Contacts of the strand formed by residues 10 - 15 (chain A) in PDB entry 1Z83
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 ILE 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.1 18.6 - - + +
6A LYS* 6.0 0.2 - - - -
8A THR 3.5 7.2 + - - +
9A ASN* 1.3 77.5 - - - +
11A ILE* 1.3 61.5 + - - +
12A PHE* 3.9 29.6 - - + -
80A MET* 4.2 22.4 - - + -
90A PHE* 3.7 7.9 - - + -
92A ILE* 4.2 10.1 - - + -
105A PHE* 4.0 14.8 - - + -
109A ILE* 4.3 14.1 - - + -
110A GLY* 4.7 4.3 - - - +
111A GLN 4.4 11.0 - - - +
112A PRO* 3.7 11.0 - - + +
113A THR* 2.8 35.9 + - - +
114A LEU 3.3 6.4 + - - +
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Residues in contact with ILE 11 (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 ASN* 5.1 2.7 - - + -
10A ILE* 1.3 78.5 - - - +
12A PHE* 1.3 73.1 + - - +
13A VAL* 3.5 2.7 + - + +
28A ILE* 5.9 0.4 - - + -
34A TYR* 3.6 31.6 - - + +
90A PHE 2.8 14.8 + - - +
91A LEU* 3.5 24.3 - - + -
92A ILE 2.8 27.5 + - - -
113A THR* 5.4 1.3 - - - -
114A LEU* 3.4 26.2 - - + +
116A LEU* 4.3 18.8 - - + -
190A LEU* 4.1 24.5 - - + -
194A LEU* 6.1 0.9 - - + -
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Residues in contact with PHE 12 (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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10A ILE* 3.9 10.3 - - + -
11A ILE* 1.3 72.4 - - - +
13A VAL* 1.3 60.0 + - - +
14A VAL* 3.8 7.5 + - + -
92A ILE* 3.6 12.3 - - + +
95A TYR 3.9 9.6 - - - -
96A PRO* 3.5 26.7 - - + -
102A GLY* 5.3 0.2 - - - -
105A PHE* 3.7 51.6 - + + -
112A PRO* 3.6 32.8 - - + -
114A LEU 3.0 10.8 + - - +
115A LEU* 3.3 14.8 - - + +
116A LEU 2.8 28.4 + - - +
164A TYR* 3.7 29.8 - + - -
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Residues in contact with VAL 13 (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 ILE* 4.1 14.1 - - + +
12A PHE* 1.3 73.3 - - - +
14A VAL* 1.3 64.3 + - - +
21A LYS* 3.7 29.9 - - + +
24A GLN* 6.2 1.6 - - + -
25A CYS* 3.8 25.8 - - - -
28A ILE* 5.6 0.2 - - + -
91A LEU* 4.3 16.2 - - + -
92A ILE 2.8 16.0 + - - +
93A ASP* 4.2 6.1 - - - -
94A GLY* 3.4 23.6 + - - -
95A TYR 4.9 1.2 + - - +
116A LEU* 3.5 21.5 - - + +
118A VAL* 4.2 12.6 - - + -
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.3 10.3 - - + -
13A VAL* 1.3 78.8 - - - +
15A GLY* 1.3 61.9 + - - +
21A LYS* 3.9 4.7 - - - +
94A GLY* 6.1 0.4 - - - -
95A TYR 5.5 0.7 - - - +
96A PRO* 4.7 11.0 - - + +
115A LEU* 3.9 30.5 - - + -
116A LEU 2.9 8.2 + - - +
117A TYR* 3.5 3.9 - - - -
118A VAL* 2.9 27.0 + - - +
153A TYR* 4.6 2.9 - - + +
157A THR* 3.9 26.2 - - + +
160A VAL* 4.7 9.6 - - + -
161A ILE* 3.4 29.8 - - + -
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Residues in contact with GLY 15 (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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14A VAL* 1.3 80.6 - - - +
16A GLY* 1.3 67.4 + - - -
19A SER* 3.5 6.3 - - - -
21A LYS* 3.1 18.5 + - - +
97A ARG* 5.7 2.8 + - - -
117A TYR* 4.9 0.7 - - - -
118A VAL 3.5 15.5 - - - -
153A TYR* 3.4 22.5 - - - -
157A THR* 5.6 0.3 - - - +
631A AP5 5.5 0.2 + - - -
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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