Contacts of the strand formed by residues 1117 - 1126 (chain C) 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 SER1117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003C ALA* 3.4 4.3 - - - +
1004C ARG* 3.1 34.4 + - - +
1019C PHE* 4.3 1.0 - - - -
1050C HIS 3.1 5.4 - - - -
1051C MET* 3.8 13.7 - - - -
1052C LEU* 3.1 21.1 + - - +
1109C ILE* 3.4 18.8 - - - +
1110C TYR 2.9 25.0 + - - -
1115C LYS* 3.4 0.4 - - - +
1116C TYR* 1.3 76.9 - - - +
1118C THR* 1.3 61.1 + - - +
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Residues in contact with THR1118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A VAL* 3.8 25.4 - - + -
1088A ASN* 2.6 29.3 + - - +
1089A HIS* 3.0 20.4 - - - +
1001C SER* 5.6 2.2 - - - +
1002C ALA 3.3 11.0 - - - +
1003C ALA* 4.4 7.9 - - + -
1019C PHE* 4.6 0.2 - - - -
1023C LEU* 5.2 2.0 - - + -
1049C PHE* 3.2 1.4 - - - -
1050C HIS* 2.7 35.7 + - - +
1051C MET* 3.1 11.3 - - - +
1115C LYS 3.9 11.0 - - - +
1117C SER* 1.3 79.3 - - - +
1119C PHE* 1.3 61.7 + - - +
1120C SER* 5.2 1.1 - - - -
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Residues in contact with PHE1119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000C PHE* 3.6 24.0 - + - -
1001C SER* 3.5 0.5 - - - -
1002C ALA* 2.8 37.1 + - + +
1019C PHE* 3.4 36.8 - + + -
1030C PHE* 3.9 21.5 - + - -
1035C GLY 4.4 0.9 - - - -
1047C PHE* 4.3 6.5 - + + -
1048C ILE 3.5 11.9 - - - -
1049C PHE* 3.9 8.7 - - + -
1064C LEU* 3.8 30.1 - - + -
1100C ILE* 4.2 13.7 - - + -
1101C TRP* 4.1 14.1 - - - -
1102C LEU* 3.8 17.9 - - + -
1118C THR* 1.3 76.6 - - - +
1120C SER* 1.3 72.7 + - - +
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Residues in contact with SER1120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A HIS* 2.7 30.1 + - - -
1091A ILE* 3.6 17.9 - - - -
1000C PHE* 3.1 19.7 - - - -
1001C SER* 2.6 25.5 + - - -
1047C PHE* 3.4 6.8 - - - +
1048C ILE* 2.9 32.8 + - - +
1119C PHE* 1.3 73.8 - - - +
1121C GLY* 1.3 58.8 + - - +
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Residues in contact with GLY1121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091A ILE* 3.9 1.2 - - - +
999C ALA* 3.3 0.9 - - - -
1000C PHE* 2.9 50.3 + - - +
1037C PHE* 6.1 1.3 - - - -
1045C TYR* 5.9 0.2 - - - -
1046C VAL 3.0 13.5 - - - -
1047C PHE* 3.7 5.2 - - - -
1048C ILE* 5.9 0.2 - - - -
1120C SER* 1.3 77.7 - - - +
1122C TYR* 1.3 67.7 + - - +
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Residues in contact with TYR1122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046A VAL* 4.1 9.9 - - + +
1091A ILE* 3.4 24.2 - - + -
1122A TYR* 2.2 29.8 + + - -
1124A LEU* 3.4 40.2 - - + -
1048B ILE* 6.0 0.9 - - - +
1122B TYR* 2.5 13.3 + - - -
998C VAL* 3.2 14.6 - - - +
999C ALA* 3.8 3.1 - - + +
1037C PHE* 6.4 0.2 - - - -
1045C TYR* 3.4 11.5 - - - -
1046C VAL* 3.0 62.8 + - + +
1047C PHE* 5.0 1.8 - - - -
1048C ILE* 5.9 4.9 - - + -
1120C SER 5.6 0.2 - - - -
1121C GLY* 1.3 75.5 - - - +
1123C LEU* 1.3 70.7 + - - +
1124C LEU* 3.6 17.4 + - + -
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Residues in contact with LEU1123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124A LEU* 5.0 2.1 - - - +
1125A TYR* 3.1 25.0 + - + +
997C ARG* 4.3 14.8 - - - +
998C VAL* 2.8 37.8 + - + -
1041C VAL* 5.7 4.0 - - + -
1042C ASN 5.0 1.1 - - - +
1043C GLY* 4.3 1.6 - - - -
1044C THR 3.6 8.5 - - - +
1045C TYR* 3.7 30.8 - - + +
1122C TYR* 1.3 78.5 - - - +
1124C LEU* 1.3 61.5 + - - +
1125C TYR 3.5 30.1 - - - +
1126C GLN* 4.0 21.1 - - + +
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Residues in contact with LEU1124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122A TYR* 6.2 0.2 - - + -
1124A LEU* 5.7 2.2 - - + -
999B ALA* 4.1 9.0 - - + -
1122B TYR* 3.4 56.8 - - + -
1123B LEU 5.0 3.1 - - - +
1124B LEU* 6.0 0.4 - - - -
1044C THR* 2.8 20.3 + - + +
1046C VAL* 4.1 17.3 - - + -
1091C ILE* 4.4 5.2 - - + -
1122C TYR* 3.6 16.1 + - + -
1123C LEU* 1.3 76.7 - - - +
1125C TYR* 1.3 92.1 + - + +
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Residues in contact with TYR1125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996B MET 3.7 15.3 + - - -
997B ARG* 3.7 16.2 - - + -
998B VAL 3.4 36.5 + - - -
999B ALA* 4.5 0.4 - - + -
1026B LEU* 3.5 22.9 - - + -
1123B LEU* 2.6 33.2 + - - +
1124B LEU 5.9 0.9 - - - -
1043C GLY* 3.1 3.3 - - - -
1044C THR* 2.9 37.7 + - - +
1123C LEU* 3.5 4.8 - - - +
1124C LEU* 1.3 111.1 - - + +
1126C GLN* 1.3 68.0 + - - +
1127C ASP 4.7 0.3 - - - -
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Residues in contact with GLN1126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041C VAL* 5.0 12.3 - - + -
1042C ASN 3.9 8.7 - - - +
1123C LEU* 4.0 19.1 - - + +
1124C LEU 4.4 0.4 + - - -
1125C TYR* 1.3 78.5 - - - +
1127C ASP* 1.3 98.0 + - - +
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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