Contacts of the strand formed by residues 220 - 224 (chain A) in PDB entry 1OE5
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 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 2.9 12.2 + - + +
90A VAL* 3.2 13.5 - - + +
91A LEU 2.8 31.2 + - - +
218A VAL* 3.6 2.1 - - - +
219A LYS* 1.4 82.7 - - + +
221A VAL* 1.3 60.3 + - - +
222A ILE* 3.8 17.0 - - + -
244A THR* 3.3 37.7 - - + +
246A LYS* 3.9 17.7 - - + -
273A LEU* 4.9 10.3 - - + +
275A VAL* 3.7 30.5 - - + -
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Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.4 14.4 - - + +
93A LEU* 4.3 15.3 - - + -
209A LEU* 5.7 0.7 - - + -
213A VAL* 3.9 20.2 - - + -
218A VAL* 3.5 24.0 - - + -
220A LEU* 1.3 73.0 - - - +
222A ILE* 1.3 68.1 + - - +
223A GLY 4.4 1.3 - - - +
232A ALA* 4.1 25.1 - - + -
236A LEU* 4.0 5.6 - - + -
243A VAL* 3.9 9.0 - - + -
244A THR 2.8 12.3 + - - +
245A VAL* 3.4 10.1 - - + -
246A LYS* 2.9 28.6 + - - +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.6 24.2 - - + -
91A LEU 2.8 9.2 + - - +
92A PHE* 3.3 30.7 - - + -
93A LEU 2.8 26.5 + - - -
220A LEU* 3.8 24.2 - - + -
221A VAL* 1.3 77.1 - - - +
223A GLY* 1.3 65.6 + - - +
224A VAL* 3.3 1.6 + - - +
246A LYS* 3.5 3.1 - - + -
247A GLY 4.0 4.0 - - - +
248A ILE* 3.6 38.4 - - + +
270A LEU* 4.4 3.1 - - + -
273A LEU* 4.1 13.7 - - + -
275A VAL* 3.9 13.9 - - + -
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Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.7 10.3 - - - -
221A VAL* 3.8 4.9 + - - +
222A ILE* 1.3 69.7 - - - +
224A VAL* 1.3 62.0 + - - -
225A GLY 3.5 5.3 + - - +
228A SER* 3.9 3.6 - - - -
229A GLU* 3.7 26.2 - - - +
245A VAL* 5.1 0.2 - - - +
246A LYS 2.9 10.9 + - - -
247A GLY* 3.3 3.8 - - - -
248A ILE 3.0 25.3 + - - +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.2 4.7 - - + -
93A LEU 2.8 26.8 + - - +
94A GLY* 4.4 1.9 - - - -
95A MET* 4.7 1.2 + - - +
109A PHE* 3.7 27.1 - - + -
152A PHE* 4.1 24.0 - - + -
222A ILE 3.9 7.9 - - - +
223A GLY* 1.3 68.7 - - - -
225A GLY* 1.3 60.7 + - - +
228A SER* 3.6 13.7 + - - -
248A ILE* 4.0 20.4 - - + -
249A MET 4.0 7.4 - - - +
250A HIS* 3.1 14.5 - - + -
251A PRO* 3.7 25.4 - - + -
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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