Contacts of the strand formed by residues 21 - 29 (chain A) in PDB entry 3M4D
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 LYS 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 3.8 17.5 + - - +
20A VAL* 1.3 74.9 - - - +
22A THR* 1.3 61.1 + - - +
40A TYR* 4.8 1.1 - - - -
41A SER* 3.4 1.0 - - - -
42A PHE* 2.8 41.8 + - + +
288A LYS 5.4 3.2 + - - +
289A GLU* 3.5 48.4 + - + +
46G LYS 5.6 0.9 + - - -
47G ASN* 3.3 36.6 - - + +
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.0 13.2 - - + +
21A LYS* 1.3 79.0 - - - +
23A GLY* 1.3 58.3 + - - +
39A PHE* 4.2 4.9 - - + -
40A TYR* 3.2 14.7 + - - -
41A SER* 3.4 24.2 - - - +
11G THR 5.5 0.2 - - - +
12G THR 3.9 15.9 - - - +
13G ASP 5.2 3.4 - - - +
14G ILE* 4.2 5.8 - - + +
45G ASP* 5.0 2.3 + - - -
47G ASN* 2.9 7.7 + - - +
48G HIS* 2.7 36.3 + - - +
49G ASN* 2.9 22.5 + - - +
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Residues in contact with GLY 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 THR* 1.3 78.8 - - - +
24A ASP* 1.3 59.9 + - - -
39A PHE* 3.3 9.0 - - - -
40A TYR* 2.9 47.5 + - - -
48G HIS* 3.4 8.0 + - - -
49G ASN* 3.1 17.3 - - - -
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Residues in contact with ASP 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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23A GLY* 1.3 73.2 - - - -
25A LEU* 1.3 74.1 + - - +
26A VAL* 5.3 1.1 - - + -
37A LYS* 2.7 36.4 + - + +
38A VAL 3.4 1.6 - - - -
39A PHE* 3.7 11.6 - - - -
14G ILE* 4.1 1.9 - - - +
48G HIS* 2.7 30.2 + - - +
49G ASN* 2.7 11.0 + - - +
50G LYS* 3.0 22.9 + - + -
52G LEU* 4.1 4.9 - - - +
99G SER* 3.3 11.1 + - - +
233G THR* 4.0 21.8 - - + +
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Residues in contact with LEU 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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24A ASP* 1.3 93.4 + - - +
26A VAL* 1.3 63.0 + - - +
27A THR* 5.2 1.1 - - - -
36A LYS 3.7 0.9 - - - +
37A LYS* 3.3 3.9 - - - +
38A VAL* 2.9 44.7 + - + +
40A TYR* 4.2 8.3 - - + -
282A TYR* 3.8 37.6 + - + -
291A MET* 3.5 37.2 - - + +
292A THR* 4.1 3.8 - - - +
293A ASN* 3.8 21.5 - - - +
49G ASN* 3.6 15.0 - - - +
50G LYS* 3.9 8.5 - - - +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP 4.3 2.0 - - - -
25A LEU* 1.3 77.4 - - - +
27A THR* 1.3 69.4 + - - +
35A HIS* 3.6 26.5 - - + +
36A LYS 3.4 3.6 - - - +
37A LYS* 3.6 22.7 - - + -
293A ASN* 5.0 2.8 + - - +
50G LYS* 5.5 1.8 - - - +
97G GLN* 3.2 41.5 + - + +
98G ILE 3.6 6.7 - - - +
99G SER* 3.8 25.1 - - - +
162G ASP* 3.8 10.8 - - + -
233G THR* 4.6 6.3 - - - +
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Residues in contact with THR 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 LEU 5.2 0.3 - - - -
26A VAL* 1.3 81.7 + - - +
28A TYR* 1.3 71.7 + - - +
29A ASP* 5.5 1.3 - - + -
34A MET 3.8 0.5 - - - +
35A HIS* 3.8 0.5 - - - -
36A LYS* 2.8 46.3 + - - +
280A GLU* 2.9 40.7 + - - +
282A TYR* 4.3 3.4 + - - -
293A ASN* 3.3 10.2 + - - -
97G GLN* 5.0 1.3 - - - +
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Residues in contact with TYR 28 (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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27A THR* 1.3 80.4 - - - +
29A ASP* 1.3 63.4 + - - +
30A LYS* 3.5 36.6 + - + +
33A GLY* 3.9 14.5 - - - -
34A MET 3.2 29.8 - - - -
35A HIS* 3.7 4.0 - - - -
160G PRO 3.8 5.6 + - - -
161G THR* 3.4 46.8 - - + +
162G ASP* 3.4 35.2 + - + +
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Residues in contact with ASP 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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27A THR* 4.1 2.6 - - + +
28A TYR* 1.3 71.2 - - - +
30A LYS* 1.3 58.0 + - - +
31A GLU* 3.2 10.4 + - - +
32A ASN* 2.7 42.4 + - - -
33A GLY* 2.9 22.9 + - - -
34A MET* 2.9 26.7 + - + +
36A LYS* 4.7 5.8 - - - +
278A SER* 2.7 25.0 + - - +
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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