Contacts of the strand formed by residues 120 - 127 (chain D) in PDB entry 1OIK
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 ALA 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D LEU* 4.6 15.3 - - + -
75D LEU* 6.5 0.2 - - + -
118D PRO* 3.4 3.5 + - - +
119D LYS* 1.3 91.9 - - + +
121D SER* 1.3 66.4 + - - +
256D ILE* 4.8 3.6 - - + -
257D TRP 3.2 17.7 - - - +
259D ASN* 4.1 5.6 - - - +
281D THR* 3.6 3.3 + - - -
282D LEU* 3.0 39.0 + - + +
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASP* 3.7 6.8 + - - +
118D PRO* 5.3 0.2 - - - +
120D ALA* 1.3 72.5 + - - +
122D ILE* 1.3 64.4 + - - +
123D LEU 4.2 0.4 - - - -
255D ALA 3.8 0.3 - - - +
256D ILE* 3.3 7.6 - - - +
257D TRP* 3.2 60.4 + - - +
259D ASN* 5.9 1.0 - - - -
279D ARG* 3.5 18.4 + - - -
280D VAL 3.4 6.3 - - - -
281D THR* 2.8 22.7 + - - -
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 6.2 0.7 - - + -
68D GLN* 3.1 22.6 + - + +
71D PHE* 4.3 15.7 - - + -
72D ALA* 3.5 37.5 - - + -
75D LEU* 4.2 7.4 - - + -
121D SER* 1.3 77.6 - - - +
123D LEU* 1.3 62.0 + - - +
254D VAL* 3.9 21.5 - - + -
255D ALA 3.4 3.6 - - - -
256D ILE* 3.9 22.2 - - + -
279D ARG* 3.2 2.8 - - - -
280D VAL* 2.9 35.0 + - + +
282D LEU* 4.0 23.8 - - + -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLN* 4.4 0.2 - - - -
122D ILE* 1.3 74.7 - - - +
124D ARG* 1.3 60.3 + - - +
137D TRP* 5.2 0.9 - - + -
249D TRP* 3.7 25.5 - - + -
254D VAL* 3.2 4.9 - - - -
255D ALA 2.8 37.2 + - - +
257D TRP* 3.6 27.1 - - + -
277D VAL* 3.6 31.0 - - + -
278D ARG 3.5 8.7 - - - +
279D ARG* 3.4 24.9 - - + -
1300D AKG 3.7 42.4 - - + +
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLN 4.8 4.7 - - - -
63D LEU* 3.8 43.6 + - - +
64D ASP* 3.7 8.5 - - - +
65D ASP* 3.1 36.2 + - - +
68D GLN* 2.9 33.0 + - - +
93D LEU* 4.6 0.2 - - - +
123D LEU* 1.3 74.7 - - - +
125D SER* 1.3 72.1 + - - +
126D VAL* 3.5 22.6 + - - +
249D TRP* 4.8 0.7 - - - -
252D GLY* 5.0 4.7 - - - -
253D ASP 3.4 8.7 - - - +
254D VAL* 4.1 11.0 - - + +
277D VAL* 3.3 7.4 - - - -
278D ARG* 2.9 43.0 + - - +
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Residues in contact with SER 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ARG* 1.3 75.9 + - - +
126D VAL* 1.3 58.4 + - - +
127D VAL 4.1 4.9 + - - -
128D ALA* 3.6 26.5 - - - +
249D TRP* 3.6 27.3 - - - +
250D GLU 3.6 18.2 + - - -
251D ALA* 3.6 2.3 - - - -
252D GLY* 2.7 30.7 + - - -
253D ASP 3.0 8.9 + - - -
276D ILE 4.1 3.6 - - - -
277D VAL* 4.2 7.6 - - - +
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ARG* 3.8 37.5 - - - +
125D SER* 1.3 74.4 - - - +
127D VAL* 1.3 71.1 + - + +
128D ALA 4.3 0.2 - - - -
251D ALA* 3.8 15.9 - - - +
276D ILE* 3.0 21.9 + - + +
278D ARG* 4.1 37.7 - - + +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D SER* 4.1 3.7 + - - -
126D VAL* 1.3 87.8 - - + +
128D ALA* 1.3 65.6 + - - +
251D ALA* 5.2 0.9 - - - -
274D PRO* 3.8 28.5 - - + +
275D ARG* 3.3 9.8 - - - +
276D ILE* 2.9 60.7 + - + +
277D VAL* 5.1 0.7 - - - +
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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