Contacts of the strand formed by residues 160 - 166 (chain Y) 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 THR 160 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153Y LEU* 4.4 6.3 - - + -
154Y ASP 3.2 9.4 - - - +
155Y SER* 2.6 25.9 + - - +
159Y VAL* 1.4 71.4 - - - +
161Y HIS* 1.3 75.5 + - - +
162Y ASN* 5.0 3.1 - - - +
177Y ARG* 3.3 6.1 - - - +
178Y LEU* 2.9 46.2 + - + -
180Y LEU 3.1 16.7 + - - -
181Y ALA* 4.3 0.2 - - - +
261Y LEU* 5.1 0.2 - - - +
274Y ILE* 3.6 31.4 - - + +
277Y THR* 6.1 0.4 - - + -
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Residues in contact with HIS 161 (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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73Y HIS 5.2 0.7 - - - -
108Y ALA* 4.9 7.6 - - + -
109Y PRO* 3.6 41.3 - - + +
110Y LEU* 5.2 3.4 + - - +
152Y VAL 4.1 0.2 - - - -
153Y LEU* 3.4 4.7 - - - -
154Y ASP* 2.7 41.7 + - + +
159Y VAL* 4.0 31.5 - - + +
160Y THR* 1.3 80.1 + - - +
162Y ASN* 1.3 65.7 + - - +
163Y VAL* 4.2 12.1 - - + -
175Y ILE* 4.0 8.0 - - + +
176Y MET 3.0 16.8 - - - -
177Y ARG* 3.7 29.2 + - + +
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Residues in contact with ASN 162 (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* 4.5 5.8 - - + +
152Y VAL 3.2 7.1 + - - +
153Y LEU* 3.6 21.2 - - - +
160Y THR* 5.0 2.1 - - - +
161Y HIS* 1.3 74.9 + - - +
163Y VAL* 1.3 62.6 + - - +
164Y PRO* 3.5 2.9 - - - +
175Y ILE* 3.2 24.8 - - - +
176Y MET* 2.9 13.5 + - + +
178Y LEU* 5.8 0.3 + - - +
277Y THR* 2.9 31.1 - - - +
278Y THR* 3.4 34.4 + - - +
281Y SER* 3.6 20.2 - - - +
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Residues in contact with VAL 163 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Y PRO* 3.5 33.9 - - + -
136Y ILE* 5.1 2.2 - - + -
138Y ALA* 3.4 22.0 - - + -
139Y VAL* 5.0 0.9 - - + -
151Y ILE* 4.2 1.1 - - - +
152Y VAL 2.9 29.0 + - - +
154Y ASP* 5.8 0.2 - - + -
161Y HIS* 4.2 9.9 - - + -
162Y ASN* 1.3 78.5 - - - +
164Y PRO* 1.3 63.5 - - - +
165Y ILE* 3.5 16.8 + - + +
170Y ALA* 3.6 30.7 - - + -
175Y ILE* 3.9 15.9 - - + -
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Residues in contact with PRO 164 (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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150Y GLY 3.7 7.0 - - - +
151Y ILE* 3.9 15.9 - - + -
162Y ASN 3.5 6.5 - - - +
163Y VAL* 1.3 82.3 - - - +
165Y ILE* 1.4 60.2 + - - +
170Y ALA* 3.6 0.2 - - - -
171Y LEU* 2.8 35.4 + - + +
174Y ALA* 3.7 15.5 - - + -
175Y ILE* 4.0 18.6 - - + +
281Y SER* 3.4 21.1 - - - +
285Y CYS* 3.8 21.5 - - - -
293Y LEU* 4.4 8.7 - - + -
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Residues in contact with ILE 165 (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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138Y ALA* 3.7 9.9 - - + +
139Y VAL* 3.5 40.6 - - + +
142Y LEU* 3.9 19.5 - - + -
148Y THR 3.4 16.2 - - - +
149Y THR* 3.1 24.6 - - - +
150Y GLY 2.9 12.5 + - - +
152Y VAL* 4.5 2.7 - - + -
163Y VAL* 3.6 20.6 - - + +
164Y PRO* 1.4 74.7 - - - +
166Y TYR* 1.3 62.4 + - - +
168Y GLY* 3.6 25.6 - - - +
169Y TYR 3.7 2.7 - - - -
170Y ALA* 3.6 15.7 - - + -
171Y LEU* 4.7 1.3 - - - -
293Y LEU* 4.3 2.0 - - - +
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Residues in contact with TYR 166 (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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149Y THR* 3.6 17.3 - - + -
164Y PRO 4.4 0.2 - - - -
165Y ILE* 1.3 72.4 - - - +
167Y GLU* 1.3 90.1 + - + +
168Y GLY 2.9 4.8 + - - -
169Y TYR* 3.1 27.4 + - + +
171Y LEU* 4.3 20.8 - - + +
289Y ILE* 3.7 36.7 - - + +
292Y ASP* 4.0 17.8 + - - -
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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