Contacts of the strand formed by residues 1290 - 1295 (chain D) in PDB entry 4OIN
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 LEU1290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283D ILE* 5.4 3.8 - - + -
1284D GLU* 3.8 5.6 - - - +
1285D GLU* 3.6 38.4 - - + +
1289D LYS* 1.3 76.5 - - - +
1291D SER* 1.3 85.0 + - - +
1292D VAL* 4.9 0.7 - - + -
1304D LYS* 4.3 0.5 - - - +
1305D LEU* 3.0 51.8 + - + +
1306D PRO 4.1 0.2 - - - +
1307D LYS* 3.8 39.3 - - + +
1309D ALA 4.7 4.0 - - - +
1311D LEU* 4.5 24.9 - - + -
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Residues in contact with SER1291 (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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1283D ILE* 3.9 0.2 - - - -
1284D GLU* 2.9 50.3 + - - +
1289D LYS* 5.4 1.6 - - - +
1290D LEU* 1.3 84.2 + - - +
1292D VAL* 1.3 68.3 + - - +
1293D PHE* 4.3 14.8 - - - -
1302D GLU* 5.1 0.7 - - - -
1303D TYR 3.5 11.0 - - - -
1304D LYS* 3.3 30.1 - - - +
1305D LEU* 4.8 1.3 - - - +
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Residues in contact with VAL1292 (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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1281D VAL* 3.8 27.6 - - + -
1282D ARG 4.0 2.9 - - - +
1283D ILE* 4.2 8.1 - - + -
1290D LEU* 4.9 3.1 - - + -
1291D SER* 1.3 78.5 - - - +
1293D PHE* 1.3 68.9 + - - +
1303D TYR* 2.9 45.0 + - + +
1305D LEU* 4.4 10.5 - - + -
1311D LEU* 4.1 34.5 - - + -
1313D VAL* 4.7 6.7 - - + -
1325D LEU* 4.2 24.9 - - + -
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Residues in contact with PHE1293 (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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1280D VAL 3.4 1.4 - - - +
1281D VAL* 3.4 4.7 - - - -
1282D ARG* 2.9 82.2 + - + +
1284D GLU* 4.0 31.0 - - + -
1291D SER* 4.3 10.1 - - - -
1292D VAL* 1.3 78.2 - - - +
1294D VAL* 1.3 62.9 + - - +
1295D GLU* 4.0 2.9 - - - +
1300D SER* 4.4 10.5 - - - +
1301D LYS 3.3 8.7 - - - +
1302D GLU* 3.4 47.8 - - + -
1304D LYS* 6.3 0.2 - - - -
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Residues in contact with VAL1294 (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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1275D SER* 3.4 22.9 - - - +
1277D ILE* 4.3 13.2 - - + +
1278D ASP 3.4 27.1 - - - +
1279D GLY* 3.7 12.3 - - - -
1280D VAL 3.5 2.7 - - - +
1281D VAL* 4.8 4.3 - - + -
1292D VAL* 4.2 0.9 + - + -
1293D PHE* 1.3 75.6 - - - +
1295D GLU* 1.3 62.0 + - - +
1296D SER 3.9 1.2 + - - -
1299D PHE 4.3 0.3 - - - +
1300D SER* 3.5 1.8 - - - -
1301D LYS* 2.9 38.1 + - + +
1303D TYR* 3.7 22.4 - - + -
1319D VAL* 4.3 13.2 - - + -
1325D LEU* 4.2 9.0 - - + -
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Residues in contact with GLU1295 (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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1279D GLY* 3.3 2.7 - - - -
1280D VAL* 2.9 55.3 + - + +
1282D ARG* 3.1 52.2 + - - +
1293D PHE* 4.5 4.9 - - + -
1294D VAL* 1.3 72.7 - - - +
1296D SER* 1.3 65.0 + - - +
1300D SER* 3.3 26.7 - - - +
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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