Contacts of the strand formed by residues 21 - 27 (chain A) in PDB entry 1UF1
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 GLU 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLY 5.1 6.3 - - - +
19A GLY* 3.3 12.4 - - - +
20A ASP* 1.3 89.9 + - - +
22A LYS* 1.3 62.5 + - - +
23A LYS 4.3 0.2 - - - -
71A LEU* 3.9 27.3 - - + +
72A GLU* 5.7 0.7 - - - +
99A THR* 4.7 10.1 - - + -
100A VAL 4.1 2.0 - - - -
101A LYS* 4.6 2.4 - - + +
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Residues in contact with LYS 22 (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 ASP 5.0 1.1 - - - +
21A GLU* 1.3 76.8 - - - +
23A LYS* 1.3 65.1 + - - +
24A VAL* 3.5 26.9 + - + +
62A SER* 4.1 16.6 + - - -
63A GLY* 4.0 20.7 + - - -
64A LEU* 5.3 0.7 - - - -
68A ASP* 5.6 1.6 - - - -
98A LEU 3.5 0.3 - - - +
99A THR* 3.2 6.5 - - - +
100A VAL* 2.9 48.9 + - + +
101A LYS* 5.3 1.8 - - - -
102A ASP* 5.5 12.8 - - - +
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Residues in contact with LYS 23 (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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22A LYS* 1.3 73.6 - - - +
24A VAL* 1.3 60.0 + - - +
25A ASN* 3.6 12.4 + - + +
72A GLU* 6.4 0.4 - - - -
97A ILE* 3.1 34.1 - - + -
98A LEU 4.0 1.6 - - - -
99A THR* 3.8 23.5 - - + +
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Residues in contact with VAL 24 (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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22A LYS* 3.8 32.5 - - - +
23A LYS* 1.3 73.0 - - - +
25A ASN* 1.3 59.2 + - - +
26A LEU* 3.7 9.0 + - + +
62A SER* 2.9 36.6 - - - +
64A LEU* 3.8 31.9 - - + -
96A LEU 3.0 5.7 - - - +
97A ILE* 4.0 1.6 - - - -
98A LEU* 2.6 53.5 + - + +
100A VAL* 4.3 2.7 - - + -
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Residues in contact with ASN 25 (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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23A LYS* 3.6 11.1 + - + +
24A VAL* 1.3 72.8 - - - +
26A LEU* 1.3 67.5 + - - +
27A VAL* 5.4 2.8 - - - +
62A SER* 5.0 1.9 + - - -
95A HIS* 4.2 18.4 + - - +
96A LEU 3.6 3.1 - - - -
97A ILE* 4.1 18.8 - - + +
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Residues in contact with LEU 26 (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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24A VAL* 4.1 13.5 - - + +
25A ASN* 1.3 81.1 - - - +
27A VAL* 1.3 65.4 + - - +
28A LEU* 4.1 3.8 - - + -
34A LEU* 3.0 35.9 - - + -
58A GLU* 3.2 46.7 - - + +
59A ALA* 4.1 8.5 - - - -
62A SER* 3.6 18.6 - - - +
64A LEU* 4.4 3.1 - - + -
94A ARG 3.6 1.0 - - - +
95A HIS* 3.1 9.0 - - - -
96A LEU* 2.9 39.4 + - + +
98A LEU* 4.8 1.8 - - + -
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Residues in contact with VAL 27 (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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25A ASN* 5.4 2.5 - - - +
26A LEU* 1.3 73.7 - - - +
28A LEU* 1.3 71.5 + - - +
32A ARG* 5.5 1.2 - - - -
58A GLU* 2.9 24.2 + - - +
94A ARG* 4.3 3.1 - - + +
95A HIS* 3.5 33.2 - - + +
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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