Contacts of the strand formed by residues 136 - 142 (chain A) in PDB entry 3VKO
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 ASP 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 3.4 8.0 - - + -
23A ILE* 2.6 43.6 + - - +
51A GLN 3.0 4.4 + - - -
52A ASN* 4.2 7.7 - - - +
53A GLY* 2.7 28.7 + - - -
134A LYS 4.8 1.3 - - - +
135A ILE* 1.3 75.1 - - - +
137A THR* 1.3 82.3 + - - +
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Residues in contact with THR 137 (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 VAL* 3.7 27.6 - - + -
21A GLY 3.2 13.9 + - - +
22A THR* 4.4 9.1 - - + +
23A ILE* 4.1 3.1 - - - +
50A LEU* 3.6 2.6 - - - -
51A GLN* 2.6 42.8 + - - +
53A GLY* 3.4 27.6 - - - +
54A SER* 3.9 6.7 + - - -
135A ILE* 3.8 2.3 - - - +
136A ASP* 1.3 100.5 + - - +
138A LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 138 (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 ILE* 5.9 1.6 - - + -
19A PHE* 3.9 6.5 - - + +
20A VAL* 3.5 1.0 - - - -
21A GLY 2.8 38.5 + - - +
23A ILE* 4.0 12.9 - - + +
33A ILE* 4.0 20.9 - - + -
35A ILE* 4.4 5.2 - - + -
48A VAL* 4.6 4.0 - - + -
49A ASP 3.6 3.4 - - - +
50A LEU* 4.2 20.0 - - + +
137A THR* 1.3 76.4 - - - +
139A GLY* 1.3 64.2 + - - +
140A ILE* 3.6 31.6 - - + -
149A ILE* 4.1 19.3 - - + -
151A PHE* 3.8 25.6 - - + -
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Residues in contact with GLY 139 (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 PHE 3.1 9.4 - - - -
20A VAL* 4.2 1.8 - - - -
47A GLN 3.8 0.5 - - - +
48A VAL* 3.4 4.0 - - - -
49A ASP 2.8 36.5 + - - -
51A GLN* 4.3 3.6 + - - -
138A LEU* 1.3 76.4 - - - +
140A ILE* 1.3 65.8 + - - +
141A TYR* 3.8 23.5 - - - -
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Residues in contact with ILE 140 (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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17A ILE* 3.6 10.2 - - + +
18A PRO* 3.2 5.7 - - - +
19A PHE* 2.7 37.2 + - + +
35A ILE* 4.1 17.9 - - + -
46A PHE* 4.9 0.9 - - + -
47A GLN 3.3 9.4 - - - +
48A VAL* 4.3 12.8 - - + -
138A LEU* 3.6 14.8 - - + -
139A GLY* 1.3 78.8 - - - +
141A TYR* 1.3 64.5 + - - +
144A VAL* 3.8 27.1 - - + -
146A ILE* 3.9 27.6 - - + -
149A ILE* 3.8 26.5 - - + -
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Residues in contact with TYR 141 (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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17A ILE* 4.2 5.8 - - - -
18A PRO* 3.4 24.5 - - + -
20A VAL* 3.3 34.0 - - + +
46A PHE* 3.3 6.6 - - - +
47A GLN* 2.9 51.0 + - + +
49A ASP* 3.4 26.7 - - - -
51A GLN* 2.8 27.2 + - - -
59A ARG* 5.7 2.0 - - - -
139A GLY* 3.8 13.8 - - - -
140A ILE* 1.3 74.2 - - - +
142A GLY* 1.3 64.3 + - - +
144A VAL* 4.2 2.9 - - - +
3C SIA 5.9 2.0 - - - +
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Residues in contact with GLY 142 (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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17A ILE* 3.6 15.8 - - - +
18A PRO* 5.5 1.0 - - - +
45A ARG* 3.8 9.0 - - - -
46A PHE* 4.0 2.2 - - - -
47A GLN* 5.8 1.1 - - - -
141A TYR* 1.3 80.2 - - - +
143A LYS* 1.3 64.2 + - - +
144A VAL 3.4 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