Contacts of the strand formed by residues 330 - 336 (chain A) in PDB entry 4AS7
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 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASN 3.0 7.9 + - - +
19A ILE* 3.1 23.2 - - + +
20A GLN 2.8 24.4 + - - +
100A THR* 3.3 8.6 - - - +
102A PHE* 4.0 28.0 - - + -
299A ILE* 4.2 12.8 - - + -
302A LEU* 5.9 1.3 - - - +
323A SER 5.6 0.2 - - - -
324A LEU* 3.7 22.6 + - + +
328A THR* 3.9 14.8 + - - +
329A ARG* 1.3 75.8 + - - +
331A SER* 1.3 67.2 + - - +
332A ILE* 5.2 1.1 - - + -
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Residues in contact with SER 331 (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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20A GLN* 3.1 27.3 - - - +
22A VAL* 5.9 1.6 - - - -
85A VAL* 4.0 23.1 + - - +
89A ILE* 3.3 24.7 - - - +
100A THR 3.0 7.1 + - - -
101A ILE* 3.3 8.5 - - - +
102A PHE* 2.9 28.8 + - - -
329A ARG* 4.6 2.1 + - - -
330A THR* 1.3 76.5 - - - +
332A ILE* 1.3 64.9 + - - +
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Residues in contact with ILE 332 (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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19A ILE* 5.6 2.0 - - + -
20A GLN 2.9 9.3 + - - +
21A VAL* 4.2 25.1 - - + -
22A VAL* 2.9 30.7 + - - +
102A PHE* 3.6 25.1 - - + +
104A TYR* 4.0 21.8 - - + -
295A LEU* 6.3 1.8 - - + -
299A ILE* 4.3 32.3 - - + -
330A THR* 5.2 1.6 - - + -
331A SER* 1.3 78.5 - - - +
333A ILE* 1.3 72.3 + - - +
334A ALA* 4.3 6.3 - - + +
352A TYR* 5.4 10.8 - - + -
353A ALA* 6.0 2.2 - - + -
356A ALA* 4.3 9.9 - - + -
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Residues in contact with ILE 333 (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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22A VAL* 3.6 21.3 - - + -
24A ARG* 4.1 25.6 - - + -
72A PHE* 5.9 0.7 - - + -
81A VAL* 4.2 13.5 - - + -
85A VAL* 4.3 14.8 - - + -
101A ILE* 3.9 14.1 - - + -
102A PHE 2.7 13.4 + - - +
103A ALA* 3.3 5.8 - - - +
104A TYR 2.9 25.5 + - - +
114A THR* 3.8 19.5 - - + -
115A MET* 5.0 1.6 - - + -
135A ILE* 3.7 29.4 - - + -
332A ILE* 1.3 76.5 - - - +
334A ALA* 1.3 59.1 + - - +
335A THR* 3.8 11.5 + - + +
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Residues in contact with ALA 334 (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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21A VAL* 5.5 0.4 - - + -
22A VAL 2.9 15.3 + - - +
23A VAL* 3.2 18.1 - - + +
24A ARG 2.8 23.0 + - - -
104A TYR* 3.2 12.6 - - + +
332A ILE* 3.9 6.4 + - + -
333A ILE* 1.3 71.4 - - - +
335A THR* 1.3 63.4 + - - +
349A THR* 3.9 20.4 - - + -
353A ALA* 4.3 16.2 - - + -
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Residues in contact with THR 335 (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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24A ARG* 3.2 13.5 - - + +
103A ALA* 5.1 0.9 - - + -
104A TYR 2.8 16.9 + - - -
105A GLY* 3.6 11.1 - - - -
106A GLN* 4.1 1.0 + - - +
109A THR* 2.7 42.9 + - - +
110A GLY 3.9 21.3 - - - +
111A LYS* 3.5 17.1 - - + +
114A THR* 4.2 9.4 - - - +
333A ILE* 4.2 19.1 - - + +
334A ALA* 1.3 77.5 - - - +
336A ILE* 1.3 65.0 + - - +
349A THR* 4.0 2.9 + - - +
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Residues in contact with ILE 336 (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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23A VAL* 3.8 21.5 - - + -
24A ARG 3.0 3.9 + - - +
25A CYS* 3.6 19.9 - - + -
26A ARG* 3.2 29.3 + - - +
41A VAL* 3.9 27.6 - - + -
43A CYS* 5.1 0.4 - - - -
50A VAL* 4.3 11.2 - - + -
109A THR* 3.9 9.2 - - - +
334A ALA 4.8 0.2 - - - +
335A THR* 1.3 79.0 - - - +
337A SER* 1.3 59.1 + - - +
346A THR* 3.9 32.8 - - + +
349A THR* 3.9 24.2 - - + -
350A LEU* 4.3 8.7 - - + -
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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