Contacts of the strand formed by residues 17 - 26 (chain A) in PDB entry 1PYB
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.2 27.1 - - + -
15A VAL* 2.8 26.2 + - + +
16A ASP* 1.3 72.2 - - - +
18A ARG* 1.3 63.9 + - - +
67A VAL* 4.2 1.8 - - + -
68A ILE 3.7 2.0 - - - +
69A VAL* 3.5 34.8 - - + +
87A LEU* 3.9 22.7 - - + -
108A ALA 3.4 0.5 - - - +
109A LYS* 3.8 1.2 - - - -
110A LEU* 3.0 61.7 + - + +
287B LEU* 5.3 8.7 - - + -
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASP* 3.8 15.4 + - + +
17A LEU* 1.3 80.1 - - - +
19A VAL* 1.3 64.7 + - - +
20A ALA 3.9 0.5 + - - -
41A LEU* 3.9 29.2 + - + +
44A GLU* 5.1 9.5 + - - -
67A VAL* 4.4 1.8 - - - -
68A ILE* 2.9 37.0 + - - +
70A ALA* 4.0 23.0 - - + +
107A GLY* 3.4 29.7 + - - +
108A ALA 3.2 8.7 - - - +
109A LYS* 3.6 37.6 - - + +
110A LEU* 5.2 0.2 - - - -
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 1.3 73.7 - - - +
20A ALA* 1.3 66.8 + - - +
21A LYS* 5.9 0.7 - - + -
41A LEU* 4.2 1.0 - - - +
65A LYS* 4.3 20.6 - - + -
66A ILE 3.3 8.1 - - - +
67A VAL* 3.4 29.4 - - + -
100A PRO* 5.0 5.6 - - + -
104A VAL* 4.5 15.7 - - + +
105A LYS 4.2 11.7 - - - +
106A GLU* 3.8 0.7 - - - -
107A GLY* 2.9 28.1 + - - -
108A ALA* 3.2 25.5 + - + -
110A LEU* 4.2 10.5 - - + -
289B ALA* 4.4 8.7 - - + -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG 3.9 0.2 + - - -
19A VAL* 1.3 76.8 - - - +
21A LYS* 1.3 66.7 + - - +
22A VAL 3.9 0.2 + - - -
39A LEU* 4.0 14.8 - - + +
40A SER 3.3 24.9 - - - +
41A LEU* 3.3 26.2 - - + -
64A LYS 3.7 0.5 - - - +
65A LYS* 3.4 1.7 - - - -
66A ILE* 2.9 32.4 + - - +
68A ILE* 4.3 5.8 - - + -
106A GLU* 4.9 2.0 - - - +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 5.9 0.9 - - + -
20A ALA* 1.3 75.2 - - - +
22A VAL* 1.3 63.5 + - - +
23A LEU* 3.2 8.4 + - + -
38A THR 3.6 0.2 - - - +
39A LEU* 3.7 1.2 - - - -
40A SER* 2.9 38.7 + - - +
63A GLY* 4.7 9.2 - - - +
64A LYS 3.5 5.8 - - - +
65A LYS* 3.2 39.3 - - + +
104A VAL 2.8 30.7 + - - +
105A LYS* 4.2 3.5 - - - +
106A GLU* 3.4 37.9 - - + +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 1.3 69.8 - - - +
23A LEU* 1.3 62.0 + - - +
24A SER* 3.3 26.9 - - - +
37A LEU* 3.7 29.8 - - + -
38A THR 3.6 5.6 - - - +
39A LEU* 3.9 16.8 - - + -
61A LEU* 3.0 23.1 - - + +
62A VAL* 3.6 0.6 - - - +
63A GLY* 2.8 29.0 + - - -
64A LYS 3.0 19.7 + - - +
66A ILE* 3.8 22.9 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.2 5.3 + - + +
22A VAL* 1.3 72.5 - - - +
24A SER* 1.3 66.3 + - - +
38A THR* 2.9 23.6 + - - +
39A LEU 5.3 0.4 - - - +
40A SER* 3.7 34.5 - - - +
45A GLU* 3.8 24.0 - - + +
62A VAL* 3.7 15.0 - - - +
106A GLU* 5.4 3.8 - - - +
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.3 12.7 - - - +
23A LEU* 1.3 84.2 - - - +
25A ALA* 1.3 62.7 + - - +
26A GLU* 4.3 1.3 - - - -
36A LYS 3.7 0.4 - - - +
37A LEU* 3.6 0.3 - - - -
38A THR* 2.8 43.3 + - - +
62A VAL* 4.4 11.4 - - - -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 5.1 0.4 - - + -
24A SER* 1.3 79.4 - - - +
26A GLU* 1.3 64.9 + - - +
27A ARG* 2.9 29.7 + - - +
35A LEU* 5.0 4.5 - - + -
36A LYS 3.4 6.3 - - - +
37A LEU* 3.9 21.3 - - + -
58A PRO* 4.1 31.2 - - + +
62A VAL* 4.7 4.3 - - + +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 6.2 0.7 - - - +
25A ALA* 1.3 78.3 - - - +
27A ARG* 1.3 64.9 + - - +
34A LEU* 2.8 20.2 - - - +
35A LEU* 4.1 2.6 - - - +
36A LYS* 3.0 45.6 + - + +
38A THR* 4.7 11.1 - - + +
47A THR* 4.1 19.4 - - - +
81A GLU* 4.4 4.0 - - - +
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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