Contacts of the strand formed by residues 1085 - 1094 (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 THR1085 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1074D ALA* 6.1 0.2 - - - +
1075D TYR 3.8 15.2 + - - -
1085D THR 5.1 6.7 + - - -
1087D SER* 4.7 11.6 + - - +
1084E GLU* 5.5 1.2 - - - +
1085E THR* 4.9 7.3 + - - -
1050F HIS* 4.3 22.0 - - + -
1051F MET 3.3 21.3 - - - +
1052F LEU* 3.4 19.0 - - + +
1075F TYR 4.1 3.5 - - - +
1076F ALA* 3.5 10.5 - - - +
1084F GLU* 1.3 89.7 + - - +
1086F ALA* 1.3 65.2 + - - +
1087F SER* 4.1 5.7 + - - +
1116F TYR 5.6 1.6 - - - +
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Residues in contact with ALA1086 (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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1085E THR* 5.7 0.2 - - - -
1049F PHE* 4.0 3.8 - - - -
1050F HIS* 3.7 0.5 - - - -
1051F MET* 2.8 40.7 + - + +
1060F LEU* 3.9 20.2 - - + -
1062F VAL* 4.7 3.8 - - + -
1074F ALA* 3.5 23.3 - - + +
1075F TYR 3.9 11.0 - - - +
1076F ALA* 3.6 16.5 - - + +
1085F THR* 1.3 71.2 - - - +
1087F SER* 1.3 59.9 + - - +
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Residues in contact with SER1087 (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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1087D SER* 5.6 1.7 - - - -
1050E HIS* 3.4 27.4 + - - +
1085E THR* 4.8 13.0 + - - +
1087E SER* 5.0 2.9 + - - -
1116E TYR 5.4 0.3 - - - +
1049F PHE* 3.1 20.0 - - - -
1050F HIS* 3.5 25.5 + - - -
1074F ALA* 3.5 12.6 - - - +
1085F THR* 4.0 7.6 + - - +
1086F ALA* 1.3 75.4 - - - +
1088F ASN* 1.3 66.5 + - - +
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Residues in contact with ASN1088 (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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1050E HIS* 3.5 16.5 + - - -
1115E LYS 3.5 11.5 + - - -
1116E TYR 3.1 20.0 + - - -
1118E THR* 2.6 25.5 + - - +
1048F ILE* 3.6 4.5 - - - +
1049F PHE* 3.1 53.6 + - + +
1072F VAL* 3.8 9.7 - - + +
1073F SER 2.8 24.4 + - - +
1087F SER* 1.3 77.2 + - - +
1089F HIS* 1.3 79.7 + - - +
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Residues in contact with HIS1089 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048E ILE* 3.5 42.9 + - + +
1050E HIS* 2.9 30.1 + + + -
1118E THR* 3.0 34.1 + - - +
1119E PHE 4.0 1.0 + - - -
1120E SER* 2.7 41.8 + - - -
1046F VAL* 5.9 0.9 - - + -
1047F PHE 3.1 15.7 - - - +
1048F ILE* 4.4 5.2 - - + -
1049F PHE* 5.2 1.1 - - - -
1064F LEU* 5.0 1.3 - - - -
1072F VAL* 3.5 13.9 - - - +
1088F ASN* 1.3 88.0 + - - +
1090F ALA* 1.3 70.1 + - - +
1091F ILE* 4.8 2.0 - - + -
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Residues in contact with ALA1090 (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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1001E SER* 4.2 5.6 - - - +
1023E LEU* 5.3 3.8 - - + -
1045F TYR 3.9 0.3 - - - +
1046F VAL* 3.4 3.8 - - - +
1047F PHE* 2.8 32.9 + - + +
1064F LEU* 3.6 25.6 - - + -
1071F LEU* 5.3 2.2 - - + -
1072F VAL* 4.3 12.8 - - + -
1089F HIS* 1.3 81.7 - - - +
1091F ILE* 1.3 66.0 + - - +
1092F LEU* 3.8 16.2 - - + -
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Residues in contact with ILE1091 (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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999E ALA* 4.1 7.9 - - + -
1000E PHE 4.0 6.3 - - - +
1001E SER* 3.5 17.9 + - - -
1023E LEU* 4.2 4.0 - - - +
1024E ASN* 3.2 27.2 - - - +
1048E ILE* 6.0 2.7 - - + -
1120E SER* 3.6 26.9 - - - -
1121E GLY 4.1 4.3 - - - +
1122E TYR* 3.6 32.3 - - + -
1044F THR* 3.7 20.6 - - + -
1045F TYR 3.2 10.5 - - - +
1046F VAL* 3.9 19.5 - - + -
1089F HIS* 4.8 2.0 - - + -
1090F ALA* 1.3 78.8 - - - +
1092F LEU* 1.3 66.3 + - - +
1124F LEU* 4.8 0.9 - - + -
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Residues in contact with LEU1092 (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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1023E LEU* 4.7 12.6 - - + +
1024E ASN* 4.5 4.7 - - - -
1043F GLY 3.6 0.5 - - - +
1044F THR* 3.2 7.3 - - - -
1045F TYR* 2.8 40.4 + - - +
1047F PHE* 3.7 33.2 - - + -
1066F LYS* 4.1 6.7 - - + -
1071F LEU* 3.5 41.1 - - + -
1090F ALA* 3.8 18.4 - - + -
1091F ILE* 1.3 81.0 - - - +
1093F GLN* 1.3 67.0 + - - +
1094F LEU* 3.6 19.0 + - + +
1100F ILE* 5.2 0.2 - - + -
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Residues in contact with GLN1093 (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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1023E LEU 5.1 1.8 + - - -
1024E ASN* 4.1 15.9 + - - +
1043F GLY 3.5 9.9 - - - +
1044F THR* 4.4 5.6 - - - +
1066F LYS* 4.1 9.9 + - - -
1092F LEU* 1.3 74.3 - - - +
1094F LEU* 1.3 66.8 + - - +
1095F PHE* 5.3 4.7 - - + -
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Residues in contact with LEU1094 (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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1037F PHE* 3.9 9.9 - - + -
1039F CYS* 3.9 16.8 - - + -
1042F ASN* 3.4 5.1 - - - +
1043F GLY 2.9 27.8 + - - -
1045F TYR* 3.8 23.6 - - + -
1047F PHE* 3.8 13.5 - - + -
1066F LYS* 4.1 8.1 - - + +
1092F LEU* 4.1 22.9 - - + +
1093F GLN* 1.3 82.9 - - - +
1095F PHE* 1.3 65.2 + - - +
1098F ASP* 3.8 15.0 - - + +
1100F ILE* 3.8 39.7 - - + -
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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