Contacts of the strand formed by residues 19 - 24 (chain N) 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 GLY 19 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N PHE* 2.2 45.8 + - - +
18N GLY* 1.3 75.0 - - - +
20N VAL* 1.3 65.2 + - - +
115N TYR* 4.6 2.8 - - - -
120N SER* 3.3 7.8 + - - -
192N VAL* 3.0 24.9 - - - -
193N THR* 4.2 0.9 - - - -
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Residues in contact with VAL 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N VAL 3.7 7.6 - - - +
15N LYS* 4.0 1.6 - - + +
16N PHE* 4.2 0.6 - - - -
19N GLY* 1.3 79.7 - - - +
21N VAL* 1.3 74.8 + - - +
22N ILE* 3.8 11.0 - - + -
50N MET* 3.2 5.4 - - - +
113N GLY* 4.2 5.6 - - - -
114N GLY 4.5 10.1 - - - +
115N TYR 4.8 0.2 - - - +
120N SER* 3.6 18.4 - - - +
122N LEU* 3.4 43.7 - - + -
191N THR* 5.0 0.2 - - - -
192N VAL* 2.9 45.3 + - + +
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Residues in contact with VAL 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N VAL 2.8 32.8 + - - +
16N PHE* 2.4 43.7 - - + -
20N VAL* 1.3 73.1 - - - +
22N ILE* 1.4 64.4 + - - +
166N ARG* 4.4 9.9 - - + +
169N VAL* 3.5 42.0 - - + -
189N ILE* 4.3 8.7 - - + -
190N ALA 3.6 2.7 - - - +
191N THR* 2.7 31.6 - - + -
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Residues in contact with ILE 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N VAL* 4.7 10.5 - - + -
12N LEU 3.1 18.6 - - - +
13N GLY* 4.0 6.3 - - - -
20N VAL* 3.8 6.1 - - + -
21N VAL* 1.4 79.7 - - - +
23N ALA* 1.3 62.9 + - - +
42N ILE* 4.4 19.5 - - + +
50N MET* 3.8 29.4 - - + +
51N LEU 5.5 0.2 - - - -
52N GLY 5.1 4.0 - - - +
111N VAL* 4.4 15.7 - - + +
113N GLY* 3.7 33.7 - - - +
188N GLN 4.3 0.2 - - - +
189N ILE* 4.8 0.4 - - - -
190N ALA* 2.8 37.3 + - + +
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Residues in contact with ALA 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N LEU* 3.0 32.8 + - - +
21N VAL 4.3 0.4 - - - -
22N ILE* 1.3 74.2 - - - +
24N ALA* 1.3 62.8 + - - +
42N ILE* 5.3 0.2 - - - -
169N VAL* 3.3 31.2 - - + +
173N MET* 4.0 14.4 - - + -
187N PHE* 4.4 2.5 - - + -
188N GLN 3.3 12.1 - - - +
189N ILE* 4.1 17.9 - - + +
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Residues in contact with ALA 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N SER 4.4 2.9 - - - -
11N VAL* 3.7 30.7 - - + -
23N ALA* 1.3 77.5 - - - +
25N ASP* 1.3 63.7 + - - +
26N MET* 4.2 1.7 - - - +
41N ARG* 3.8 10.1 - - + +
42N ILE* 4.3 21.7 - - + +
173N MET* 4.2 5.4 - - - -
187N PHE* 3.0 14.1 - - - +
188N GLN* 3.0 21.2 + - - +
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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