Contacts of the strand formed by residues 139 - 144 (chain D) in PDB entry 1O94
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 VAL 139 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.7 2.9 - - + -
17C PHE* 3.5 26.2 - - + -
19C ILE* 5.3 2.7 - - + -
26C VAL* 4.1 14.1 - - + -
232C MET* 3.9 15.3 - - + -
233C TYR 3.5 16.8 - - - +
234C ILE* 4.6 4.0 - - + -
235C PRO* 4.2 3.1 - - - -
119D TYR* 3.9 0.2 + - - -
133D GLY* 3.4 6.2 - - - -
134D GLY* 3.0 44.2 + - - +
135D TYR* 4.0 2.7 - - + -
137D GLN 4.0 4.7 - - - -
138D LYS* 1.3 84.7 - - + +
140D ASN* 1.3 67.0 + - - +
141D VAL* 3.9 13.7 - - + -
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Residues in contact with ASN 140 (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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231C ARG 3.9 0.3 - - - +
232C MET* 3.3 6.8 - - - +
233C TYR* 2.8 75.7 + - + +
235C PRO* 3.9 23.2 - - - +
119D TYR* 2.6 40.2 + - - -
120D ILE* 4.1 6.7 - - - +
131D THR* 3.7 8.4 - - + +
132D ARG 3.5 2.2 - - - -
137D GLN 5.5 0.3 - - - +
139D VAL* 1.3 76.6 - - - +
141D VAL* 1.3 62.5 + - - +
142D GLU 4.1 0.4 - - - -
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLN* 5.7 0.7 - - - +
229C VAL* 4.0 27.6 - - + -
231C ARG 3.6 3.8 - - - +
232C MET* 3.7 28.0 - - + -
130D ALA 3.5 1.0 - - - +
131D THR* 3.2 5.4 - - - -
132D ARG* 2.7 43.7 + - + +
133D GLY 3.9 6.1 - - - +
134D GLY* 3.8 26.9 - - - -
139D VAL* 3.9 2.7 - - + -
140D ASN* 1.3 78.8 - - - +
142D GLU* 1.3 61.1 + - - +
143D VAL* 3.8 11.1 + - + +
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Residues in contact with GLU 142 (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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229C VAL* 3.8 1.0 - - - -
230C ARG* 2.9 48.6 + - + -
231C ARG* 2.5 59.3 + - + +
233C TYR* 4.1 13.3 + - + -
122D GLU* 5.1 4.0 - - - +
124D GLN* 4.9 3.9 - - - +
129D VAL* 4.0 18.2 - - + +
130D ALA 3.3 3.1 - - - -
131D THR* 3.5 19.2 + - - +
140D ASN 4.1 0.6 - - - -
141D VAL* 1.3 72.8 - - - +
143D VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 143 (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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227C SER* 4.3 15.7 - - - +
228C ARG 3.4 14.8 - - - +
229C VAL* 4.1 13.0 - - + -
230C ARG* 4.3 3.4 - - - +
115D ALA* 4.2 12.3 - - + -
129D VAL* 3.3 6.6 - - - +
130D ALA* 2.7 49.5 + - + +
132D ARG* 5.2 11.2 - - + -
141D VAL* 4.2 17.3 - - + +
142D GLU* 1.3 80.8 - - - +
144D ASP* 1.3 61.1 + - - +
145D PHE* 3.8 23.2 - - + -
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Residues in contact with ASP 144 (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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227C SER* 3.6 3.1 - - - -
228C ARG* 2.8 79.3 + - - +
230C ARG* 2.8 30.4 + - - +
127D GLU* 5.2 9.0 - - + +
128D LEU 3.4 18.6 - - - +
129D VAL* 4.2 4.7 - - + -
143D VAL* 1.3 75.0 - - - +
145D PHE* 1.3 66.4 + - - +
146D PRO* 3.5 4.5 - - - +
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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