Contacts of the strand formed by residues 131 - 136 (chain 9) 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 ALA 131 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029 PRO* 3.2 12.4 - - + +
1039 THR 2.9 21.8 + - - -
1249 PHE* 3.8 3.4 - - - -
1299 VAL* 3.4 6.6 - - - +
1309 PRO* 1.3 81.8 - - + +
1329 MET* 1.3 64.1 + - - +
3569 TRP* 4.0 22.0 - - + -
3579 ILE 3.0 20.6 - - - +
3589 THR* 3.9 10.1 - - + -
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Residues in contact with MET 132 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039 THR* 3.2 18.4 - - - +
1059 LEU* 3.7 15.9 - - + -
1199 MET 4.0 0.7 - - - +
1209 THR* 3.8 28.7 - - - +
1239 MET* 3.6 35.7 - - + -
1249 PHE* 3.4 33.9 - - + -
1299 VAL* 4.2 6.3 - - + -
1319 ALA* 1.3 73.7 - - - +
1339 TYR* 1.3 64.0 + - - +
1349 VAL* 4.1 10.3 - - + -
3569 TRP* 3.4 6.9 - - - -
3579 ILE* 2.8 31.0 + - - +
3709 VAL* 4.3 11.2 - - - -
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Residues in contact with TYR 133 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039 THR 3.3 2.2 + - - -
1049 LEU* 3.5 15.4 - - + +
1059 LEU* 2.8 28.1 + - - +
1329 MET* 1.3 81.9 - - - +
1349 VAL* 1.3 74.5 + - - +
1359 ALA* 4.2 12.3 - - + -
3469 LEU* 4.5 4.4 - - + +
3529 PHE* 3.3 32.5 - + + -
3559 MET* 3.5 41.8 - - + +
3569 TRP* 3.9 16.6 - - + -
3579 ILE* 5.1 2.7 - - + -
3709 VAL* 4.7 4.5 - - - -
3729 ARG* 2.9 44.2 + - - -
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Residues in contact with VAL 134 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059 LEU* 3.4 5.8 - - + +
1069 THR 4.4 2.9 - - - -
1079 GLU* 3.6 48.0 - - + +
1169 ARG* 3.2 42.9 + - + +
1199 MET* 4.3 18.2 - - + -
1209 THR* 4.5 6.3 - - - +
1329 MET* 4.1 20.6 - - + -
1339 TYR* 1.3 87.7 - - - +
1359 ALA* 1.3 56.3 + - - +
3709 VAL* 4.6 9.6 - - + +
3729 ARG* 4.5 3.9 + - - +
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Residues in contact with ALA 135 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049 LEU* 4.2 6.7 - - + -
1059 LEU 2.9 11.3 + - - +
1069 THR* 3.3 4.9 - - - -
1079 GLU* 3.0 23.6 + - - +
1169 ARG* 4.9 0.2 - - - +
1339 TYR* 4.0 17.5 - - + -
1349 VAL* 1.3 73.2 - - - +
1369 ILE* 1.3 62.1 + - - +
1399 VAL* 6.1 1.3 - - + -
1409 LEU* 3.6 38.1 - - + -
3469 LEU* 4.7 1.6 - - + -
3729 ARG* 5.9 0.7 - - - +
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Residues in contact with ILE 136 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079 GLU* 3.7 25.1 - - + +
1089 ALA 4.6 2.2 - - - +
1099 PRO* 4.2 32.8 - - + +
1169 ARG* 4.0 15.4 - - - +
1359 ALA* 1.3 72.4 - - - +
1379 GLN* 1.3 69.8 + - - +
1389 ALA* 4.2 7.9 - - + +
1399 VAL* 3.2 38.7 + - + +
1409 LEU* 3.2 11.0 + - - +
1639 VAL* 5.1 1.6 - - + -
1709 ALA* 4.8 14.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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