Contacts of the strand formed by residues 8 - 12 (chain W) in PDB entry 1O1F
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 8 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7W ALA* 1.3 75.3 - - - +
9W VAL* 1.3 66.4 + - - +
10W CYS* 4.1 1.8 - - + -
20W GLY 3.6 4.5 - - - +
21W PHE* 3.5 35.4 - - + -
90W PHE* 4.0 25.4 - - + -
94W LEU* 4.2 14.4 - - + -
96W VAL* 4.0 19.1 - - + -
98W PRO* 5.3 2.9 - - + -
101W HIS* 3.7 36.3 - - + +
102W PRO 2.8 11.8 + - - +
103W THR* 4.2 12.3 - - + +
104W LEU* 2.9 24.3 + - - +
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Residues in contact with VAL 9 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W LEU* 1.3 78.2 - - - +
10W CYS* 1.3 65.3 + - - +
11W ASP 4.9 0.2 - - - +
19W ALA* 3.2 12.0 - - - -
20W GLY 3.0 11.2 + - - -
22W ALA* 4.2 15.3 - - + -
94W LEU* 6.4 0.2 - - - -
104W LEU* 3.3 27.1 - - + +
106W THR* 5.4 3.1 - - + -
340W TRP* 2.8 57.4 + - + +
343W GLY* 3.9 25.8 - - - +
344W SER* 3.9 9.9 - - - +
347W ALA* 4.5 0.9 - - + -
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Residues in contact with CYS 10 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W LEU* 5.9 1.3 - - + -
9W VAL* 1.3 76.3 - - - +
11W ASP* 1.3 59.2 + - - +
12W ASN* 3.5 25.3 + - - -
17W VAL* 4.1 16.8 - - - -
18W LYS 3.6 2.7 - - - -
19W ALA* 4.5 4.3 - - + +
86W TRP* 4.0 17.5 - - - -
89W THR* 4.7 11.4 - - + -
90W PHE* 5.8 6.1 - - + -
103W THR* 4.9 6.1 - - + -
104W LEU 2.9 7.6 + - - +
105W LEU* 3.5 20.6 - - + +
106W THR* 3.4 22.7 + - - +
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Residues in contact with ASP 11 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W VAL* 4.0 0.8 - - + -
10W CYS* 1.3 73.1 - - - +
12W ASN* 1.3 66.5 + - - +
13W GLY* 5.3 0.3 - - - -
17W VAL* 3.5 6.2 - - - -
18W LYS* 2.8 59.2 + - + +
106W THR* 2.9 27.3 + - + +
137W GLN* 4.2 7.3 - - - +
339W VAL* 3.4 33.5 - - + +
340W TRP* 4.0 17.5 + - + +
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Residues in contact with ASN 12 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W CYS* 3.5 19.3 + - - -
11W ASP* 1.3 78.0 + - - +
13W GLY* 1.3 58.8 + - - +
17W VAL* 4.5 9.8 - - - +
71W ILE* 3.5 23.7 - - + +
74W GLY* 5.3 2.9 - - - +
76W ILE* 5.5 3.4 - - + +
82W MET* 3.5 11.9 - - + +
86W TRP* 2.9 38.5 + - - +
105W LEU* 4.3 7.5 - - - +
106W THR* 3.7 21.0 + - - +
119W MET* 4.8 3.4 - - - +
137W GLN* 4.1 15.1 + - - +
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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