Contacts of the strand formed by residues 28 - 34 (chain A) in PDB entry 5YXK
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 LEU 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.1 15.0 - - + -
19A ASN* 4.7 3.1 - - - +
23A GLN* 3.9 24.5 - - - +
24A SER 3.7 12.3 - - - +
25A LEU* 3.1 18.9 + - + +
26A SER 3.5 0.4 - - - -
27A GLU* 1.3 86.4 - - - +
29A VAL* 1.3 64.4 + - - +
30A VAL* 4.0 12.8 - - + -
43A VAL 3.7 2.3 - - - +
45A LEU* 2.8 27.1 + - - +
68A TRP* 4.1 26.0 - - + -
87A ILE* 4.4 4.3 - - + -
88A HIS 3.1 16.4 - - - +
89A HIS* 4.0 0.2 - - - -
90A LYS 4.7 0.2 - - - +
98A ILE* 3.7 25.6 - - + -
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Residues in contact with VAL 29 (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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28A LEU* 1.3 76.4 - - - +
30A VAL* 1.3 60.6 + - - +
31A PHE* 4.3 14.8 - - + -
42A GLU* 3.7 23.6 - - - +
43A VAL 3.6 4.9 - - - +
44A TYR* 3.9 26.9 - - + -
45A LEU* 4.1 10.3 - - + -
88A HIS* 2.7 47.3 + - + +
90A LYS* 4.5 13.7 - - + -
95A MET* 3.9 31.2 - - + -
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Residues in contact with VAL 30 (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 LEU* 4.6 6.5 - - + -
28A LEU* 4.3 9.9 - - + -
29A VAL* 1.3 78.6 - - - +
31A PHE* 1.3 66.6 + - - +
32A TRP* 4.6 3.0 - - + +
42A GLU* 3.3 2.0 - - - +
43A VAL* 2.7 48.1 + - + +
63A PHE* 4.5 15.5 - - + -
68A TRP* 3.6 33.2 - - + -
85A CYS* 4.1 14.4 - - - -
86A ILE 3.4 9.0 - - - +
87A ILE* 4.0 22.9 - - + -
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Residues in contact with PHE 31 (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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29A VAL* 4.3 12.8 - - + -
30A VAL* 1.3 78.9 - - - +
32A TRP* 1.3 66.7 + - - +
33A GLN* 3.6 39.3 - - + -
39A VAL* 4.4 15.0 - - + -
41A ASN 3.1 15.0 - - - +
42A GLU* 3.9 15.9 - - + -
52A SER* 6.2 1.3 - - - -
84A GLN 3.6 0.7 - - - +
85A CYS* 3.5 2.9 - - - -
86A ILE* 2.9 45.9 + - + -
88A HIS* 3.4 28.9 - + - -
95A MET* 4.2 15.7 - - + -
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Residues in contact with TRP 32 (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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13A LEU* 3.0 57.0 - - + -
14A PRO 3.6 13.2 - - - -
15A CYS* 3.2 26.1 - - - -
30A VAL* 4.6 2.4 - - + +
31A PHE* 1.3 82.7 - - - +
33A GLN* 1.3 57.0 + - - +
39A VAL* 3.3 5.7 - - - +
40A LEU* 2.8 37.8 + - + -
41A ASN* 3.0 15.0 + - + +
43A VAL* 6.3 0.7 - - + -
63A PHE* 3.4 25.7 - + - -
68A TRP 4.2 2.0 - - - -
69A THR 4.3 0.4 - - - -
70A LEU* 3.5 48.9 - - + -
83A TYR* 5.0 5.6 - + + -
84A GLN 3.2 16.8 - - - -
85A CYS* 3.7 14.9 - - + -
101A MET 5.3 1.3 - - - -
103A SER* 5.3 2.2 - - - -
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Residues in contact with GLN 33 (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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31A PHE* 3.6 17.8 - - + -
32A TRP* 1.3 74.1 - - - +
34A ASP* 1.3 66.1 + - - +
37A ASN* 3.0 41.6 + - - +
38A LEU 3.2 5.8 - - - +
39A VAL* 3.8 23.8 - - + +
40A LEU* 3.9 4.7 - - - -
83A TYR* 3.4 4.9 - - - +
84A GLN* 2.8 48.4 + - + +
86A ILE* 2.8 31.8 - - + +
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Residues in contact with ASP 34 (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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33A GLN* 1.3 78.2 - - - +
35A GLN* 1.3 62.1 + - + +
36A GLU* 2.7 22.7 + - - +
37A ASN* 2.9 19.8 + - - +
38A LEU* 2.9 48.3 + - - +
40A LEU* 3.7 7.8 - - + +
56A LYS* 4.5 3.8 + - - -
57A TYR* 2.8 30.1 + - - +
82A LEU 3.6 7.0 - - - -
83A TYR* 4.0 12.3 - - + -
84A GLN* 5.8 0.7 - - - +
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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