Contacts of the strand formed by residues 128 - 135 (chain A) in PDB entry 2GO0
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 ARG 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 3.6 28.5 - - + +
21A LYS* 3.0 34.1 - - - +
22A SER* 3.1 4.3 - - - +
126A ASN 3.1 2.7 + - - +
127A VAL* 1.3 80.5 - - - +
129A LEU* 1.3 68.0 + - - +
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Residues in contact with LEU 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 PRO* 3.5 7.7 - - - +
21A LYS 3.2 14.8 + - - +
63A TYR* 3.3 43.7 - - + +
64A VAL 4.0 0.2 - - - +
65A TRP* 3.2 59.9 - - + +
110A SER* 4.3 7.6 - - - +
123A TYR* 4.8 9.4 - - + -
127A VAL* 3.7 20.2 - - + -
128A ARG* 1.3 76.9 - - - +
130A PRO* 1.3 74.4 - - + +
131A TYR* 3.1 9.9 + - - +
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Residues in contact with PRO 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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16A LEU* 4.9 2.5 - - + -
17A PHE 3.6 14.1 - - - +
18A LEU* 4.6 9.0 - - - +
19A SER 4.0 5.2 - - - +
20A PRO* 4.0 6.0 - - + -
57A ILE* 3.4 35.9 - - + -
61A TYR* 3.5 29.2 - - + -
63A TYR 3.6 14.1 - - - +
64A VAL* 2.8 22.2 - - + +
65A TRP 3.0 6.2 + - - -
129A LEU* 1.3 94.0 - - + +
131A TYR* 1.3 59.1 + - - +
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Residues in contact with TYR 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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16A LEU* 3.2 4.4 - - - +
17A PHE* 2.9 68.3 + + + +
19A SER* 3.2 23.6 - - - -
21A LYS* 3.4 43.6 + - + +
26A ALA* 3.6 19.5 - - + -
29A ALA* 4.7 3.5 - - - +
30A CYS* 4.7 6.2 + - + -
33A ARG* 5.0 1.7 + - - -
38A LEU* 3.8 6.3 - - + -
64A VAL* 3.6 5.8 - - - -
65A TRP* 3.7 21.3 - - + +
129A LEU 3.7 8.5 - - - +
130A PRO* 1.3 75.6 - - - +
132A VAL* 1.3 78.5 + - - +
133A CYS* 4.2 13.7 - - + -
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Residues in contact with VAL 132 (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 TYR* 4.3 8.1 - - + -
15A ALA 3.4 16.6 - - - +
16A LEU* 3.9 5.4 - - + -
38A LEU* 3.7 5.4 - - - +
39A VAL* 3.2 40.6 + - + -
50A VAL* 4.3 8.3 - - + -
53A LEU* 3.5 25.8 - - + -
54A VAL* 3.2 34.8 - - + -
64A VAL* 4.4 5.4 - - + -
65A TRP 4.0 5.1 + - - -
131A TYR* 1.3 91.7 - - - +
133A CYS* 1.3 72.7 + - - +
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Residues in contact with CYS 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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13A CYS 3.2 2.6 - - - +
14A TYR* 3.2 3.6 - - - -
15A ALA 3.0 30.2 + - - +
17A PHE* 4.7 0.9 - - + -
30A CYS* 2.0 50.9 - - + -
33A ARG* 3.2 44.0 - - - +
39A VAL 4.1 2.2 - - - +
131A TYR* 4.2 8.3 - - + -
132A VAL* 1.3 82.8 - - - +
134A LYS* 1.3 61.3 + - - +
135A PHE* 3.4 3.8 - - + -
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Residues in contact with LYS 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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12A HIS* 3.4 32.6 + - + +
13A CYS 3.3 5.4 - - - -
14A TYR* 3.3 39.9 + - + -
35A SER 5.1 1.6 - - - +
36A GLY* 2.8 25.8 - - - -
37A ASN 3.3 17.5 + - - +
39A VAL* 4.3 2.3 - - - +
40A SER* 3.2 22.6 + - - +
86A SER* 3.0 43.2 + - - +
87A SER* 4.5 1.4 - - - +
133A CYS* 1.3 74.0 - - - +
135A PHE* 1.3 67.9 + - - +
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Residues in contact with PHE 135 (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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3A PRO* 4.0 25.6 - - + -
12A HIS* 3.4 8.9 - - - +
13A CYS* 2.7 65.4 + - + +
14A TYR 4.8 0.2 - - - -
15A ALA* 4.0 15.0 - - + -
33A ARG* 3.6 50.5 - - + -
34A PRO* 4.2 9.6 - - + -
36A GLY* 3.9 5.8 - - - -
133A CYS* 3.4 13.2 - - - -
134A LYS* 1.3 82.6 - - - +
136A THR* 1.3 69.1 + - - +
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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