Contacts of the strand formed by residues 150 - 155 (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 GLY 150 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Y LEU* 3.8 14.3 - - - +
149Y THR* 1.3 77.4 - - - +
151Y ILE* 1.3 62.2 + - - +
164Y PRO* 3.7 0.7 - - - +
165Y ILE* 2.9 29.1 + - - +
293Y LEU* 3.8 12.6 - - - +
296Y ASN* 3.2 20.9 - - - -
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Residues in contact with ILE 151 (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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142Y LEU* 4.4 0.4 - - - +
150Y GLY* 1.3 75.1 - - - +
152Y VAL* 1.3 65.6 + - - +
153Y LEU 4.0 0.3 + - - -
162Y ASN* 4.5 6.3 - - + +
163Y VAL 3.7 8.5 - - - +
164Y PRO* 3.9 22.0 - - + -
278Y THR* 3.6 30.1 - - + +
281Y SER* 3.6 21.3 - - - +
282Y ILE* 3.7 12.1 - - + -
293Y LEU* 3.4 33.2 - - + +
296Y ASN 2.8 9.1 + - - +
297Y ASN* 3.4 21.3 - - - +
298Y VAL* 2.9 23.4 + - - +
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Residues in contact with VAL 152 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138Y ALA* 3.3 41.5 - - + +
141Y SER* 4.3 2.7 - - - -
142Y LEU* 3.8 31.0 - - + +
151Y ILE* 1.3 73.9 - - - +
153Y LEU* 1.3 67.9 + - - +
154Y ASP* 3.6 10.0 + - + -
161Y HIS 4.1 0.2 - - - -
162Y ASN* 3.2 7.6 - - - +
163Y VAL* 2.9 30.9 + - - +
165Y ILE* 4.5 1.3 - - + -
297Y ASN* 5.6 0.2 - - - -
298Y VAL* 3.1 14.4 - - + +
300Y SER* 3.6 25.1 - - - +
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Residues in contact with LEU 153 (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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151Y ILE 4.0 0.8 + - - -
152Y VAL* 1.3 71.1 - - - +
154Y ASP* 1.3 59.6 + - - +
155Y SER* 5.1 1.8 - - - -
160Y THR* 4.4 8.5 - - + -
161Y HIS 3.4 8.1 - - - +
162Y ASN* 3.6 24.5 - - - +
274Y ILE* 3.6 40.4 - - + +
278Y THR* 3.9 9.9 - - - +
297Y ASN* 4.5 13.1 - - - +
298Y VAL 2.9 8.0 + - - +
299Y MET* 3.6 34.6 - - + -
300Y SER 3.1 24.1 + - - +
304Y THR* 4.0 13.7 - - + -
309Y ILE* 5.7 5.4 - - + -
313Y MET* 4.5 3.4 - - + -
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Residues in contact with ASP 154 (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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109Y PRO* 5.9 2.7 - - + +
137Y GLN* 4.0 25.8 - - - +
138Y ALA* 4.1 10.8 + - + -
152Y VAL* 3.6 13.8 + - + +
153Y LEU* 1.3 73.4 - - - +
155Y SER* 1.4 64.4 + - - +
156Y GLY 5.1 0.4 + - - -
159Y VAL 4.0 1.5 - - - +
160Y THR* 3.2 4.0 - - - +
161Y HIS* 2.7 50.2 + - + +
300Y SER* 3.0 30.2 + - - +
301Y GLY* 4.0 4.5 + - - -
339Y VAL* 4.3 9.3 - - - +
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Residues in contact with SER 155 (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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153Y LEU* 5.1 3.6 - - - -
154Y ASP* 1.4 75.9 + - - +
156Y GLY* 1.3 60.6 + - - +
159Y VAL 3.6 4.4 + - - -
160Y THR* 2.6 27.7 + - - +
180Y LEU 4.6 0.3 + - - -
181Y ALA* 4.5 2.3 - - - +
261Y LEU* 4.8 4.3 - - - +
274Y ILE* 5.5 1.2 - - - +
300Y SER 3.1 8.7 + - - -
301Y GLY* 3.2 13.3 - - - -
303Y THR* 3.1 38.8 + - - +
304Y THR* 3.6 19.7 - - - -
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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