Contacts of the strand formed by residues 131 - 136 (chain 0) 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 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020 PRO* 3.2 12.2 - - + +
1030 THR 2.9 22.3 + - - -
1240 PHE* 3.8 3.4 - - - -
1290 VAL* 3.4 5.5 - - - +
1300 PRO* 1.3 82.5 - - + +
1320 MET* 1.3 64.2 + - - +
3560 TRP* 4.0 21.3 - - + -
3570 ILE 3.0 21.8 - - - +
3580 THR* 3.9 9.4 - - + -
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Residues in contact with MET 132 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030 THR* 3.2 18.8 - - - +
1050 LEU* 3.7 16.8 - - + -
1190 MET 4.0 0.7 - - - +
1200 THR* 3.8 29.6 - - - +
1230 MET* 3.6 36.1 - - + -
1240 PHE* 3.4 32.5 - - + -
1290 VAL* 4.2 6.7 - - + -
1310 ALA* 1.3 75.6 - - - +
1330 TYR* 1.3 63.1 + - - +
1340 VAL* 4.1 9.6 - - + -
3560 TRP* 3.4 6.1 - - - -
3570 ILE* 2.8 30.6 + - - +
3700 VAL* 4.3 11.4 - - - -
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Residues in contact with TYR 133 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030 THR 3.3 2.2 + - - +
1040 LEU* 3.5 15.3 - - + +
1050 LEU* 2.8 27.5 + - - +
1320 MET* 1.3 82.2 - - - +
1340 VAL* 1.3 74.8 + - - +
1350 ALA* 4.2 12.1 - - + -
3460 LEU* 4.5 4.6 - - + +
3520 PHE* 3.3 32.7 - + + -
3550 MET* 3.5 40.8 - - + +
3560 TRP* 3.9 16.4 - - + -
3570 ILE* 5.1 2.7 - - + -
3700 VAL* 4.7 3.8 - - - -
3720 ARG* 2.9 44.1 + - - -
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Residues in contact with VAL 134 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050 LEU* 3.4 4.9 - - + -
1060 THR 4.4 2.5 - - - -
1070 GLU* 3.6 47.6 - - + +
1160 ARG* 3.2 43.1 + - + +
1190 MET* 4.3 18.4 - - + -
1200 THR* 4.5 7.0 - - - +
1320 MET* 4.1 20.2 - - + -
1330 TYR* 1.3 88.0 - - - +
1350 ALA* 1.3 57.0 + - - +
3700 VAL* 4.6 9.2 - - + +
3720 ARG* 4.5 4.1 + - - +
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Residues in contact with ALA 135 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040 LEU* 4.2 7.0 - - + -
1050 LEU 2.9 10.9 + - - +
1060 THR* 3.3 4.3 - - - -
1070 GLU* 3.0 23.7 + - - -
1160 ARG* 4.9 0.2 - - - +
1330 TYR* 4.0 17.7 - - + -
1340 VAL* 1.3 74.2 - - - +
1360 ILE* 1.3 63.0 + - - +
1390 VAL* 6.1 1.3 - - + -
1400 LEU* 3.6 37.7 - - + -
3460 LEU* 4.7 1.6 - - + -
3720 ARG* 5.9 0.2 - - - +
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Residues in contact with ILE 136 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070 GLU* 3.7 26.2 - - + +
1080 ALA 4.6 2.0 - - - +
1090 PRO* 4.2 31.6 - - + +
1160 ARG* 4.0 15.4 - - - +
1350 ALA* 1.3 72.0 - - - +
1370 GLN* 1.3 69.6 + - - +
1380 ALA* 4.2 8.1 - - + +
1390 VAL* 3.2 38.2 + - + +
1400 LEU* 3.2 11.0 + - - +
1630 VAL* 5.1 1.3 - - + -
1700 ALA* 4.8 15.0 - - + -
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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