Contacts of the strand formed by residues 1043 - 1052 (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 GLY1043 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041F VAL 3.3 3.2 + - - -
1042F ASN* 1.3 75.4 - - - +
1044F THR* 1.3 62.6 + - - -
1045F TYR* 3.3 13.8 - - - -
1093F GLN* 3.5 4.2 - - - -
1094F LEU 2.9 31.5 + - - -
1123F LEU* 4.3 0.2 - - - -
1125F TYR 3.0 13.0 - - - -
1126F GLN* 4.2 0.7 - - - -
1127F ASP 3.7 12.4 + - - -
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Residues in contact with THR1044 (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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996E MET 5.0 0.5 + - - -
999E ALA* 4.3 9.4 - - + -
1024E ASN* 3.8 17.1 + - - +
1026E LEU* 3.8 18.8 - - + +
1043F GLY* 1.3 71.7 - - - -
1045F TYR* 1.3 56.8 + - - +
1091F ILE* 3.7 26.9 - - + -
1092F LEU 3.2 10.5 - - - +
1093F GLN* 4.4 5.3 - - - +
1123F LEU* 3.5 4.0 - - - +
1124F LEU* 2.8 36.2 + - + -
1125F TYR* 2.7 29.6 + - - +
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Residues in contact with TYR1045 (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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998F VAL* 4.3 6.1 - - + -
1037F PHE* 3.6 25.1 - + - -
1039F CYS* 3.9 12.8 - - - -
1040F PRO* 3.5 11.3 - - - +
1041F VAL* 2.8 45.8 + - - +
1043F GLY 3.3 18.8 - - - -
1044F THR* 1.3 73.4 - - - +
1046F VAL* 1.3 63.9 + - - +
1047F PHE* 3.5 24.7 - + + -
1090F ALA 3.9 0.5 - - - +
1091F ILE* 3.2 5.5 - - - +
1092F LEU 2.8 35.4 + - - +
1094F LEU* 3.8 17.0 - - + -
1122F TYR 3.5 17.7 - - - -
1123F LEU* 3.4 31.4 - - + +
1124F LEU 4.3 0.2 - - - +
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Residues in contact with VAL1046 (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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1048E ILE* 5.1 12.6 - - + -
1122E TYR* 4.2 11.0 - - + -
1045F TYR* 1.3 75.1 - - - +
1047F PHE* 1.3 74.5 + - - +
1048F ILE* 5.7 3.1 - - + -
1089F HIS* 5.9 0.7 - - + -
1090F ALA 3.4 7.9 - - - +
1091F ILE* 3.9 29.4 - - + -
1121F GLY* 3.1 4.7 - - - -
1122F TYR* 3.1 74.0 + - + +
1124F LEU* 4.4 12.8 - - + -
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Residues in contact with PHE1047 (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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1000F PHE* 4.0 16.6 - + - -
1037F PHE* 3.7 27.6 - + - -
1045F TYR* 3.5 31.6 - + + -
1046F VAL* 1.3 82.0 - - - +
1048F ILE* 1.3 60.7 + - - +
1049F PHE* 5.7 0.7 - - + -
1064F LEU* 4.1 18.4 - - + -
1089F HIS* 3.1 7.4 - - - +
1090F ALA 2.8 31.3 + - - +
1092F LEU* 3.7 29.6 - - + -
1094F LEU* 3.8 3.4 - - + -
1100F ILE* 3.5 38.4 - - + -
1119F PHE* 4.4 7.9 - + + -
1120F SER 3.4 6.5 - - - +
1121F GLY* 3.7 13.7 - - - -
1122F TYR 5.0 0.2 - - - -
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Residues in contact with ILE1048 (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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1046D VAL* 6.4 2.2 - - + -
