Contacts of the strand formed by residues 18 - 23 (chain f) 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 PRO 18 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16f GLY 4.3 0.4 - - - +
17f LYS* 1.3 93.3 - - + +
19f VAL* 1.3 62.5 + - - +
30f LYS* 5.8 4.3 - - + -
31f GLY* 3.5 11.9 - - - +
32f TYR* 3.6 34.1 - - + +
74f GLY* 4.1 0.9 - - - -
75f VAL* 3.0 49.2 + - + +
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Residues in contact with VAL 19 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14f LEU* 3.5 38.4 - - + +
17f LYS 3.7 7.9 - - - +
18f PRO* 1.3 78.8 - - - +
20f MET* 1.3 63.0 + - - +
21f VAL* 4.7 1.6 - - + -
29f TYR 4.0 0.5 - - - +
30f LYS* 3.4 4.7 - - - +
31f GLY 2.9 41.7 + - - +
33f LEU* 3.6 23.8 - - + +
44f LEU* 4.5 12.3 - - + -
72f ILE* 4.2 15.5 - - + -
73f ARG 3.3 11.4 - - - +
74f GLY* 4.5 0.2 - - - -
75f VAL* 4.0 6.3 - - - +
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Residues in contact with MET 20 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19f VAL* 1.3 75.8 - - - +
21f VAL* 1.3 63.5 - - - +
22f LYS* 4.2 1.7 + - + +
28f GLU* 3.5 36.3 - - + +
29f TYR 3.4 3.4 - - - +
30f LYS* 3.5 42.6 - - + +
50f TYR* 3.7 27.1 - - + -
71f TYR* 4.2 3.5 - - + +
72f ILE* 3.6 1.8 - - - -
73f ARG* 2.9 62.0 + - - +
75f VAL 3.9 13.6 + - - +
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Residues in contact with VAL 21 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19f VAL* 4.7 1.8 - - + -
20f MET* 1.3 75.6 - - - +
22f LYS* 1.3 58.8 + - - +
23f LEU* 3.9 15.3 + - + +
28f GLU* 3.2 4.7 - - - +
29f TYR* 2.9 36.5 + - - +
42f MET* 3.9 23.6 - - - -
44f LEU* 4.2 14.4 - - + -
64f ILE* 4.0 20.6 - - + -
69f VAL* 3.2 35.0 - - + -
71f TYR 3.6 3.4 - - - +
72f ILE* 4.3 12.1 - - + +
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Residues in contact with LYS 22 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41e MET* 4.8 8.3 - - - -
63e GLU* 4.1 20.3 + - - -
20f MET* 4.2 1.0 + - + -
21f VAL* 1.3 73.7 - - - +
23f LEU* 1.3 65.1 + - - +
26f GLY* 3.4 25.6 + - - -
27f MET 3.9 2.7 - - - +
28f GLU* 3.8 26.7 + - + +
53f GLY 5.9 0.8 - - - +
69f VAL* 3.8 1.6 - - - +
70f LEU* 2.7 46.4 + - + +
71f TYR* 2.7 61.4 + - + +
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Residues in contact with LEU 23 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107d ILE* 4.1 21.1 - - + -
108d VAL* 4.5 3.6 - - + -
21f VAL* 3.9 21.5 - - + +
22f LYS* 1.3 87.4 - - - +
24f LYS* 1.3 65.0 + - - +
25f TRP* 2.9 10.7 + - + +
26f GLY* 3.0 13.9 + - - -
27f MET* 2.9 27.1 + - + +
29f TYR* 3.3 38.8 - - + -
64f ILE* 3.9 16.4 - - + -
68f ASN* 3.3 21.5 - - + +
69f VAL* 4.0 3.4 - - - -
70f LEU* 4.0 4.3 - - - +
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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