Contacts of the helix formed by residues 102 - 115 (chain P) in PDB entry 1ZD2
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 ASN 102 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12P GLY 5.4 0.2 + - - -
13P VAL* 3.1 28.7 + - - +
14P LEU 2.6 15.7 + - - +
15P ALA 4.3 0.4 - - - +
16P LEU* 3.3 29.2 - - + +
100P LYS 3.2 3.2 + - - -
101P ILE* 1.3 69.3 - - - +
103P ARG* 1.3 63.1 + - - +
104P PRO* 3.1 22.5 - - - +
105P MET* 3.0 14.9 + - - +
106P LEU* 3.1 12.0 + - - +
203P VAL* 6.1 0.4 - - - +
206P THR* 3.2 32.0 + - - +
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Residues in contact with ARG 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P ILE* 2.8 42.0 + - - +
102P ASN* 1.3 68.8 - - - +
104P PRO* 1.3 73.4 - - + +
105P MET 3.1 0.2 + - - -
106P LEU* 3.1 19.4 + - - +
107P GLN* 2.9 26.5 + - - +
142P GLU* 2.8 38.4 + - - -
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Residues in contact with PRO 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ASN* 3.1 20.2 - - - +
103P ARG* 1.3 95.1 - - + +
105P MET* 1.3 55.0 + - - +
107P GLN* 3.5 14.5 + - + +
108P ALA* 2.9 28.1 + - - +
206P THR* 4.1 11.2 - - + -
207P ASP* 5.4 5.4 - - - +
210P LEU* 4.3 15.9 - - + +
221P LEU 5.6 0.9 - - - +
222P LEU* 5.9 1.8 - - + -
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Residues in contact with MET 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 3.9 19.1 - - + -
13P VAL* 3.0 46.4 - - + +
14P LEU* 3.7 15.7 - - + -
102P ASN* 3.0 14.8 + - - +
104P PRO* 1.3 78.6 - - - +
106P LEU* 1.3 67.8 + - - +
108P ALA* 3.0 5.7 + - - +
109P ALA* 2.9 21.7 + - - +
183P LEU* 5.7 1.6 - - - -
203P VAL* 4.0 24.7 - - + -
206P THR* 3.7 19.7 - - + +
209P ALA* 4.5 4.7 - - + -
210P LEU* 3.4 24.5 - - + -
213P LEU* 5.6 0.2 - - - -
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P LEU* 4.0 9.1 - - + +
101P ILE* 3.9 27.8 - - + -
102P ASN 3.1 6.0 + - - +
103P ARG* 3.6 24.5 - - - +
105P MET* 1.3 76.0 - - - +
107P GLN* 1.3 57.0 + - - +
109P ALA* 3.1 2.5 + - - +
110P LEU* 2.8 41.0 + - + +
142P GLU* 4.6 0.2 - - - +
143P LEU* 3.6 19.3 - - + -
146P HIS* 3.8 28.9 - - + +
147P PHE* 3.8 25.1 - - + -
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Residues in contact with GLN 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P ARG* 2.9 15.1 + - - +
104P PRO* 3.7 13.7 - - - +
106P LEU* 1.3 75.3 - - - +
108P ALA* 1.3 66.6 + - - +
110P LEU* 3.2 14.0 + - + +
111P MET* 3.0 24.7 + - + +
221P LEU 5.5 2.9 - - - +
222P THR* 3.4 26.9 - - + +
223P PRO 3.7 0.7 - - - +
224P ALA* 4.4 1.9 - - - +
225P PRO* 2.9 42.8 - - + +
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Residues in contact with ALA 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 5.0 0.4 - - + -
104P PRO 2.9 15.6 + - - +
105P MET* 3.3 8.7 - - - +
107P GLN* 1.3 76.3 - - - +
109P ALA* 1.3 63.6 - - - +
111P MET* 3.4 4.6 + - - +
112P LEU* 3.1 27.5 + - - +
210P LEU* 3.8 25.1 - - + -
213P LEU* 4.7 3.4 - - + -
221P LEU* 3.7 33.5 - - + +
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Residues in contact with ALA 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 3.7 25.2 - - + -
14P LEU* 4.7 0.7 - - + -
105P MET 2.9 12.1 + - - +
106P LEU* 3.2 9.4 - - - +
108P ALA* 1.3 76.1 - - - +
110P LEU* 1.3 64.1 + - + +
112P LEU* 3.1 8.9 + - - +
113P ARG 3.0 17.3 + - - -
119P THR* 3.7 8.1 - - + +
146P HIS 5.6 0.4 - - - -
147P PHE* 3.6 36.3 - - + -
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Residues in contact with LEU 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P LEU* 2.8 51.1 + - + +
107P GLN* 3.5 12.3 - - + +
109P ALA* 1.3 74.5 - - - +
111P MET* 1.3 54.8 + - - +
113P ARG* 2.9 12.3 + - - +
114P LYS* 2.7 36.6 + - - +
146P HIS* 3.3 51.8 - - + +
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Residues in contact with MET 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P GLN* 3.0 13.2 + - + +
108P ALA* 3.4 10.8 - - - +
110P LEU* 1.3 75.6 - - - +
112P LEU* 1.3 65.5 + - - +
114P LYS* 3.0 37.9 + - + +
115P LYS* 3.0 50.1 + - + +
219P ILE* 4.1 9.9 - - + -
220P GLN 4.1 9.0 - - - +
221P LEU* 3.7 20.9 - - + -
222P THR* 5.2 12.8 - - + -
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Residues in contact with LEU 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P ALA* 3.5 27.1 - - + -
8P PHE* 4.1 7.2 - - + -
108P ALA 3.1 12.1 + - - +
109P ALA 3.1 7.9 + - - +
111P MET* 1.3 79.3 - - - +
113P ARG* 1.3 65.3 + - - +
115P LYS* 3.0 12.8 + - - -
117P PHE* 3.0 37.2 + - + +
119P THR* 4.7 2.2 - - + -
213P LEU* 3.8 29.2 - - + -
217P THR* 3.9 24.2 - - + +
219P ILE* 3.8 26.7 - - + -
221P LEU* 4.1 9.6 - - + -
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Residues in contact with ARG 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P ALA 3.0 6.3 + - - +
110P LEU* 2.9 15.6 + - - +
112P LEU* 1.3 77.4 - - - +
114P LYS* 1.3 62.7 + - - +
115P LYS 2.9 1.6 + - - -
116P GLY* 2.9 13.3 + - - -
117P PHE* 3.2 25.8 + - - +
119P THR* 3.8 16.4 + - + +
145P MET 3.0 24.4 + - - -
146P HIS* 3.3 25.0 - - - +
147P PHE 3.6 4.6 + - - -
148P ASP* 2.9 45.8 + - - +
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Residues in contact with LYS 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P LEU 2.7 16.3 + - - +
111P MET* 3.0 28.9 + - + +
113P ARG* 1.3 72.1 - - - +
115P LYS* 1.3 57.1 + - + +
116P GLY 3.4 2.2 + - - -
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Residues in contact with LYS 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P MET* 3.0 41.2 + - + +
112P LEU 3.0 5.4 + - - +
113P ARG 2.9 1.8 + - - -
114P LYS* 1.3 79.7 - - + +
116P GLY* 1.3 56.9 + - - +
117P PHE* 3.5 9.9 + - - -
219P ILE* 3.5 46.6 - - + +
220P GLN* 4.5 16.6 + - - +
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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