.2 - - - +
121D GLN* 1.3 63.8 + - + +
123D TYR 4.4 3.6 - - - -
124D LYS* 3.4 67.3 - - - +
127D PHE* 4.5 9.8 - - + -
159E ASP* 5.9 1.0 + - - -
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Residues in contact with GLN 121 (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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66D THR* 3.7 27.8 + - + +
67D ASP* 5.4 4.8 - - - +
117D SER 3.7 10.0 + - - +
118D LEU* 3.4 34.1 + - - +
120D GLN* 1.3 80.4 - - + +
122D SER* 1.3 64.5 + - - +
124D LYS* 5.7 0.7 - - - -
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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