Contacts of the strand formed by residues 109 - 116 (chain b) in PDB entry 5A0Q
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 THR 109 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11b VAL* 5.6 0.2 - - - +
53b ALA* 4.0 0.2 - - - -
54b SER* 3.2 34.2 + - - +
107b TRP 4.0 2.8 + - - -
108b ASN* 1.3 75.7 + - - +
110b MET* 1.4 59.6 + - - +
124b TYR* 3.3 41.7 - - + +
125b VAL 3.4 8.1 - - - +
126b ASP* 4.2 2.3 + - - -
127b MET* 3.7 19.2 + - - +
139b THR* 3.8 19.4 - - + +
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Residues in contact with MET 110 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43b MET* 4.3 3.8 - - - -
51b LEU* 3.8 24.2 - - + -
52b GLY 3.2 11.9 - - - +
53b ALA* 3.6 27.4 - - + -
60b PHE* 4.3 11.9 - - - -
63b LEU* 3.6 36.3 - - + -
92b LEU* 3.8 23.6 - - + -
96b MET* 4.0 10.8 - - + -
108b ASN* 4.2 16.2 - - + +
109b THR* 1.4 77.2 - - - +
111b VAL* 1.4 60.5 + - - +
112b ILE* 4.1 3.7 - - - +
124b TYR* 3.5 2.4 - - - -
125b VAL* 3.0 34.5 + - + +
139b THR* 4.8 0.9 - - - -
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Residues in contact with VAL 111 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11b VAL* 4.6 15.5 - - + +
12b LEU 5.1 0.2 - - - +
13b GLY* 4.4 6.7 - - - +
22b ILE* 4.4 15.3 - - + +
50b MET 4.0 0.3 - - - +
51b LEU* 3.3 3.1 - - - -
52b GLY 3.1 28.7 + - - -
109b THR 4.4 0.2 + - - -
110b MET* 1.4 70.7 - - - +
112b ILE* 1.4 62.0 + - - +
113b GLY 4.0 1.6 + - - +
122b LEU* 4.2 19.3 - - + -
123b GLY 3.4 11.0 - - - +
124b TYR* 4.7 2.7 - - + -
137b LEU* 3.8 36.8 - - + +
139b THR* 3.7 26.4 - - + +
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Residues in contact with ILE 112 (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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49b THR* 5.3 2.9 - - - +
50b MET 3.4 17.9 - - - +
51b LEU* 3.5 37.0 - - + -
85b PRO* 4.5 15.2 - - + +
88b ILE* 4.1 12.8 - - + -
89b HIS* 3.3 44.9 - - + +
92b LEU* 4.0 5.6 - - + -
110b MET 4.1 2.2 - - - +
111b VAL* 1.4 71.3 - - - +
113b GLY* 1.3 57.0 + - - +
114b GLY 3.7 0.3 + - - -
121b PHE* 3.3 10.7 - - - +
122b LEU* 4.3 0.9 - - - -
123b GLY 3.0 33.7 + - - +
125b VAL* 3.7 15.5 - - + -
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Residues in contact with GLY 113 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20b VAL* 4.2 4.9 - - - -
22b ILE* 3.7 20.7 - - - +
49b THR* 3.4 1.5 - - - -
50b MET* 3.0 38.2 + - - +
111b VAL* 4.0 0.4 - - - +
112b ILE* 1.3 71.4 - - - +
114b GLY* 1.3 58.4 + - - -
121b PHE 3.5 5.6 - - - -
122b LEU* 4.0 12.6 - - - -
192b VAL* 3.7 7.6 - - - +
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Residues in contact with GLY 114 (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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20b VAL* 4.5 4.2 - - - +
49b THR* 3.7 24.5 - - - -
85b PRO* 3.5 13.8 - - - +
112b ILE 3.7 1.2 + - - -
113b GLY* 1.3 74.0 - - - -
115b TYR* 1.3 64.9 + - - -
116b ALA 3.4 1.9 + - - -
120b SER* 4.5 1.8 - - - -
121b PHE 3.0 32.0 + - - +
192b VAL* 4.6 2.5 - - - -
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Residues in contact with TYR 115 (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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18b GLY* 4.1 19.7 - - - -
19b GLY 4.6 5.8 - - - +
20b VAL* 5.3 0.4 - - + -
48b SER* 3.5 17.9 + - - +
49b THR* 4.9 1.8 - - - +
85b PRO* 5.3 0.4 - - - -
114b GLY* 1.3 70.2 - - - -
116b ALA* 1.3 59.2 + - - +
117b ASP 4.2 2.3 + - - -
118b GLY* 2.8 49.1 + - - -
119b GLU 3.3 16.2 - - - -
120b SER* 3.6 15.9 - - - +
192b VAL* 3.5 27.6 - - + +
193b THR 5.1 0.4 - - - +
194b GLU* 3.7 45.0 - - + +
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Residues in contact with ALA 116 (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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84b SER* 5.0 6.7 - - - -
85b PRO* 3.6 31.4 - - + -
86b ARG* 5.3 4.0 - - - +
114b GLY 3.4 0.4 + - - -
115b TYR* 1.3 73.0 - - - +
117b ASP* 1.4 73.7 + - + +
118b GLY 3.4 1.1 - - - -
119b GLU* 2.7 32.3 + - - +
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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