Contacts of the strand formed by residues 150 - 155 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142X LEU* 3.8 14.5 - - - +
149X THR* 1.3 78.2 - - - +
151X ILE* 1.3 62.4 + - - +
164X PRO* 3.7 0.7 - - - +
165X ILE* 2.9 29.2 + - - +
293X LEU* 3.8 12.6 - - - +
296X ASN* 3.2 21.1 - - - -
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Residues in contact with ILE 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X LEU* 4.4 0.4 - - - +
150X GLY* 1.3 74.6 - - - +
152X VAL* 1.3 65.0 + - - +
153X LEU 4.0 0.5 + - - -
162X ASN* 4.5 6.3 - - + +
163X VAL 3.7 8.5 - - - +
164X PRO* 3.9 22.7 - - + -
278X THR* 3.6 30.3 - - + +
281X SER* 3.6 22.0 - - - +
282X ILE* 3.7 13.0 - - + -
293X LEU* 3.4 33.2 - - + +
296X ASN 2.8 8.5 + - - +
297X ASN* 3.4 21.3 - - - +
298X VAL* 2.9 23.7 + - - +
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Residues in contact with VAL 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138X ALA* 3.3 41.3 - - + +
141X SER* 4.3 2.5 - - - -
142X LEU* 3.8 30.5 - - + +
151X ILE* 1.3 73.5 - - - +
153X LEU* 1.3 68.4 + - - +
154X ASP* 3.6 10.0 + - + -
161X HIS 4.1 0.2 - - - -
162X ASN* 3.2 7.3 - - - +
163X VAL* 2.9 30.9 + - - +
165X ILE* 4.5 1.6 - - + -
297X ASN* 5.6 0.2 - - - -
298X VAL* 3.1 14.1 - - + +
300X SER* 3.6 25.4 - - - +
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Residues in contact with LEU 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X ILE 4.0 0.8 + - - -
152X VAL* 1.3 72.0 - - - +
154X ASP* 1.3 59.9 + - - +
155X SER* 5.1 1.8 - - - -
160X THR* 4.4 8.1 - - + -
161X HIS 3.4 8.1 - - - +
162X ASN* 3.6 23.8 - - - +
274X ILE* 3.6 40.8 - - + +
278X THR* 3.9 10.1 - - - +
297X ASN* 4.5 13.5 - - - +
298X VAL 2.9 8.2 + - - +
299X MET* 3.6 33.4 - - + -
300X SER 3.1 24.8 + - - +
304X THR* 4.0 13.5 - - + -
309X ILE* 5.7 5.2 - - + -
313X MET* 4.5 3.8 - - + -
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Residues in contact with ASP 154 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X PRO* 5.9 2.1 - - - +
137X GLN* 4.0 26.2 - - - +
138X ALA* 4.1 11.0 + - + -
152X VAL* 3.6 13.8 + - + +
153X LEU* 1.3 72.9 - - - +
155X SER* 1.4 63.9 + - - +
156X GLY 4.4 0.6 + - - -
159X VAL 4.0 1.8 - - - +
160X THR* 3.2 3.8 - - - +
161X HIS* 2.7 51.1 + - + +
163X VAL* 5.8 0.2 - - + -
300X SER* 3.0 29.4 + - - +
301X GLY* 4.0 4.2 + - - -
339X VAL* 4.3 9.7 - - - +
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Residues in contact with SER 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LEU* 5.1 3.1 - - - -
154X ASP* 1.4 76.5 + - - +
156X GLY* 1.3 60.1 + - - +
159X VAL 3.6 4.4 + - - -
160X THR* 2.6 27.2 + - - +
180X LEU 4.6 0.3 + - - -
181X ALA* 4.5 2.3 - - - +
261X LEU* 4.8 4.9 - - - +
274X ILE* 5.5 1.1 - - - +
300X SER 3.1 8.3 + - - -
301X GLY* 3.2 14.1 - - - -
303X THR* 3.1 38.4 + - - +
304X 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