Contacts of the strand formed by residues 19 - 25 (chain A) in PDB entry 4B7B
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY* 2.9 10.3 + - - +
18A ASN* 1.3 87.7 - - + +
20A GLN* 1.3 65.1 + - - +
21A VAL* 4.7 7.6 - - + -
299A ILE* 4.1 24.7 - - + +
302A LEU* 3.7 35.4 - - + +
303A VAL* 3.9 26.0 - - + +
328A THR* 6.1 1.3 - - + -
330A THR* 3.2 28.0 - - + +
331A SER* 5.5 0.2 - - - -
332A ILE* 5.3 2.9 - - + -
357A LYS* 2.8 31.1 + - + +
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Residues in contact with GLN 20 (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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16A GLY 3.6 2.2 + - - -
17A LYS* 2.4 38.0 + - - +
18A ASN 5.4 1.1 - - - -
19A ILE* 1.3 87.1 + - - +
21A VAL* 1.3 62.8 + - - +
22A VAL* 4.3 8.5 - - + -
69A ASP* 3.0 34.0 - - + +
70A MET* 6.5 0.7 - - + -
85A VAL* 6.4 0.4 - - + -
330A THR 2.9 7.1 + - - +
331A SER* 3.2 20.6 - - - +
332A ILE 3.2 22.2 + - - -
357A LYS* 3.7 2.9 + - - +
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Residues in contact with VAL 21 (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* 4.7 5.2 - - + -
20A GLN* 1.3 76.2 - - - +
22A VAL* 1.3 67.9 + - - +
68A PHE* 3.5 14.6 - - + +
69A ASP* 3.0 35.5 + - - +
332A ILE* 3.6 31.9 - - + +
353A ALA* 3.6 39.7 - - + +
356A ALA* 4.6 0.9 - - + -
357A LYS* 3.7 33.0 - - + +
359A ILE* 5.8 1.6 - - + -
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Residues in contact with VAL 22 (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* 4.8 7.9 - - + -
21A VAL* 1.3 84.1 - - - +
23A VAL* 1.3 65.7 + - - +
68A PHE* 4.6 0.4 - - - -
69A ASP* 4.5 5.4 - - + -
70A MET* 3.3 42.6 - - + +
72A PHE* 4.1 16.2 - - + -
85A VAL* 4.1 11.4 - - + -
331A SER* 6.1 1.1 - - - -
332A ILE 3.1 14.0 + - - +
333A ILE* 3.7 28.5 - - + -
334A ALA* 3.0 28.8 + - - +
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Residues in contact with VAL 23 (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* 1.3 81.6 - - - +
24A ARG* 1.3 65.1 + - - +
25A CYS* 4.2 2.2 + - + +
50A VAL* 3.8 22.7 - - + -
68A PHE* 3.7 40.2 - - + -
70A MET 2.9 10.6 + - - +
71A VAL* 4.7 3.6 - - + -
72A PHE* 3.0 32.2 + - - +
334A ALA* 3.4 21.1 - - + +
336A ILE* 3.9 22.7 - - + -
350A LEU* 4.1 7.4 - - + -
353A ALA* 5.1 0.2 - - + -
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Residues in contact with ARG 24 (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* 1.3 75.2 - - - +
25A CYS* 1.3 66.5 + - - +
26A ARG* 3.6 1.8 + - - +
72A PHE* 4.1 20.0 - - + -
73A GLY 6.0 0.4 - - - +
76A THR* 4.4 11.7 + - + +
77A LYS* 4.1 4.0 - - - +
78A GLN* 2.9 41.6 + - - +
81A VAL* 3.7 28.2 - - - +
109A THR 4.7 0.9 - - - +
113A PHE* 3.8 13.3 - - - -
114A THR* 2.7 43.1 + - - +
333A ILE* 4.2 19.5 - - + +
334A ALA 2.9 10.1 + - - -
335A THR* 3.4 12.1 - - + +
336A ILE 3.2 21.3 + - - -
1364A ADP 3.8 19.2 + - - +
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Residues in contact with CYS 25 (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* 4.1 2.0 - - - +
24A ARG* 1.3 73.8 - - - +
26A ARG* 1.3 62.0 + - - +
27A PRO* 4.6 0.5 - - - +
41A VAL* 3.9 10.3 - - - -
43A CYS* 3.6 12.6 - - - -
72A PHE 3.8 10.7 + - - +
73A GLY 4.5 4.5 - - - +
74A ALA* 5.5 0.9 - - - -
336A ILE* 3.4 17.7 - - + +
338A PRO* 3.6 28.7 - - - -
1364A ADP 5.4 0.5 + - - -
1366A CD 2.7 30.3 - - - -
1367A CD 2.7 25.8 - - - -
1376A CL 3.7 6.2 - - + +
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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