Contacts of the helix formed by residues 87 - 99 (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 SER 87 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68P GLU* 4.6 4.6 + - - -
85P ASN 3.7 5.4 + - - -
86P PHE* 1.3 80.6 - - - +
88P ILE* 1.3 57.8 + - - +
89P LYS* 3.4 10.2 + - - +
90P GLU* 2.8 36.2 + - - +
91P ILE* 2.8 36.7 + - - +
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Residues in contact with ILE 88 (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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23P LEU* 5.9 2.0 - - + -
37P LEU* 5.1 1.8 - - + -
63P TRP* 4.2 6.1 - - + -
64P ILE* 4.0 20.4 - - + +
67P MET* 3.8 37.5 - - + +
68P GLU* 3.8 25.3 + - + +
71P CYS* 3.7 15.3 - - - -
86P PHE* 3.5 35.1 - - + -
87P SER* 1.3 72.0 - - - +
89P LYS* 1.3 62.9 + - - +
91P ILE* 3.3 6.6 + - + -
92P PHE* 3.0 42.4 + - + +
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Residues in contact with LYS 89 (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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64P ILE* 3.8 35.5 - - + +
68P GLU* 4.8 1.1 + - - +
87P SER* 3.4 7.8 + - - +
88P ILE* 1.3 80.8 - - - +
90P GLU* 1.3 66.2 + - + +
92P PHE* 3.7 2.0 - - - +
93P ASP* 2.9 51.7 + - - +
130P ARG* 4.9 6.7 - - - +
131P ALA* 5.0 3.2 - - - +
132P GLU* 3.1 28.0 + - - -
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Residues in contact with GLU 90 (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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85P ASN 6.0 0.2 - - - +
87P SER* 2.8 33.2 + - - +
89P LYS* 1.3 77.5 - - + +
91P ILE* 1.3 64.5 + - + +
93P ASP* 4.0 7.8 - - - +
94P LYS* 3.4 39.6 + - - +
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Residues in contact with ILE 91 (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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22P VAL* 4.6 15.4 - - + +
23P LEU* 5.6 4.0 - - + -
26P THR* 3.3 43.1 - - + +
30P LEU* 5.1 0.4 - - + -
37P LEU* 4.7 2.0 - - + -
86P PHE* 3.4 31.0 - - + -
87P SER 2.8 21.2 + - - +
88P ILE* 3.5 8.1 - - + +
89P LYS 3.1 0.2 - - - -
90P GLU* 1.3 80.8 - - + +
92P PHE* 1.3 75.4 + - + +
94P LYS* 3.3 6.2 - - - +
95P ALA* 2.9 23.9 + - - +
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Residues in contact with PHE 92 (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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19P VAL* 4.7 20.0 - - + -
22P VAL* 5.6 2.9 - - + -
23P LEU* 4.6 15.9 - - + -
41P PHE* 4.0 19.7 - + - -
60P LEU* 5.2 10.1 - - + -
63P TRP* 3.5 34.8 - + - -
64P ILE* 6.1 3.8 - - + -
67P MET* 4.2 8.1 - - + -
88P ILE* 3.0 41.2 + - + +
89P LYS* 3.9 3.1 - - - +
91P ILE* 1.3 85.6 - - + +
93P ASP* 1.3 69.2 + - - +
94P LYS 3.1 1.8 - - - -
95P ALA* 4.0 6.1 - - + -
96P ILE* 2.8 41.6 + - + +
126P TRP* 5.4 7.2 - + - -
130P ARG* 5.6 3.6 - - - -
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Residues in contact with ASP 93 (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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64P ILE* 5.6 0.2 - - - +
89P LYS* 2.9 52.9 + - - +
90P GLU* 3.8 6.1 + - - +
92P PHE* 1.3 75.2 - - - +
94P LYS* 1.3 63.6 + - - +
96P ILE* 3.9 1.2 - - - +
97P SER* 3.1 27.5 + - - -
130P ARG* 2.8 43.5 + - - +
132P GLU* 2.9 23.1 - - + +
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Residues in contact with LYS 94 (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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90P GLU* 3.4 32.1 + - - +
91P ILE* 3.3 10.7 + - - +
92P PHE 3.1 0.2 - - - -
93P ASP* 1.3 80.6 - - - +
95P ALA* 1.3 63.6 + - - +
97P SER* 3.4 6.3 + - - -
98P ALA* 3.1 25.7 + - - +
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Residues in contact with ALA 95 (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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17P PRO 4.8 2.1 - - - +
19P VAL* 3.8 20.4 - - + +
22P VAL* 3.5 43.2 - - + +
25P ARG* 6.1 0.2 - - - +
91P ILE 2.9 15.3 + - - +
92P PHE* 3.1 8.0 + - - +
94P LYS* 1.3 75.9 - - - +
96P ILE* 1.3 62.6 + - - +
98P ALA* 3.1 19.5 - - - +
99P ARG* 3.2 9.2 + - - +
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Residues in contact with ILE 96 (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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19P VAL* 3.7 24.9 - - + -
60P LEU* 4.4 4.3 - - + -
92P PHE* 2.8 30.9 + - + +
93P ASP 3.9 2.7 - - - +
95P ALA* 1.3 67.7 - - - +
97P SER* 1.3 59.2 + - - +
98P ALA 2.9 4.3 - - - -
99P ARG* 2.9 36.0 + - - +
126P TRP* 3.5 27.6 - - + -
128P ASP* 4.3 0.2 - - - +
130P ARG* 3.6 43.1 - - - +
135P GLY* 5.7 1.3 - - - -
136P LEU* 4.0 24.5 - - + +
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Residues in contact with SER 97 (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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93P ASP 3.1 16.6 + - - -
94P LYS* 3.4 8.5 + - - +
96P ILE* 1.3 79.7 - - - +
98P ALA* 1.3 63.0 + - - +
99P ARG 3.5 4.2 + - - +
100P LYS* 3.2 22.9 + - - -
132P GLU* 6.5 1.1 - - - -
135P GLY* 6.0 6.5 - - - -
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Residues in contact with ALA 98 (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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17P PRO* 4.0 14.6 - - + +
94P LYS 3.1 20.6 + - - +
95P ALA* 3.1 12.1 - - - +
96P ILE 2.9 0.4 - - - -
97P SER* 1.3 76.8 + - - +
99P ARG* 1.3 63.4 + - - +
100P LYS* 3.5 14.8 + - - +
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Residues in contact with ARG 99 (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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10P LEU* 4.6 11.4 - - - +
11P ASP* 3.2 29.9 + - - +
15P ALA* 3.5 21.2 - - + +
16P LEU 3.2 27.4 - - - +
17P PRO* 3.6 12.1 - - - +
19P VAL* 3.1 34.3 - - + +
95P ALA 3.2 2.2 + - - +
96P ILE* 2.9 23.5 + - - +
97P SER 3.6 3.5 - - - +
98P ALA* 1.3 81.6 - - - +
100P LYS* 1.3 64.4 + - - +
126P TRP* 4.9 9.7 - - - -
136P LEU* 2.8 39.4 - - - +
139P LEU* 4.3 17.8 - - + +
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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