Contacts of the strand formed by residues 28 - 36 (chain t) in PDB entry 4PJO
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 28 (chain t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20t MET* 3.5 32.5 - - + +
21t VAL 3.2 12.1 - - - +
22t LYS* 3.8 31.8 + - + +
26t GLY 4.1 1.5 - - - +
27t MET* 1.3 80.3 - - - +
29t TYR* 1.3 67.4 + - - +
49t GLU* 3.6 3.8 - - - +
50t TYR* 2.8 42.6 + - + +
53t GLY* 3.5 32.2 + - - +
71t TYR* 4.7 8.3 + - - -
73t ARG* 4.6 6.4 + - - -
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Residues in contact with TYR 29 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40n GLY* 4.4 1.6 - - - -
41n ILE* 4.3 7.1 - - + +
45r ASN* 4.4 4.7 + - - -
107r ILE* 5.5 0.2 - - - +
108r VAL* 4.0 20.9 - - + +
20t MET* 3.5 3.8 - - - -
21t VAL* 2.9 46.6 + - + +
23t LEU* 3.3 39.5 - - + -
27t MET* 3.6 23.8 - - + +
28t GLU* 1.3 76.6 - - - +
30t LYS* 1.3 59.6 + - - +
44t LEU* 3.8 6.4 - - + +
47t THR* 3.8 15.9 - - + -
48t GLU 3.4 6.3 - - - -
49t GLU* 2.7 34.2 + - + -
59t LEU* 3.5 25.6 - - + -
62t VAL* 5.3 3.6 - - + -
64t ILE* 4.3 10.1 - - + -
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Residues in contact with LYS 30 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18t PRO* 5.8 4.5 - - + -
19t VAL 3.4 9.4 - - - +
20t MET* 3.5 24.7 - - + +
29t TYR* 1.3 73.1 - - - +
31t GLY* 1.3 61.8 + - - +
46t ASN 3.6 1.9 - - - +
47t THR* 3.1 6.4 - - - -
48t GLU* 2.8 44.5 + - + +
50t TYR* 3.2 41.7 + - + -
75t VAL* 4.0 22.8 - - + +
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Residues in contact with GLY 31 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18t PRO* 4.1 1.8 - - - -
19t VAL* 2.9 34.2 + - - +
30t LYS* 1.3 78.8 - - - +
32t TYR* 1.3 68.4 + - - -
33t LEU 3.1 5.2 + - - -
44t LEU* 4.1 12.3 - - - +
45t ALA 3.4 11.2 - - - -
46t ASN 4.0 4.3 - - - -
47t THR* 4.3 2.2 - - - -
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Residues in contact with TYR 32 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16t GLY* 3.7 22.2 - - - +
17t LYS 3.7 5.4 - - - -
18t PRO* 4.1 28.6 - - + +
31t GLY* 1.3 74.1 - - - -
33t LEU* 1.3 67.2 + - - +
34t VAL* 3.1 8.0 + - + +
44t LEU* 3.5 0.8 - - - -
45t ALA* 2.8 45.1 + - + +
46t ASN* 4.7 14.1 - - + -
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Residues in contact with LEU 33 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11t LEU* 4.3 7.9 - - + +
14t LEU* 4.0 28.0 - - + +
15t THR* 4.0 10.8 - - + +
16t GLY* 2.9 29.3 + - - -
17t LYS 3.2 4.8 + - - -
19t VAL* 3.6 17.0 - - + -
31t GLY 3.1 7.5 + - - -
32t TYR* 1.3 70.7 - - - +
34t VAL* 1.3 59.7 + - - +
35t SER 3.4 25.8 - - - +
36t VAL* 3.7 18.2 - - + -
42t MET* 4.4 5.2 - - + -
43t GLN 3.6 8.7 - - - +
44t LEU* 4.4 13.2 - - + -
72t ILE* 3.7 26.9 - - + -
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Residues in contact with VAL 34 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26r THR 5.8 0.9 - - - +
15t THR* 4.3 12.2 - - - -
16t GLY 5.1 0.8 + - - +
32t TYR* 3.2 18.4 - - + +
33t LEU* 1.3 73.7 - - - +
35t SER* 1.3 63.7 + - - +
43t GLN* 3.0 41.5 + - + +
44t LEU 4.0 2.5 - - - -
45t ALA* 3.6 24.0 - - + +
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Residues in contact with SER 35 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26r THR 4.0 8.7 - - - -
27r GLY* 3.5 18.3 + - - -
28r PRO* 3.4 8.6 - - - +
15t THR* 5.0 4.7 - - - -
33t LEU* 3.4 4.2 - - - +
34t VAL* 1.3 80.7 - - - +
36t VAL* 1.3 76.4 + - - +
43t GLN* 2.6 54.2 + - - +
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Residues in contact with VAL 36 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27r GLY* 5.0 2.8 - - - -
28r PRO* 3.6 6.4 - - - +
8t LYS* 5.7 5.6 - - + +
11t LEU* 4.3 32.1 - - + -
12t ASN* 4.8 11.7 - - - +
15t THR* 5.1 5.3 - - + +
33t LEU* 3.7 25.6 - - + -
35t SER* 1.3 85.9 - - - +
37t ASP* 1.3 68.5 + - - +
40t MET* 4.7 3.8 - - + -
41t ASN 3.2 15.9 - - - +
42t MET* 3.8 12.1 - - + -
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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