Contacts of the strand formed by residues 16 - 21 (chain Y) in PDB entry 1O18
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 16 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13Y GLY* 3.1 17.9 + - - -
15Y GLY* 1.3 82.2 - - - +
17Y VAL* 1.3 58.4 + - - +
18Y LYS* 2.7 39.5 + - + +
30Y VAL* 3.8 16.6 - - + -
31Y PHE* 3.5 29.2 - - - +
32Y PRO* 3.8 8.5 - - + -
33Y SER* 4.6 2.0 - - - -
157Y ASP* 5.2 5.5 - - + +
210Y ARG* 6.1 2.2 - - - +
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Residues in contact with VAL 17 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y CYS* 4.1 24.0 - - - -
11Y ASP 3.5 11.2 - - - +
12Y ASN* 4.6 9.0 - - - +
13Y GLY 4.6 0.4 - - - +
16Y LEU* 1.3 74.9 - - - +
18Y LYS* 1.3 69.4 + - - +
29Y ALA 3.6 1.1 - - - +
30Y VAL* 3.2 24.3 - - - +
31Y PHE* 3.0 39.0 + - + +
33Y SER* 4.0 13.2 - - - +
82Y MET* 5.8 0.4 - - + -
85Y ILE* 3.7 28.7 - - + -
89Y THR* 4.5 7.6 - - + +
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Residues in contact with LYS 18 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Y CYS* 3.6 0.3 - - - -
11Y ASP* 2.8 61.8 + - + +
13Y GLY* 4.3 7.7 - - - -
16Y LEU* 2.7 40.7 + - + +
17Y VAL* 1.3 76.8 - - - +
19Y ALA* 1.3 61.3 + - - +
27Y PRO* 4.0 6.3 - - + -
29Y ALA 3.3 5.2 - - - -
30Y VAL* 4.2 7.0 - - + -
336Y LYS 5.1 4.3 - - - +
337Y TYR* 3.8 33.9 - - + -
340Y TRP* 3.4 22.2 - - + -
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Residues in contact with ALA 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y VAL 3.2 11.4 - - - +
10Y CYS* 4.6 5.4 - - + -
17Y VAL* 4.7 3.8 - - + -
18Y LYS* 1.3 73.6 - - - +
20Y GLY* 1.3 53.1 + - - +
27Y PRO* 3.2 4.2 - - - +
28Y ARG 2.6 30.8 + - - -
29Y ALA* 2.7 27.4 + - + +
89Y THR* 3.6 31.2 - - + -
94Y LEU* 4.0 6.3 - - + -
340Y TRP* 3.6 4.5 - - - +
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Residues in contact with GLY 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y LEU* 3.6 7.1 - - - +
9Y VAL 3.0 25.3 + - - -
19Y ALA* 1.3 79.1 - - - +
21Y PHE* 1.3 65.3 + - - -
24Y ASP* 4.4 0.2 - - - -
28Y ARG* 3.7 18.4 - - - -
94Y LEU* 3.6 13.2 - - - +
340Y TRP* 3.6 10.8 - - - -
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Residues in contact with PHE 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y THR 3.8 22.7 - - - +
7Y ALA 3.5 2.0 - - - -
8Y LEU* 3.5 28.9 - - + -
20Y GLY* 1.3 74.6 - - - -
22Y ALA* 1.3 66.7 + - - +
24Y ASP* 3.0 33.6 + - - +
28Y ARG* 3.5 38.4 - - + +
94Y LEU* 4.3 28.5 - - + -
96Y VAL* 3.7 26.0 - - + -
101Y HIS* 4.6 7.4 - + - -
340Y TRP* 3.5 9.2 - - - -
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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