Contacts of the strand formed by residues 13 - 18 (chain F) in PDB entry 1S89
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 HIS 13 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F PRO* 4.0 16.6 - - + +
11F ARG* 4.1 6.9 + - - -
12F LYS* 1.3 70.2 - - - +
14F ILE* 1.3 61.6 + - - +
41F VAL* 3.4 25.7 - - + +
43F TYR* 3.3 32.1 - - + -
82F LYS* 3.1 26.9 + - - +
83F ILE* 3.8 3.4 - - - -
84F ASP* 2.7 55.7 + - - +
85F VAL 3.3 6.1 + - - +
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Residues in contact with ILE 14 (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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12F LYS* 4.1 14.1 - - + +
13F HIS* 1.3 75.9 - - - +
15F ALA* 1.3 62.4 + - - +
16F LEU* 3.8 25.7 - - + +
37F LEU* 4.1 20.9 - - + -
40F HIS* 3.8 25.1 - - + -
41F VAL 2.7 12.8 + - - +
42F LEU* 3.6 8.9 - - + +
43F TYR* 2.7 36.7 + - - +
83F ILE* 4.6 0.4 - - - -
85F VAL* 3.7 17.9 - - + +
87F ILE* 4.0 12.6 - - + -
132F PHE* 3.8 24.0 - - + -
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Residues in contact with ALA 15 (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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13F HIS 4.1 0.2 + - - -
14F ILE* 1.3 74.3 - - - +
16F LEU* 1.3 60.2 + - - +
17F VAL* 4.1 2.2 - - + -
43F TYR* 3.5 9.0 - - + -
44F ALA* 5.9 0.2 - - - -
74F VAL* 3.9 17.0 - - + -
83F ILE* 3.9 19.7 - - + -
85F VAL 3.0 11.7 + - - +
86F LEU* 3.7 22.4 - - + +
87F ILE* 3.0 30.1 + - - +
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Residues in contact with LEU 16 (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 ILE* 3.8 12.6 - - + +
15F ALA* 1.3 73.4 - - - +
17F VAL* 1.3 63.7 + - - +
26F LEU* 4.3 15.0 - - + -
29F TRP* 4.5 13.0 - - + -
30F VAL* 4.4 9.9 - - + -
37F LEU* 5.3 4.5 - - + -
42F LEU* 4.2 27.8 - - + -
43F TYR 2.8 16.8 + - - +
44F ALA* 3.1 29.1 - - + +
45F THR 3.6 2.1 + - - -
48F THR* 3.7 4.9 - - - +
52F ILE* 3.9 24.0 - - + -
60F VAL* 5.5 1.8 - - + -
87F ILE* 3.6 34.3 - - + -
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Residues in contact with VAL 17 (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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15F ALA* 4.7 0.9 - - + -
16F LEU* 1.3 84.5 - - - +
18F ALA* 1.3 65.2 + - - +
26F LEU* 4.2 5.1 - - - +
44F ALA* 5.3 0.4 - - - -
45F THR* 3.7 24.7 - - + +
48F THR* 4.4 1.1 - - - -
71F ASP* 4.0 8.1 - - - +
74F VAL* 4.7 12.3 - - + -
86F LEU* 4.4 17.3 - - + -
87F ILE 2.9 7.6 + - - +
88F PHE* 3.1 25.0 - - + -
89F PHE 2.9 24.3 + - - -
105F LEU* 5.0 4.9 - - + -
206F PGA 3.3 26.2 - - - +
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Residues in contact with ALA 18 (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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17F VAL* 1.3 79.1 - - - +
19F HIS* 1.3 67.2 + - - +
22F CYS 4.2 1.8 - - - -
23F LYS* 2.9 34.5 + - + +
26F LEU* 3.6 32.1 - - + -
48F THR* 3.4 10.3 + - - +
88F PHE* 4.6 0.4 - - - -
89F PHE* 3.5 12.6 - - + +
206F PGA 3.4 12.7 - - - +
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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