Contacts of the helix formed by residues 93 - 105 (chain A) in PDB entry 2Z4U
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE* 1.3 80.9 - - - +
94A SER* 1.3 60.7 + - - +
95A THR* 3.5 7.2 + - - -
96A GLU* 3.0 31.2 + - - +
97A SER* 2.8 28.0 + - - -
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE 3.9 0.2 + - - -
93A SER* 1.3 74.1 - - - +
95A THR* 1.3 62.5 + - - +
97A SER* 3.4 7.1 + - - -
98A THR* 3.1 26.0 + - - -
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 3.3 7.1 + - - -
94A SER* 1.3 80.3 - - - +
96A GLU* 1.3 65.8 + - + +
98A THR* 3.3 9.5 + - - -
99A ASP* 3.2 29.1 + - - +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 3.8 20.8 + - - +
67A ARG* 2.8 47.3 + - - +
74A MET* 3.7 15.8 - - + +
92A ILE* 3.8 14.2 - - + +
93A SER* 3.0 23.4 + - - +
95A THR* 1.3 80.2 - - + +
97A SER* 1.3 57.5 + - - +
99A ASP* 3.1 4.8 + - - +
100A VAL* 2.9 29.6 + - - +
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.8 19.1 - - - +
92A ILE* 3.8 17.8 - - - +
93A SER 2.8 17.9 + - - -
94A SER* 3.6 9.0 - - - -
96A GLU* 1.3 76.5 - - - +
98A THR* 1.3 60.9 + - - +
100A VAL* 3.2 4.0 + - - +
101A GLU* 2.9 35.2 + - - +
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A SER 3.1 15.3 + - - -
95A THR* 3.5 11.6 - - - -
97A SER* 1.3 74.1 - - - +
99A ASP* 1.3 68.2 + - - +
101A GLU* 3.4 18.6 + - - +
102A ASN* 3.0 39.9 + - - +
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 5.2 5.2 + - - +
49A TYR* 2.7 41.4 + - + +
65A MET* 4.1 1.3 - - - -
95A THR* 3.2 19.3 + - - +
96A GLU* 3.1 10.4 + - - +
98A THR* 1.3 83.0 - - - +
100A VAL* 1.3 55.2 + - - +
102A ASN* 3.4 5.5 + - - +
103A THR* 2.7 38.6 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A MET* 3.6 19.1 - - + -
74A MET* 3.6 34.3 - - + +
75A GLY* 4.9 3.6 - - - -
88A ILE* 3.7 26.2 - - + -
92A ILE* 3.7 12.6 - - + -
96A GLU 2.9 19.3 + - - +
97A SER 3.2 6.0 + - - +
99A ASP* 1.3 72.0 - - - +
101A GLU* 1.3 66.1 + - - +
104A LEU* 3.0 47.9 + - + +
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TYR* 4.0 29.6 + - + -
88A ILE* 3.9 15.1 - - + +
97A SER* 2.9 27.5 + - - +
98A THR* 3.5 22.4 + - - +
100A VAL* 1.3 75.5 - - - +
102A ASN* 1.4 60.6 + - - +
105A CYS* 3.0 34.1 + - - +
111A ARG* 3.2 23.6 + - - +
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Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A THR* 3.0 35.0 + - - +
99A ASP* 4.0 5.4 + - - +
101A GLU* 1.4 76.7 - - - +
103A THR* 1.3 62.3 + - - +
105A CYS 4.1 1.3 - - - -
106A PRO* 3.2 30.1 - - + +
111A ARG* 3.0 29.1 + - - +
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A VAL* 3.8 31.6 - - + +
49A TYR* 4.4 6.8 - - - -
51A LEU* 3.8 33.2 - - + +
65A MET* 3.6 19.0 - - + +
99A ASP* 2.7 25.8 + - - +
102A ASN* 1.3 80.2 - - - +
104A LEU* 1.3 65.3 + - - +
106A PRO* 3.8 8.7 - - - +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.9 23.5 - - + +
63A THR* 3.7 25.6 - - + +
65A MET* 3.9 13.9 - - + +
75A GLY 4.3 1.6 - - - -
76A TYR 3.6 31.4 - - - +
77A SER* 3.8 22.0 + - - +
84A CYS* 3.3 12.5 - - - -
86A TYR* 4.3 9.4 - - + -
87A HIS 4.9 1.3 - - - +
100A VAL* 3.0 36.6 + - + +
101A GLU 4.5 0.2 - - - +
103A THR* 1.3 78.4 - - - +
105A CYS* 1.3 63.6 + - - +
106A PRO* 3.5 5.9 - - - +
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Residues in contact with CYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER* 4.4 1.3 - - - -
84A CYS* 2.1 58.1 - - + -
85A ARG 4.3 0.2 - - - -
86A TYR* 3.9 24.0 - - + -
101A GLU 3.0 14.2 + - - +
102A ASN 3.8 0.2 - - - -
104A LEU* 1.3 78.9 - - - +
106A PRO* 1.3 63.2 - - - +
107A ASN 3.1 5.0 + - - +
111A ARG* 2.8 43.8 + - + -
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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