Contacts of the strand formed by residues 21 - 29 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS 5.5 0.9 - - - +
47B ASN* 3.5 36.1 - - + +
19C THR* 3.9 17.2 + - - +
20C VAL* 1.3 74.4 - - - +
22C THR* 1.3 63.0 + - - +
40C TYR* 4.8 0.4 - - - -
41C SER* 3.4 0.9 - - - -
42C PHE* 2.8 42.6 + - + +
288C LYS 5.5 3.8 + - - +
289C GLU* 3.5 48.4 + - + +
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Residues in contact with THR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR 3.9 16.6 - - - +
13B ASP 5.3 2.5 - - - +
14B ILE* 4.2 6.3 - - + +
45B ASP* 5.0 1.9 + - - -
47B ASN* 2.9 8.4 + - + +
48B HIS* 2.6 34.8 + - - +
49B ASN* 2.9 22.0 + - - +
20C VAL* 4.0 13.9 - - + +
21C LYS* 1.3 79.3 - - - +
23C GLY* 1.3 59.9 + - - +
39C PHE* 4.1 7.0 - - - -
40C TYR* 3.2 15.4 + - - -
41C SER* 3.6 22.9 - - - +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS* 3.4 8.0 + - - -
49B ASN* 3.0 17.7 - - - -
22C THR* 1.3 79.5 - - - +
24C ASP* 1.3 60.9 + - - -
39C PHE* 3.3 9.2 - - - -
40C TYR* 2.9 46.0 + - - -
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Residues in contact with ASP 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.1 3.6 - - - +
48B HIS* 2.7 28.3 + - + +
49B ASN* 2.7 14.7 + - - +
50B LYS* 2.9 23.7 + - + -
52B LEU* 4.1 7.4 - - - +
99B SER* 3.3 11.4 + - - +
233B THR* 4.0 16.6 - - + -
23C GLY* 1.3 71.8 - - - -
25C LEU* 1.3 68.7 + - - +
26C VAL* 5.3 1.3 - - + -
37C LYS* 2.7 37.2 + - - +
38C VAL 3.4 2.0 - - - -
39C PHE* 3.7 15.1 - - - -
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASN* 3.7 15.3 - - - +
50B LYS* 4.1 9.2 - - - +
24C ASP* 1.3 85.4 + - - +
26C VAL* 1.3 61.8 + - - +
27C THR* 5.3 1.3 - - - +
36C LYS 3.8 0.7 - - - +
37C LYS* 3.3 2.9 - - - -
38C VAL* 2.8 43.8 + - + +
40C TYR* 4.2 7.9 - - + -
282C TYR* 3.8 34.3 + - + -
291C MET* 3.4 38.1 - - + +
292C THR* 4.1 4.7 - - + -
293C ASN* 3.9 20.4 - - - +
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS* 4.5 2.6 - - - +
97B GLN* 3.3 41.2 + - - +
98B ILE 3.6 17.0 - - - +
99B SER* 3.9 13.9 - - - +
162B ASP* 3.8 8.3 - - + -
233B THR* 4.6 4.9 - - - +
24C ASP* 5.3 1.8 - - + -
25C LEU* 1.3 77.5 - - - +
27C THR* 1.3 68.0 + - - +
35C HIS* 3.4 29.2 - - + +
36C LYS 3.3 4.0 - - - +
37C LYS* 3.6 22.7 - - + -
293C ASN* 5.2 3.0 + - - -
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLN* 5.1 1.1 - - - +
25C LEU* 5.3 0.9 - - - +
26C VAL* 1.3 80.5 + - - +
28C TYR* 1.3 70.3 + - - +
29C ASP* 5.5 0.9 - - + -
34C MET 3.7 0.9 - - - +
35C HIS* 3.9 0.2 - - - -
36C LYS* 2.7 57.7 + - - +
280C GLU* 2.8 39.9 + - - +
282C TYR* 4.3 4.8 + - - -
293C ASN* 3.7 8.1 + - - +
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PRO 3.9 6.0 + - - -
161B THR* 3.4 48.1 - - + +
162B ASP* 3.4 35.7 + - + +
27C THR* 1.3 81.1 - - - +
29C ASP* 1.3 63.8 + - - +
30C LYS* 3.6 46.3 + - + +
33C GLY* 3.8 15.3 - - - -
34C MET* 3.1 31.2 - - - -
35C HIS* 3.7 3.6 - - + -
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Residues in contact with ASP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C THR* 4.1 1.9 - - + -
28C TYR* 1.3 72.2 - - - +
30C LYS* 1.3 56.6 + - - +
31C GLU* 3.2 10.4 + - - +
32C ASN* 2.7 45.1 + - + -
33C GLY* 2.9 23.7 + - - -
34C MET* 3.0 23.7 + - + +
36C LYS* 4.7 5.8 - - - +
278C SER* 2.8 26.5 + - - +
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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