1048D ILE* 3.6 30.3 - - + -
1089D HIS* 3.2 31.7 - - + +
1091D ILE* 5.8 1.3 - - + -
1048E ILE* 4.9 13.9 - - + -
1050E HIS* 5.3 2.9 - - + -
1046F VAL* 5.7 4.3 - - + -
1047F PHE* 1.3 77.1 - - - +
1049F PHE* 1.3 69.6 + - - +
1050F HIS* 3.7 24.2 - - + -
1088F ASN 3.6 12.8 - - - +
1089F HIS* 4.2 5.8 - - + +
1119F PHE* 3.5 1.4 - - - -
1120F SER* 3.0 37.5 + - - +
1122F TYR* 6.3 2.7 - - + -
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Residues in contact with PHE1049 (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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1089D HIS* 3.9 2.0 - - - -
1048F ILE* 1.3 80.7 - - - +
1050F HIS* 1.3 67.3 + - - +
1051F MET* 4.3 4.7 - - + -
1062F VAL* 3.8 25.8 - - + -
1064F LEU* 4.1 25.1 - - + -
1072F VAL* 4.5 2.7 - - + -
1073F SER 4.8 1.1 - - - -
1074F ALA* 3.8 22.0 - - + -
1086F ALA 4.0 9.0 - - - -
1087F SER* 3.1 26.3 - - - -
1088F ASN* 3.1 48.1 + - + +
1089F HIS* 5.3 0.2 - - - -
1102F LEU* 3.7 40.6 - - + -
1118F THR 3.2 13.5 - - - +
1119F PHE* 3.7 4.5 - + + -
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Residues in contact with HIS1050 (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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1048D ILE* 5.1 1.5 - - + +
1050D HIS* 5.0 1.8 + - - -
1087D SER* 3.1 39.3 + - - +
1088D ASN* 3.6 30.3 + - - +
1089D HIS* 2.8 32.0 + - - -
1050E HIS* 5.0 4.8 + - - -
1048F ILE* 3.7 23.8 - - + +
1049F PHE* 1.3 71.8 - - - +
1051F MET* 1.3 63.0 + - - +
1085F THR* 4.3 10.1 - - + -
1086F ALA 3.7 3.6 - - - -
1087F SER* 3.5 23.3 + - - -
1116F TYR 4.2 8.1 - - - +
1117F SER* 3.1 3.8 - - - -
1118F THR* 2.7 36.8 + - - +
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Residues in contact with MET1051 (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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1004F ARG* 6.0 0.2 - - - -
1017F ILE* 4.3 8.7 - - - -
1019F PHE* 3.8 14.8 - - + -
1049F PHE* 4.3 11.0 - - + -
1050F HIS* 1.3 78.6 - - - +
1052F LEU* 1.3 60.8 + - - +
1053F LYS 3.8 0.3 + - - -
1060F LEU* 3.8 18.5 - - + +
1062F VAL* 4.1 16.4 - - + -
1084F GLU 3.7 0.5 - - - +
1085F THR* 3.3 5.4 - - - +
1086F ALA 2.8 41.9 + - - +
1102F LEU* 3.7 18.6 - - + -
1109F ILE* 3.5 29.8 - - + -
1117F SER* 3.9 11.7 - - - -
1118F THR 3.2 38.4 - - - +
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Residues in contact with LEU1052 (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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1075D TYR* 4.2 19.7 - - + +
1202D GOL 5.0 1.6 - - - +
1050F HIS 4.2 0.4 - - - -
1051F MET* 1.3 73.5 - - - +
1053F LYS* 1.3 60.8 + - - +
1060F LEU* 4.4 1.6 - - - -
1083F HIS* 3.8 25.8 - - + +
1084F GLU* 3.5 19.5 - - - +
1085F THR* 3.4 22.7 - - + +
1109F ILE* 3.5 5.0 - - - -
1110F TYR* 2.8 45.6 + - + -
1116F TYR* 3.7 47.4 + - + +
1117F SER* 3.1 10.4 + - - +
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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