Contacts of the strand formed by residues 16 - 21 (chain B) in PDB entry 2Q53
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 SER 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 1.3 95.6 + - - +
17B PHE* 1.3 64.8 + - - +
85B LYS* 4.1 31.4 - - - +
86B MSE 2.9 14.6 + - - -
87B ASN* 3.7 12.5 + - - -
88B LYS* 3.7 18.1 - - - +
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 1.3 75.1 - - - +
18B LEU* 1.3 76.9 + - - +
19B TYR* 3.7 15.0 - - + -
85B LYS* 3.6 2.8 - - - +
86B MSE 2.6 51.1 + - + +
87B ASN 3.0 29.2 - - - -
88B LYS* 3.7 20.2 - - + -
90B ASN* 4.0 3.6 - - + -
91B LEU* 3.8 35.4 - - + -
94B LEU* 3.5 32.8 - - + -
123B ARG* 4.1 15.7 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 1.3 83.9 - - - +
19B TYR* 1.3 54.2 + - - +
41B PHE* 4.1 29.4 - - + -
83B VAL* 4.2 4.9 - - + -
84B TRP 3.3 10.3 - - - +
85B LYS* 4.0 23.1 - - + -
120B ILE* 3.5 29.2 - - + -
121B THR 4.0 11.7 - - - +
122B CYS* 3.4 13.5 - - + +
123B ARG* 2.8 35.5 + - - +
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.7 19.9 + + + -
18B LEU* 1.3 72.2 - - - +
20B PHE* 1.3 72.2 + - - +
21B ALA* 3.4 28.0 + - + +
23B GLY 5.9 0.2 + - - -
25B ASN* 3.2 24.5 + - - +
31B ILE* 3.9 27.8 - - + -
82B VAL 3.6 2.9 - - - +
83B VAL* 3.4 1.7 - - - -
84B TRP* 2.7 46.4 + + + +
86B MSE 4.1 12.1 - - - -
94B LEU* 3.8 18.6 - - + -
98B GLU* 4.5 7.3 + - - -
122B CYS* 4.4 0.9 - - - -
123B ARG* 3.3 11.0 - - + -
124B SER* 4.5 0.7 - - - -
125B TYR* 3.7 29.4 - + - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 1.3 75.0 - - - +
21B ALA* 1.3 65.0 + - - +
22B TYR* 4.2 9.9 + + - -
44B ALA* 3.6 13.2 - - + -
46B LEU* 3.8 39.9 - - + -
71B ILE* 5.7 0.2 - - + -
79B VAL* 3.9 9.0 - - + -
80B TRP 4.0 1.1 - - - -
81B GLY* 3.5 38.8 - - - -
82B VAL 3.9 0.9 - - - -
83B VAL* 3.7 19.7 - - + +
110B VAL* 4.2 11.2 - - + -
112B VAL* 3.8 20.2 - - + -
122B CYS* 4.0 17.4 - - + +
123B ARG 2.9 14.7 + - - +
124B SER* 2.6 35.8 + - - -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.4 36.9 + - + +
20B PHE* 1.3 75.7 - - - +
22B TYR* 1.3 63.7 + - - +
23B GLY 4.9 0.2 - - - +
25B ASN* 3.7 27.8 - - + +
26B LEU* 3.9 2.0 - - - +
81B GLY* 3.3 24.1 - - - -
82B VAL 3.1 18.9 + - - +
84B TRP* 4.2 1.8 - - + -
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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