Contacts of the strand formed by residues 1021 - 1026 (chain F) 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 LEU1021 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002F ALA* 3.3 4.3 - - - +
1003F ALA* 2.8 34.8 + - + +
1005F THR* 3.7 19.7 - - + +
1020F ASP* 1.3 90.5 + - - +
1022F LEU* 1.3 68.0 + - - +
1023F LEU* 3.9 24.2 - - + -
1032F LEU* 3.5 10.4 - - - +
1115F LYS* 3.9 24.9 - - + -
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Residues in contact with LEU1022 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001F SER 3.5 8.1 - - - +
1002F ALA* 4.0 7.6 - - + -
1021F LEU* 1.3 81.0 - - - +
1023F LEU* 1.3 61.6 + - - +
1024F ASN 3.4 25.4 - - - +
1025F ASN* 4.1 23.8 - - + +
1030F PHE* 3.8 27.6 - - + +
1032F LEU* 3.4 36.5 - - + +
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Residues in contact with LEU1023 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071D LEU* 4.5 14.4 - - + +
1072D VAL* 3.9 26.2 - - + -
1090D ALA* 4.7 3.8 - - + -
1091D ILE 4.1 6.5 - - - +
1092D LEU* 3.8 29.6 - - + +
1093D GLN* 4.8 2.9 + - - +
1001F SER* 2.6 30.6 + - - +
1002F ALA 4.0 3.1 - - - +
1003F ALA* 3.7 32.8 - - + +
1021F LEU* 3.9 13.7 - - + -
1022F LEU* 1.3 74.3 - - - +
1024F ASN* 1.3 63.9 + - - +
1115F LYS* 4.5 4.7 - - + -
1118F THR* 5.3 1.8 - - + -
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Residues in contact with ASN1024 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044D THR* 3.8 13.9 - - - +
1091D ILE* 3.4 20.4 - - - +
1093D GLN* 3.3 33.6 - - - +
999F ALA* 3.1 37.0 + - - +
1000F PHE* 3.3 2.1 - - - -
1001F SER* 3.0 28.0 + - - +
1022F LEU* 3.2 14.8 - - - +
1023F LEU* 1.3 82.6 - - - +
1025F ASN* 1.3 65.9 + - - +
1026F LEU* 4.0 8.1 + - - +
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Residues in contact with ASN1025 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999F ALA 3.5 4.5 - - - -
1000F PHE* 4.2 3.2 - - - +
1022F LEU* 4.1 20.3 - - + +
1024F ASN* 1.3 77.4 + - - +
1026F LEU* 1.3 60.8 + - - +
1027F GLY 3.1 0.7 + - - -
1028F GLU* 3.0 41.7 + - + +
1029F THR* 3.4 6.9 + - - -
1030F PHE* 3.4 46.6 + - - +
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Residues in contact with LEU1026 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044D THR* 3.5 17.9 - - - +
1093D GLN* 4.1 7.9 - - - +
1125D TYR* 3.5 37.2 - - + -
996F MET 3.7 20.4 - - - +
997F ARG* 2.9 22.4 - - - +
998F VAL* 3.2 4.5 - - - +
999F ALA* 2.8 32.7 + - + +
1024F ASN* 4.0 10.8 + - - +
1025F ASN* 1.3 72.4 - - - +
1027F GLY* 1.3 61.0 + - - +
1028F GLU 3.4 0.8 + - - -
1029F THR* 4.6 2.3 + - - +
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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