Contacts of the strand formed by residues 19 - 25 (chain H) in PDB entry 5Y39
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 19 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12H LYS 4.2 1.3 - - - +
13H LEU* 3.5 47.0 - - + +
16H VAL* 3.2 27.1 + - + +
17H GLU 3.4 1.6 + - - -
18H GLY* 1.3 73.5 - - - +
20H HIS* 1.3 62.1 + - - +
21H ALA 3.8 7.2 - - - +
22H ILE* 4.2 5.4 - - + -
37H ASN* 3.5 10.6 + - - -
92H PHE* 3.7 27.8 - - + -
93H ILE 3.8 14.1 - - - +
94H ALA* 3.9 12.9 - - + +
98H ALA* 4.4 0.6 - - - +
103H ILE* 4.4 7.9 - - + -
106H LEU* 3.7 29.6 - - + -
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Residues in contact with HIS 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.4 6.0 - - - +
18H GLY* 2.9 25.8 + - - -
19H LEU* 1.3 75.0 + - - +
21H ALA* 1.3 58.2 + - + +
37H ASN* 3.0 39.4 + - - +
39H ASN* 3.7 38.2 + - + +
40H ALA* 3.7 25.6 - - + +
41H PRO* 4.2 8.7 - - + -
78H TYR* 5.7 2.0 - - + -
93H ILE* 2.8 16.2 + - + +
94H ALA 4.0 4.5 - - - -
95H SER* 3.5 31.7 + - - -
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Residues in contact with ALA 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 4.0 2.4 - - - +
19H LEU* 3.7 4.3 - - - +
20H HIS* 1.3 78.7 - - - +
22H ILE* 1.3 66.9 + - - +
23H VAL* 4.6 2.0 - - + -
35H VAL 3.4 5.4 - - - -
36H ALA* 3.7 22.2 - - + -
40H ALA* 4.2 4.5 - - + -
45H LEU* 3.7 22.7 - - + -
91H SER 4.5 0.2 - - - -
92H PHE* 3.5 3.5 - - - -
93H ILE* 2.9 39.2 + - + +
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H LEU* 4.3 34.5 - - + +
12H LYS* 4.9 2.5 - - + -
13H LEU* 3.7 20.0 - - + -
19H LEU* 4.2 7.6 - - + -
21H ALA* 1.3 76.9 - - - +
23H VAL* 1.3 67.3 + - - +
24H VAL* 4.2 4.4 + - + -
33H ILE* 4.2 1.4 - - - +
34H LYS* 3.8 0.5 - - - -
35H VAL* 2.8 45.6 + - + +
90H VAL* 4.8 2.5 - - + -
91H SER 3.4 7.4 - - - +
92H PHE* 3.8 32.3 - - + -
106H LEU* 4.4 7.0 - - + -
110H LEU* 4.6 4.0 - - + -
114H PHE* 4.5 20.9 - - + -
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Residues in contact with VAL 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ALA* 4.6 3.8 - - + -
22H ILE* 1.3 77.4 - - - +
24H VAL* 1.3 63.2 + - - +
25H SER* 3.8 0.5 + - - -
31H PRO* 3.9 20.2 - - + -
33H ILE 3.4 14.8 - - - +
34H LYS* 4.1 15.9 - - + -
45H LEU* 3.7 29.8 - - + -
50H LEU* 3.7 32.5 - - + -
89H VAL 3.2 4.5 - - - +
91H SER* 2.8 44.0 + - - +
93H ILE* 4.7 4.9 - - + -
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Residues in contact with VAL 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H LEU* 5.1 0.2 - - + -
22H ILE* 4.7 4.3 - - + -
23H VAL* 1.3 71.3 - - - +
25H SER* 1.3 55.7 + - - +
31H PRO* 3.6 1.4 - - - +
32H VAL* 2.7 38.0 + - + -
33H ILE* 2.9 38.6 + - + +
88H LEU* 4.0 37.0 - - + -
89H VAL 3.5 4.0 - - - +
90H VAL* 4.5 8.1 - - + -
114H PHE* 3.4 38.1 - - + -
117H LEU* 4.8 7.4 - - + -
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Residues in contact with SER 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H VAL 4.7 0.7 - - - -
24H VAL* 1.3 76.0 - - - +
26H ASP* 1.3 79.9 + - - +
29H GLY* 3.1 22.9 - - - -
30H VAL 3.0 17.2 + - - -
31H PRO* 4.3 0.9 - - - -
32H VAL* 3.9 7.6 - - - +
50H LEU* 4.2 17.2 - - - +
88H LEU* 3.4 11.1 - - - +
89H VAL* 2.8 40.6 + - - +
91H SER* 5.1 0.2 - - - -
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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