Contacts of the strand formed by residues 126 - 134 (chain A) in PDB entry 3W58
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLY* 5.3 5.9 - - - -
19A VAL* 4.4 11.7 - - + -
20A ARG 4.3 0.9 - - - -
21A GLY* 3.5 39.9 - - - -
22A GLU 3.3 11.7 - - - -
23A VAL* 3.7 22.9 - - + -
30A PHE* 3.3 43.1 - + + -
31A VAL 5.4 0.7 - - - +
32A LEU* 5.8 7.2 - - + -
85A ALA* 3.7 15.0 - - + -
87A VAL* 5.8 6.7 - - + -
122A ALA* 4.4 17.2 - - + +
123A ASP 4.7 4.0 - - - +
124A GLY 3.0 11.8 + - - +
125A ASP* 1.3 74.6 - - - +
127A LYS* 1.3 63.3 + - - +
128A ILE* 3.9 27.2 + - + -
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Residues in contact with LYS 127 (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 GLY* 3.0 4.5 - - - -
22A GLU* 2.9 44.2 + - + +
125A ASP 5.8 0.4 - - - -
126A PHE* 1.3 77.1 - - - +
128A ILE* 1.3 65.7 + - - +
129A LYS* 3.4 26.8 + - - +
10B ASN* 5.3 10.5 - - - +
12B LYS* 5.0 11.7 - - - +
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Residues in contact with ILE 128 (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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4A LEU* 3.6 35.8 - - + +
19A VAL* 3.7 25.4 - - + -
20A ARG 3.8 3.6 - - - +
21A GLY* 4.1 1.1 - - - -
32A LEU* 4.4 10.1 - - + -
120A MET* 4.5 7.4 - - + -
122A ALA* 3.6 29.3 - - + +
126A PHE* 3.9 13.8 + - + -
127A LYS* 1.3 73.4 - - - +
129A LYS* 1.3 67.2 + - - +
130A CYS 3.8 9.9 - - - +
131A VAL* 3.6 27.1 - - + -
9B LEU 5.3 4.0 - - - +
133B PHE* 4.0 11.2 - - + -
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Residues in contact with LYS 129 (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 ARG* 2.9 13.4 + - + +
21A GLY* 4.3 7.4 - - - -
22A GLU* 4.4 13.5 - - + +
127A LYS* 3.6 35.1 - - - +
128A ILE* 1.3 79.7 - - - +
130A CYS* 1.3 63.0 + - + +
10B ASN* 5.9 3.0 + - - +
15B GLU* 4.4 16.4 + - - -
132B ALA* 3.3 0.9 - - - +
133B PHE* 2.7 61.2 + - + +
134B ASP* 5.3 0.2 - - - +
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Residues in contact with CYS 130 (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 VAL* 3.5 1.4 - - - -
20A ARG* 3.0 42.9 + - + +
128A ILE* 3.7 2.4 - - - +
129A LYS* 1.3 83.2 - - + +
131A VAL* 1.3 71.7 + - - +
132A ALA* 5.1 0.9 - - - -
202A BME 2.4 48.4 - - + -
130B CYS* 5.4 4.0 - - - -
131B VAL 3.3 13.2 - - - +
132B ALA* 4.0 13.5 - - + -
133B PHE* 4.8 0.4 - - - -
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Residues in contact with VAL 131 (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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4A LEU* 4.1 8.5 - - + -
9A LEU* 5.5 0.2 - - + -
17A LEU* 3.8 24.7 - - + -
18A ARG 3.3 6.3 - - - +
19A VAL* 4.7 3.1 - - + -
120A MET* 4.1 23.1 - - + -
128A ILE* 3.6 20.6 - - + -
130A CYS* 1.3 80.9 - - - +
132A ALA* 1.3 63.4 + - - +
133A PHE* 3.9 20.7 - - + -
202A BME 3.7 1.5 - - - -
4B LEU* 6.2 1.1 - - + -
130B CYS* 3.2 3.6 - - - +
131B VAL* 2.9 39.1 + - + +
133B PHE* 5.6 3.4 - - + -
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Residues in contact with ALA 132 (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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16A CYS 3.5 2.6 - - - +
17A LEU* 3.5 5.9 - - - +
18A ARG* 2.9 34.1 + - + -
131A VAL* 1.3 75.2 - - - +
133A PHE* 1.3 64.5 + - - +
134A ASP* 3.7 13.4 - - - +
202A BME 3.3 30.3 - - - +
129B LYS 3.4 5.8 - - - +
130B CYS* 3.9 12.8 - - + -
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Residues in contact with PHE 133 (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 LEU* 3.5 46.9 - - + -
11A LEU* 4.5 14.8 - - + -
15A GLU* 5.8 3.1 - - + +
16A CYS 3.5 2.9 - - - -
17A LEU* 3.6 26.2 - - + -
131A VAL* 3.9 22.2 - - + -
132A ALA* 1.3 70.4 - - - +
134A ASP* 1.3 65.5 + - - +
4B LEU* 4.0 24.0 - - + -
128B ILE* 3.4 29.6 - - + +
129B LYS* 2.8 38.7 + - + +
130B CYS* 5.1 0.2 - - - -
131B VAL* 5.8 0.4 - - + -
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Residues in contact with ASP 134 (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 GLY 4.4 1.2 - - - +
15A GLU* 3.3 27.0 - - - +
16A CYS* 2.6 48.6 + - + +
18A ARG* 3.3 39.9 + - - +
132A ALA* 3.7 11.3 - - - +
133A PHE* 1.3 79.9 - - - +
18C ARG* 4.6 11.4 + - - -
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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