Contacts of the strand formed by residues 1129 - 1135 (chain C) in PDB entry 2CKJ
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 SER1129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021C LEU* 4.4 2.4 - - - +
1022C LEU 3.4 6.1 - - - -
1023C HIS* 3.0 33.9 + - - -
1098C ILE* 4.3 0.7 - - - -
1101C ARG* 3.1 19.0 + - - -
1127C SER* 3.2 12.2 + - - -
1128C LEU* 1.4 78.8 - - - +
1130C ALA* 1.3 61.6 + - - +
1021D LEU* 6.2 0.3 - - - +
1071D THR 4.5 2.4 + - - -
1072D VAL* 5.2 1.6 - - - +
1073D PRO* 3.7 15.4 - - - +
1131D THR* 4.0 22.6 - - - +
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Residues in contact with ALA1130 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021C LEU* 3.8 6.6 - - - -
1022C LEU* 3.0 32.9 + - - +
1094C ALA* 4.1 9.9 - - - +
1097C THR* 4.8 9.4 - - + -
1098C ILE* 3.7 21.3 - - + +
1101C ARG* 4.3 13.5 - - - +
1129C SER* 1.3 78.6 + - - +
1131C THR* 1.3 67.1 + - - +
1131D THR* 4.5 6.1 - - - -
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Residues in contact with THR1131 (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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1020C ALA 3.4 14.1 - - - +
1021C LEU* 4.3 10.0 - - + +
1094C ALA* 3.1 21.8 - - - +
1097C THR* 4.5 4.7 + - - -
1130C ALA* 1.3 73.8 - - - +
1132C GLY* 1.3 61.5 + - - +
1133C PHE* 6.4 0.2 - - - -
1021D LEU* 5.6 2.5 - - + -
1101D ARG* 5.4 5.1 + - - -
1127D SER* 5.4 3.8 - - - +
1129D SER* 4.0 36.9 + - - +
1130D ALA* 4.4 7.5 - - - +
1131D THR* 4.0 18.4 + - + +
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Residues in contact with GLY1132 (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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1019C GLY* 3.3 1.3 - - - -
1020C ALA 2.8 34.7 + - - -
1090C ALA* 3.1 24.0 - - - +
1093C ALA* 4.1 3.6 - - - -
1094C ALA* 3.9 7.0 - - - -
1131C THR* 1.3 84.7 - - - +
1133C PHE* 1.4 58.6 + - - -
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Residues in contact with PHE1133 (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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1017C GLN* 4.1 26.9 - - + -
1018C ALA 3.6 13.2 - - - -
1019C GLY* 4.3 3.8 - - - -
1089C GLN* 5.0 0.3 - - - +
1090C ALA* 4.1 2.9 - - - -
1093C ALA* 4.1 15.1 - - - +
1132C GLY* 1.4 74.0 - - - +
1134C TYR* 1.4 110.5 + - - +
1135C ARG* 4.4 0.7 - - + -
1101D ARG* 6.3 0.2 - - - +
1125D THR* 4.3 18.6 - - + -
1126D VAL* 3.7 7.4 - - - -
1127D SER* 3.1 54.5 - - - +
1128D LEU 5.0 0.7 - - - -
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Residues in contact with TYR1134 (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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1017C GLN* 3.2 23.6 - - - -
1018C ALA 3.1 11.6 + - - +
1085C ASP* 4.4 4.0 - - + -
1086C LEU* 3.9 32.3 - - + +
1089C GLN* 3.3 54.3 + - + -
1090C ALA 4.3 3.8 - - - +
1133C PHE* 1.4 95.9 - - - +
1135C ARG* 1.3 79.9 + - + +
1136C THR* 4.1 13.1 + - - +
1137C PRO* 4.4 9.2 - - + +
1152C HIS* 5.1 1.0 + - - -
1252C LYS 4.9 8.5 + - - -
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Residues in contact with ARG1135 (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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1016C ASN 3.4 8.7 - - - +
1133C PHE* 5.0 0.7 - - + -
1134C TYR* 1.3 97.6 - - - +
1136C THR* 1.3 72.3 + - - +
1137C PRO* 3.7 18.1 - - + +
1138C ASN 6.2 0.2 - - - +
1124D ASP* 4.4 16.6 + - - -
1125D THR* 3.0 45.3 + - + +
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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