Contacts of the strand formed by residues 65 - 72 (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 ARG 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 4.0 8.3 + - - -
27A VAL* 5.7 4.9 - - - +
70A PHE* 4.8 2.0 - - - -
25B ARG* 3.6 9.9 - - - +
47B GLU* 2.9 69.8 + - + +
49B ARG* 3.6 9.3 - - - +
64B LYS* 1.3 80.8 - - - +
66B VAL* 1.3 67.8 + - - +
67B LEU* 4.0 10.6 - - + +
19K ILE* 3.7 23.9 - - + +
20K PRO* 2.8 59.0 + - + -
21K TYR* 4.6 0.8 - - - +
22K LEU* 3.4 32.3 + - + +
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Residues in contact with VAL 66 (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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44B ASP* 5.7 1.3 - - - -
45B CYS 4.2 2.0 - - - -
46B ASP* 4.0 27.6 - - - +
64B LYS* 4.5 13.0 - - + -
65B ARG* 1.3 78.2 - - - +
67B LEU* 1.3 68.1 + - - +
68B GLY* 3.8 4.0 - - - +
16K ARG* 3.6 32.6 - - - +
19K ILE* 3.8 13.7 - - - +
20K PRO* 5.2 3.9 - - - +
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Residues in contact with LEU 67 (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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70A PHE* 4.1 9.2 - - + -
72A ILE* 3.0 48.8 - - + +
27B PHE* 3.6 38.8 - - + -
45B CYS* 3.0 14.9 + - - +
47B GLU* 3.8 12.1 - - + +
65B ARG* 4.0 31.4 - - + +
66B VAL* 1.3 82.2 - - - +
68B GLY* 1.3 61.3 + - - +
70B VAL* 3.6 21.3 - - + -
16K ARG* 4.0 9.8 - - - -
19K ILE* 4.3 10.1 - - + +
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Residues in contact with GLY 68 (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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75A ASP* 4.1 0.9 - - - -
42B LEU 3.5 0.3 - - - +
44B ASP* 3.3 10.6 + - - -
45B CYS* 2.7 43.5 + - - +
66B VAL* 3.8 3.8 - - - +
67B LEU* 1.3 77.7 - - - +
69B LEU* 1.3 59.1 + - - -
16K ARG* 3.6 28.9 - - - -
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Residues in contact with LEU 69 (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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9A VAL* 4.6 10.5 - - + -
72A ILE* 3.4 3.5 - - - -
73A LEU* 2.8 57.2 + - + +
74A PRO 3.7 18.2 - - - +
75A ASP* 3.3 19.8 + - + +
77A LEU* 3.8 19.1 - - + -
78A LYS* 4.2 12.1 - - + +
83A LEU* 5.1 1.1 - - + -
41B ILE* 3.8 19.5 - - + -
42B LEU 3.5 14.1 - - - +
43B CYS* 3.6 27.4 - - - +
44B ASP 4.5 0.6 - - - +
67B LEU 3.7 2.2 + - - -
68B GLY* 1.3 70.1 - - - -
70B VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 70 (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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70A PHE* 4.0 7.6 - - + -
71A LEU 3.3 11.0 - - - +
72A ILE* 4.6 2.7 - - + -
73A LEU* 5.5 0.7 - - - -
27B PHE* 3.8 28.5 - - + -
40B LEU 3.7 0.5 - - - +
41B ILE* 3.4 8.1 - - - +
42B LEU* 2.9 38.1 + - + +
45B CYS* 3.5 28.9 - - + -
67B LEU* 3.6 27.1 - - + +
68B GLY 3.6 0.9 - - - +
69B LEU* 1.3 81.2 - - - +
71B LEU* 1.3 69.9 + - - +
72B LEU* 4.0 2.2 + - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A PRO* 3.1 32.1 - - + +
7A ILE* 5.0 0.4 - - + -
10A LEU* 3.8 24.9 - - + +
39A MET* 3.5 34.3 - - + -
70A PHE* 3.2 4.0 - - - -
71A LEU* 2.8 52.4 + - + +
73A LEU* 4.1 15.1 - - + +
39B ASN* 5.1 2.7 - - + -
40B LEU 3.3 6.1 - - - +
41B ILE* 3.8 16.2 - - + -
70B VAL* 1.3 74.1 - - - +
72B LEU* 1.3 61.8 + - - +
73B ARG 3.8 0.2 + - - -
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Residues in contact with LEU 72 (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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69A ARG 3.6 17.5 - - - +
70A PHE* 4.0 5.4 - - + -
19B CYS* 4.8 2.0 - - + -
21B LEU* 4.0 44.4 - - + -
27B PHE* 4.0 20.0 - - + -
39B ASN* 3.1 6.2 - - - +
40B LEU* 3.0 60.7 + - + -
42B LEU* 5.2 2.9 - - + -
70B VAL* 3.9 3.7 + - + -
71B LEU* 1.3 73.2 - - - +
73B ARG* 1.3 72.5 + - - +
74B GLY* 5.6 0.2 - - - -
76B ASN* 4.5 5.4 - - + -
77B LEU* 4.1 17.0 - - + +
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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