Contacts of the strand formed by residues 131 - 136 (chain 8) in PDB entry 1O1F
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 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028 PRO* 3.2 12.0 - - + +
1038 THR 2.9 22.3 + - - -
1248 PHE* 3.8 3.6 - - - -
1298 VAL* 3.4 6.1 - - - +
1308 PRO* 1.3 81.6 - - + +
1328 MET* 1.3 64.0 + - - +
3568 TRP* 4.0 21.5 - - + -
3578 ILE 3.0 21.3 - - - +
3588 THR* 3.9 9.4 - - + -
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Residues in contact with MET 132 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038 THR* 3.2 18.4 - - + +
1058 LEU* 3.7 16.2 - - + -
1198 MET 4.0 0.9 - - - +
1208 THR* 3.8 29.2 - - - +
1238 MET* 3.6 35.4 - - + -
1248 PHE* 3.4 33.7 - - + -
1298 VAL* 4.2 7.2 - - + -
1318 ALA* 1.3 75.1 - - - +
1338 TYR* 1.3 64.1 + - - +
1348 VAL* 4.1 10.3 - - + -
3568 TRP* 3.4 6.6 - - - -
3578 ILE* 2.8 30.4 + - - +
3708 VAL* 4.3 11.7 - - - -
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Residues in contact with TYR 133 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038 THR 3.3 2.2 + - - +
1048 LEU* 3.5 15.1 - - + +
1058 LEU* 2.8 27.5 + - - +
1328 MET* 1.3 81.7 - - - +
1348 VAL* 1.3 75.1 + - - +
1358 ALA* 4.2 12.3 - - + -
3468 LEU* 4.5 4.7 - - + +
3528 PHE* 3.3 33.6 - + + -
3558 MET* 3.5 41.1 - - + +
3568 TRP* 3.9 15.7 - - + -
3578 ILE* 5.1 2.9 - - + -
3708 VAL* 4.7 4.9 - - + -
3728 ARG* 2.9 44.6 + - - -
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Residues in contact with VAL 134 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058 LEU* 3.4 5.8 - - + +
1068 THR 4.4 2.9 - - - -
1078 GLU* 3.6 47.6 - - + +
1168 ARG* 3.2 42.5 + - + +
1198 MET* 4.3 17.7 - - + -
1208 THR* 4.5 6.5 - - - +
1328 MET* 4.1 20.4 - - + -
1338 TYR* 1.3 87.1 - - - +
1358 ALA* 1.3 56.3 + - - +
3708 VAL* 4.6 8.9 - - + +
3728 ARG* 4.5 3.5 + - - +
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Residues in contact with ALA 135 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048 LEU* 4.2 6.5 - - + -
1058 LEU 2.9 10.8 + - - +
1068 THR* 3.3 4.0 - - - -
1078 GLU* 3.0 24.3 + - - +
1168 ARG* 4.9 0.2 - - - +
1338 TYR* 4.0 19.1 - - + -
1348 VAL* 1.3 72.9 - - - +
1368 ILE* 1.3 61.4 + - - +
1398 VAL* 6.1 1.6 - - + -
1408 LEU* 3.6 37.5 - - + -
3468 LEU* 4.7 1.8 - - + -
3728 ARG* 5.9 0.7 - - - +
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Residues in contact with ILE 136 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078 GLU* 3.7 25.8 - - + +
1088 ALA 4.6 2.2 - - - +
1098 PRO* 4.2 31.0 - - + +
1168 ARG* 4.0 15.5 - - - +
1358 ALA* 1.3 72.6 - - - +
1378 GLN* 1.3 69.4 + - - +
1388 ALA* 4.2 8.3 - - + +
1398 VAL* 3.2 38.1 + - + +
1408 LEU* 3.2 10.6 + - - +
1638 VAL* 5.1 1.3 - - + -
1708 ALA* 4.8 15.3 - - + -
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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