Contacts of the strand formed by residues 999 - 1003 (chain E) in PDB entry 4OUL
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 999 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998E VAL* 1.3 78.6 - - - +
1000E PHE* 1.3 59.8 + - - +
1024E ASN* 3.4 18.7 + - - +
1025E ASN 3.5 0.3 - - - -
1026E LEU* 2.7 44.9 + - + +
1029E THR* 5.5 0.2 - - - -
1121E GLY 3.3 8.3 - - - +
1122E TYR* 3.7 13.0 - - + -
1044F THR* 4.3 5.4 - - + -
1091F ILE* 4.1 12.3 - - + -
1124F LEU* 4.1 9.0 - - + -
1125F TYR* 4.3 2.0 - - + -
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Residues in contact with PHE1000 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998E VAL* 5.5 0.7 - - + -
999E ALA* 1.3 75.1 - - - +
1001E SER* 1.3 64.1 + - - +
1002E ALA 4.7 1.3 - - - -
1022E LEU* 4.9 0.4 - - + -
1024E ASN* 3.3 13.7 - - - +
1025E ASN* 4.1 5.8 - - - +
1029E THR* 4.2 4.7 - - - +
1030E PHE* 3.5 50.7 - + + -
1037E PHE* 3.5 39.0 - + + -
1047E PHE* 4.0 8.5 - + - -
1119E PHE* 3.7 38.4 - + - -
1120E SER* 3.2 9.1 - - - -
1121E GLY* 2.9 59.6 + - - +
1091F ILE* 4.0 2.8 - - - +
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Residues in contact with SER1001 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000E PHE* 1.3 75.7 - - - +
1002E ALA* 1.3 58.1 + - - +
1022E LEU* 3.5 3.7 - - - -
1023E LEU* 2.7 43.8 + - - +
1024E ASN* 2.9 14.3 + - - +
1118E THR* 5.5 2.4 - - - +
1119E PHE 3.5 2.0 + - - -
1120E SER* 2.5 25.7 + - - -
1072F VAL* 6.1 0.3 - - - +
1089F HIS* 4.5 0.9 + - - -
1090F ALA* 4.2 4.3 - - - -
1091F ILE* 3.5 36.2 + - - -
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Residues in contact with ALA1002 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000E PHE* 5.1 0.4 - - + -
1001E SER* 1.3 75.2 + - - +
1003E ALA* 1.3 62.6 + - - +
1019E PHE* 3.7 28.8 - - + -
1021E LEU 3.4 7.9 - - - +
1022E LEU* 4.0 5.6 - - + -
1023E LEU* 4.0 2.7 - - - -
1030E PHE* 3.8 22.9 - - + -
1118E THR* 3.1 8.0 - - - -
1119E PHE* 2.8 36.6 + - + +
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Residues in contact with ALA1003 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002E ALA* 1.3 76.2 - - - +
1004E ARG* 1.3 59.9 + - - +
1005E THR* 4.0 0.4 - - + -
1019E PHE* 3.5 7.6 - - - +
1020E ASP* 3.2 26.7 + - - +
1021E LEU* 2.8 17.9 + - + +
1023E LEU* 3.6 19.5 - - + -
1115E LYS* 3.7 30.5 - - + -
1117E SER 3.3 10.5 - - - +
1118E THR* 4.3 2.9 - - + -
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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