Contacts of the strand formed by residues 40 - 46 (chain A) in PDB entry 1VJZ
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 PHE 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A TRP* 3.5 54.1 - + + -
9A ARG 3.4 8.2 + - - +
10A GLY* 3.3 4.2 - - - -
11A PHE 3.2 17.6 + - - -
33A MSE 4.1 2.8 - - - +
38A PHE 3.9 0.6 - - - -
39A ASN* 1.3 82.7 - - - +
41A VAL* 1.3 72.7 + - - +
42A ARG* 3.5 25.4 - - + -
79A ILE* 3.7 3.5 - - - +
80A HIS* 3.5 28.5 - + - -
82A CYS* 3.5 26.7 - - + -
256A PHE* 3.3 32.1 - + - -
289A PHE 4.5 1.1 - - - -
290A ALA* 3.7 15.9 - - + -
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Residues in contact with VAL 41 (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 PHE 3.1 10.3 - - - +
13A LEU* 3.9 15.0 - - + -
30A PHE* 4.0 8.5 - - + -
33A MSE 3.2 35.7 - - + -
40A PHE* 1.3 85.1 - - - +
42A ARG* 1.3 58.9 + - - +
43A ILE* 3.7 20.4 - - + -
79A ILE* 3.6 6.9 - - + +
80A HIS 2.9 9.9 + - - +
81A ILE* 3.5 28.0 - - + -
82A CYS* 2.8 25.6 + - - +
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Residues in contact with ARG 42 (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 PHE 2.9 6.1 + - - -
12A ASN* 3.0 37.0 + - - +
13A LEU 2.9 26.5 + - - -
40A PHE* 3.5 17.2 - - + -
41A VAL* 1.3 74.3 - - - +
43A ILE* 1.3 64.6 + - - +
44A PRO* 3.4 8.8 - - + +
82A CYS* 3.3 21.8 - - - +
84A SER* 3.4 18.2 + - - -
135A ASN* 2.9 30.6 + - - -
138A ASN* 2.8 26.1 + - - +
174A ILE* 6.5 0.2 - - - -
176A ASP* 3.7 3.0 + - - -
196A SER* 5.5 1.2 + - - -
198A ARG* 3.3 13.2 - - - +
256A PHE* 5.4 0.9 - - - -
258A GLY* 3.7 16.7 - - - -
259A GLU* 2.9 29.1 + - - +
292A TRP* 4.1 3.2 - - - -
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Residues in contact with ILE 43 (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 LEU* 3.9 11.0 - - + +
25A PHE* 3.5 41.3 - - + -
41A VAL* 3.7 24.0 - - + -
42A ARG* 1.3 77.1 - - - +
44A PRO* 1.3 68.9 - - - +
45A MSE 3.3 22.6 + - + +
67A ILE* 4.5 4.3 - - + -
70A VAL* 3.8 17.7 - - + -
81A ILE* 4.0 24.7 - - + -
82A CYS 2.9 10.2 + - - +
83A ILE* 4.2 7.9 - - + -
84A SER* 2.9 24.9 + - - +
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Residues in contact with PRO 44 (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 ASN* 3.9 8.3 - - + +
13A LEU 3.4 14.9 - - - +
14A LEU* 4.1 7.4 - - + -
16A ALA* 3.5 5.7 + - - +
17A PHE* 3.4 25.5 + - + +
42A ARG* 3.4 19.1 - - + +
43A ILE* 1.3 83.6 - - - +
45A MSE 1.3 60.0 + - - +
84A SER* 3.7 12.5 - - - +
86A HIS* 3.8 31.0 - - + -
292A TRP* 3.9 24.7 - - + -
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Residues in contact with MSE 45 (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 ALA* 3.2 12.1 - - + +
17A PHE 4.7 0.2 - - - -
43A ILE* 3.4 22.2 - - + +
44A PRO* 1.3 74.8 - - - +
46A CYS* 1.3 59.8 + - - +
47A HIS 3.8 0.2 + - - -
50A TRP* 3.9 33.2 - - + -
64A PHE* 4.5 4.0 - - + -
67A ILE* 3.6 33.7 - - - -
83A ILE* 4.1 29.2 - - + -
84A SER 2.7 24.9 + - - +
85A LEU* 3.6 11.7 - - + +
86A HIS* 2.7 31.0 + - - +
87A ARG 3.1 8.3 + - - +
117A TRP* 5.2 1.1 - - + -
120A ILE* 4.1 16.4 - - + -
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Residues in contact with CYS 46 (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 ALA 2.9 12.5 + - - +
17A PHE 3.5 21.0 + - - +
18A SER 4.0 4.9 - - - -
19A ILE* 3.7 37.0 - - - -
45A MSE 1.3 70.6 - - - +
47A HIS* 1.3 66.6 + - - +
48A LEU* 3.1 14.8 - - - -
49A LEU* 3.0 23.4 + - + +
50A TRP* 3.5 5.6 - - - -
87A ARG* 4.1 24.5 - - + -
96A GLU* 4.4 2.2 - - - -
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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