Contacts of the helix formed by residues 95 - 106 (chain I) in PDB entry 1DZG
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 CYS 95 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20I MET 4.2 4.7 - - - -
21I CYS* 2.0 55.0 - - - -
94I ALA* 1.3 75.0 - - - +
96I ASN* 1.3 83.4 + - + +
97I ASP 3.1 0.3 + - - -
98I THR* 2.8 24.1 + - - -
99I LEU* 3.3 11.6 + - - +
350I LYS* 3.0 10.0 + - + +
352I PRO* 3.7 15.3 - - + -
801I NAG 5.1 4.7 - - - -
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Residues in contact with ASN 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I CYS* 1.3 81.7 - - - +
97I ASP* 1.3 67.9 + - + +
99I LEU* 4.1 8.3 - - - +
100I GLN* 3.5 20.6 + - - +
350I LYS* 4.5 13.6 - - + +
801I NAG 1.4 73.0 + - - +
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Residues in contact with ASP 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ASN* 1.3 83.3 - - + +
98I THR* 1.3 70.4 + - - +
99I LEU 3.4 0.7 - - - -
100I GLN* 3.8 20.2 + - - +
101I GLN* 3.1 28.9 + - - +
342I ASP* 3.6 20.6 - - - +
350I LYS* 5.5 0.2 - - - +
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Residues in contact with THR 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I ALA* 3.9 4.0 - - + -
95I CYS 2.8 12.4 + - - -
97I ASP* 1.3 78.4 - - - +
99I LEU* 1.3 64.9 + - - +
101I GLN* 3.6 2.9 - - - +
102I LEU* 3.0 25.9 + - - +
340I LEU* 4.8 0.7 - - - +
342I ASP* 3.9 13.2 - - + +
343I LEU* 3.6 48.6 - - + +
348I LYS 4.0 2.1 + - - -
349I SER* 4.2 0.2 - - - -
350I LYS* 3.0 34.0 + - - +
351I LEU* 3.8 10.5 - - + -
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Residues in contact with LEU 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I CYS 4.5 3.6 - - - +
22I ILE 3.7 22.9 - - - +
23I TYR* 3.6 27.6 - - + -
91I LYS* 4.0 28.5 - - + +
94I ALA* 3.7 13.0 - - - +
95I CYS* 3.3 28.8 + - - +
96I ASN 4.1 8.5 - - - +
98I THR* 1.3 78.3 - - - +
100I GLN* 1.3 63.6 + - - +
102I LEU* 3.1 8.3 + - - +
103I MET* 2.9 24.8 + - + +
116I SER* 3.7 25.8 - - - +
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Residues in contact with GLN 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I TYR* 3.6 38.2 - - + -
96I ASN 3.5 16.4 + - - +
97I ASP* 4.0 18.9 + - - +
98I THR 3.4 0.8 - - - -
99I LEU* 1.3 83.1 - - - +
101I GLN* 1.3 64.2 + - - +
103I MET* 3.3 2.8 + - - +
104I GLU* 3.0 48.5 + - - +
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Residues in contact with GLN 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ASP* 3.1 19.2 + - + +
98I THR* 3.6 3.2 - - - +
100I GLN* 1.3 75.4 - - - +
102I LEU* 1.3 65.3 + - - +
104I GLU* 3.1 13.9 + - - +
105I VAL* 2.8 27.9 + - + +
339I GLY 3.2 26.6 + - - +
340I LEU* 3.8 9.0 - - + +
341I VAL* 3.4 11.9 + - - +
342I ASP* 3.1 47.7 + - - +
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Residues in contact with LEU 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I PHE* 3.8 18.2 - - + +
90I THR* 4.6 1.3 - - + -
91I LYS* 3.4 40.8 - - + +
94I ALA* 3.9 18.2 - - + -
98I THR 3.0 12.7 + - - +
99I LEU 3.1 8.0 + - - +
101I GLN* 1.3 76.0 - - - +
103I MET* 1.3 67.4 + - - +
106I PHE* 3.3 39.9 + - + +
108I PHE* 5.1 2.2 - - - -
340I LEU* 3.4 33.8 - - + +
343I LEU* 3.9 20.0 - - + -
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Residues in contact with MET 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I TYR* 3.7 35.2 - - + -
25I SER* 4.8 0.4 - - - -
91I LYS* 3.4 32.3 - - - +
99I LEU* 2.9 26.1 + - + +
100I GLN 3.6 5.4 - - - +
102I LEU* 1.3 73.1 - - - +
104I GLU* 1.3 65.0 + - - +
106I PHE 3.2 7.6 + - - -
108I PHE* 3.2 55.3 + - + +
109I ASP* 3.9 6.1 - - - +
114I LYS 4.5 10.5 - - - +
116I SER* 4.1 12.3 - - - +
119I ILE* 3.9 19.5 - - + -
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Residues in contact with GLU 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I TYR* 4.1 13.0 + - + +
100I GLN* 3.0 48.4 + - - +
101I GLN* 3.5 17.3 - - - +
103I MET* 1.3 75.3 - - - +
105I VAL* 1.3 63.6 + - + +
107I LYS* 3.4 18.0 + - - +
109I ASP* 3.7 27.4 - - - +
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Residues in contact with VAL 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I PHE* 3.4 25.6 - - + -
101I GLN* 2.8 26.2 + - + +
102I LEU 3.9 2.7 - - - +
104I GLU* 1.3 73.7 - - + +
106I PHE* 1.3 68.2 + - + +
107I LYS* 3.3 12.6 + - - +
335I LEU* 4.8 4.5 - - + +
338I MET* 4.3 29.5 - - + +
339I GLY* 3.8 11.9 - - - +
340I LEU* 3.7 36.1 - - + +
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Residues in contact with PHE 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ALA 4.3 3.6 - - - +
55I ASN* 5.1 0.5 + - - +
58I PHE* 3.4 49.6 - + + +
83I ILE* 3.9 12.1 - - + -
84I SER* 4.2 13.9 + - - +
87I PHE* 3.4 30.5 - + + -
102I LEU* 3.3 43.1 - - + +
103I MET 3.2 1.6 + - - -
105I VAL* 1.3 79.6 - - + +
107I LYS* 1.3 60.8 + - - +
108I PHE* 2.9 42.1 + + + -
335I LEU* 3.5 19.5 - - + -
340I LEU* 3.8 9.9 - - + -
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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