Contacts of the strand formed by residues 101 - 106 (chain A) in PDB entry 1ZA3
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 THR 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLN* 2.5 33.7 + - - +
8A PRO* 2.8 35.7 + - + +
9A SER 3.5 3.4 - - - -
10A SER* 4.6 1.1 - - - +
11A LEU* 4.4 6.5 - - + -
21A ILE* 3.3 39.1 - - + +
84A ALA 3.8 1.0 - - - +
85A THR* 3.3 4.1 - - - -
86A TYR* 2.7 42.6 + - - +
100A GLY* 1.3 72.5 - - - -
102A LYS* 1.3 62.8 + - - +
103A VAL 3.9 0.4 + - - -
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Residues in contact with LYS 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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9A SER 2.8 18.2 + - - +
10A SER* 3.2 11.5 - - - -
11A LEU 2.8 28.1 + - - +
83A PHE* 6.5 1.1 - - + -
84A ALA 4.0 2.7 - - - -
85A THR* 3.6 28.3 - - + +
100A GLY 5.9 1.1 - - - +
101A THR* 1.3 73.9 - - - +
103A VAL* 1.3 62.6 + - - +
104A GLU* 5.1 1.3 - - - +
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Residues in contact with VAL 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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11A LEU* 3.6 32.3 - - + -
19A VAL* 4.4 4.9 - - + -
21A ILE* 3.8 16.6 - - + -
75A ILE* 4.8 0.7 - - + -
78A LEU* 4.1 22.2 - - + -
82A ASP 4.0 13.5 - - - +
83A PHE* 3.3 21.3 - - - -
84A ALA 3.0 21.6 + - - +
86A TYR* 3.7 24.0 - - + -
101A THR 4.8 0.2 - - - +
102A LYS* 1.3 73.1 - - - +
104A GLU* 1.3 65.5 + - - +
105A ILE* 4.2 9.2 - - + -
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Residues in contact with GLU 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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11A LEU 3.0 10.9 + - - +
12A SER* 3.0 24.4 + - - +
13A ALA 3.2 23.4 + - - +
83A PHE* 4.2 5.2 - - + -
102A LYS 5.1 1.1 - - - +
103A VAL* 1.3 77.2 - - - +
105A ILE* 1.3 88.8 + - - +
139A TYR* 3.2 22.7 + - - -
140A PRO* 5.8 0.2 - - - +
141A ARG* 5.4 2.6 + - - +
165A GLN* 2.8 27.5 + - - +
172A TYR* 3.1 21.4 + - - +
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Residues in contact with ILE 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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13A ALA 3.4 7.4 - - - +
15A VAL* 4.0 23.1 - - + +
78A LEU* 3.3 28.3 - - + -
79A GLN 3.4 16.4 - - - +
80A PRO* 3.5 22.0 - - + +
82A ASP 4.1 2.0 - - - -
83A PHE* 3.7 24.9 - - + +
103A VAL* 4.2 2.9 - - + -
104A GLU* 1.3 91.6 + - - +
106A LYS* 1.3 70.7 + - - +
107A ARG 3.6 1.9 + - - -
139A TYR* 3.9 2.8 - - - -
165A GLN* 2.9 17.6 - - - +
170A SER* 3.3 23.8 - - - +
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Residues in contact with LYS 106 (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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12A SER* 4.7 13.5 - - - +
13A ALA* 2.9 23.0 + - - +
14A SER* 2.8 35.1 + - - +
15A VAL* 4.2 5.7 + - - +
104A GLU* 3.5 3.2 + - - -
105A ILE* 1.3 77.8 - - - +
107A ARG* 1.3 71.0 + - - +
139A TYR* 3.6 21.5 - - + +
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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