Contacts of the strand formed by residues 103 - 107 (chain 4) in PDB entry 1O19
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 THR 103 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84 LEU* 3.9 19.2 - - + +
104 CYS* 4.9 4.0 - - + -
904 PHE* 4.4 18.2 - - + -
1014 HIS 3.4 9.2 + - - -
1024 PRO* 1.3 73.6 + - - +
1044 LEU* 1.4 60.3 + - - +
1054 LEU* 3.7 28.1 + - + +
1234 MET* 4.6 7.9 - - - -
1294 VAL* 3.4 19.6 - - - +
1314 ALA 2.9 11.4 + - - -
1324 MET* 3.2 28.6 - - - +
1334 TYR 3.3 2.3 + - - -
3564 TRP* 3.8 3.8 - - - -
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Residues in contact with LEU 104 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84 LEU 2.9 16.5 + - - +
94 VAL* 3.3 22.0 - - + -
104 CYS* 2.9 26.2 + - - +
1034 THR* 1.4 69.4 - - - +
1054 LEU* 1.3 80.1 + - - +
1064 THR* 4.1 10.5 - - + -
1334 TYR* 3.5 31.2 - - + +
1354 ALA* 4.2 7.4 - - + -
3434 GLY* 4.3 11.0 - - - +
3464 LEU* 4.2 16.2 - - + -
3474 ALA* 4.2 13.5 - - + -
3524 PHE* 4.1 12.6 - - + -
3564 TRP* 3.9 13.2 - - + -
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Residues in contact with LEU 105 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104 CYS* 3.5 34.3 - - + +
124 ASN* 4.3 7.4 - - - +
864 TRP* 4.4 9.2 - - + +
904 PHE* 6.1 0.4 - - + -
1034 THR* 3.9 20.0 - - + +
1044 LEU* 1.3 80.4 - - - +
1064 THR* 1.3 64.6 + - - +
1194 MET* 3.7 29.2 - - + +
1234 MET* 3.7 35.0 - - + -
1324 MET* 3.7 13.7 - - + -
1334 TYR 2.8 10.2 + - - +
1344 VAL* 3.4 3.3 - - + -
1354 ALA 2.9 23.6 + - - -
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Residues in contact with THR 106 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 VAL* 5.4 2.2 - - + -
104 CYS 3.4 9.6 + - - +
114 ASP* 2.9 31.3 + - + +
124 ASN* 3.7 19.0 + - - +
1044 LEU* 4.1 6.5 - - + -
1054 LEU* 1.3 81.8 - - - +
1074 GLU* 1.3 62.2 + - - +
1194 MET* 4.1 7.4 - - - +
1344 VAL* 4.4 2.7 - - - -
1354 ALA 3.3 6.1 - - - -
1374 GLN* 3.8 17.5 + - - +
1404 LEU* 3.4 31.9 - - + -
3394 VAL* 4.2 9.0 - - + +
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Residues in contact with GLU 107 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064 THR* 1.3 73.7 - - - +
1084 ALA* 1.3 64.4 + - - +
1094 PRO 5.3 0.5 - - - +
1114 ASN* 2.9 43.0 + - - +
1164 ARG* 3.1 50.7 + - - +
1194 MET* 5.0 3.1 - - - -
1344 VAL* 3.6 13.4 - - + +
1354 ALA 3.0 12.9 + - - +
1364 ILE* 3.7 14.0 - - + +
1374 GLN* 3.0 36.3 + - - +
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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
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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