Contacts of the strand formed by residues 77 - 84 (chain B) 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 LEU 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B CYS* 3.9 19.1 - - + -
20B ILE 3.7 11.9 - - - +
22B GLN* 4.4 0.3 - - - +
38B MET* 3.8 27.1 - - + +
40B LEU* 3.7 22.4 - - + -
72B LEU* 4.1 15.5 - - + +
73B ARG 3.9 1.8 + - - -
74B GLY* 3.0 15.7 + - - +
75B GLU 3.9 4.3 - - - +
76B ASN* 1.3 78.9 - - - +
78B VAL* 1.3 70.8 + - - +
79B SER 3.7 15.7 - - - +
80B MET* 4.0 18.4 - - + -
61C ARG* 3.6 16.1 - - + -
64C ASN* 3.1 13.5 - - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341 U 6.1 0.2 - - - +
20B ILE* 3.0 22.4 + - + +
21B LEU 3.8 16.2 - - - +
22B GLN* 3.8 20.4 - - + -
77B LEU* 1.3 76.9 - - - +
79B SER* 1.3 65.2 + - - +
19C LEU* 3.5 31.4 - - + -
21C ASN* 4.3 17.3 - - - +
60C ILE* 3.4 4.0 - - - +
61C ARG* 2.8 31.9 + - - +
64C ASN* 3.4 18.3 - - - +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG 3.9 0.9 - - - +
19B CYS* 3.4 3.8 - - - -
20B ILE* 3.0 51.2 + - - +
77B LEU* 3.7 4.5 - - - +
78B VAL* 1.3 88.3 - - - +
80B MET* 1.3 63.1 + - - +
19C LEU* 5.4 2.0 - - - -
45C MET* 4.5 5.0 - - - -
58C LEU* 3.8 19.1 - - - +
59C SER 3.0 14.4 - - - -
60C ILE* 4.5 5.8 - - - -
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Residues in contact with MET 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 3.5 37.2 - - + -
17B MET* 4.7 19.1 - - - +
18B ARG 3.6 4.3 - - - +
19B CYS* 3.5 24.2 - - + -
31B PHE* 4.5 11.7 - - + -
38B MET* 4.2 6.1 - - + -
40B LEU* 3.2 44.4 - - + -
77B LEU* 4.0 14.6 - - + -
79B SER* 1.3 76.7 - - - +
81B THR* 1.3 61.5 + - - +
57C THR* 5.4 0.3 + - - -
58C LEU* 3.4 5.9 - - - -
59C SER* 2.8 42.4 + - - +
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B MET* 2.9 10.3 - - - +
18B ARG* 2.8 56.1 + - + +
20B ILE* 5.6 3.1 - - + +
80B MET* 1.3 72.9 - - - +
82B VAL* 1.3 73.7 + - - +
83B GLU* 5.5 0.9 - - - +
55C LEU* 4.0 33.4 - - + +
56C GLU 5.0 0.5 + - - -
57C THR* 2.6 33.0 + - - +
58C LEU* 4.3 2.9 - - + +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B HIS* 3.5 28.7 - - + -
15B TYR* 3.8 20.0 - - + -
16B ARG 4.0 0.9 - - - +
17B MET* 2.5 32.7 - - + +
81B THR* 1.3 85.1 + - - +
83B GLU* 1.3 63.9 + - - +
84B GLY* 3.7 24.0 - - - +
57C THR* 3.9 16.8 - - + +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 2.7 28.5 + - + +
18B ARG* 3.0 46.9 + - - +
28B ILE* 3.7 33.7 - - + +
81B THR* 3.6 2.1 + - - +
82B VAL* 1.3 76.0 - - - +
84B GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TYR* 3.5 10.7 - - - -
16B ARG* 3.0 32.0 + - - +
82B VAL* 3.7 6.0 - - - +
83B GLU* 1.3 79.1 - - - +
85B PRO* 1.4 72.6 - - - +
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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