Contacts of the strand formed by residues 1023 - 1031 (chain C) in PDB entry 5DFV
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 THR1023 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012C PRO* 4.0 4.5 - - - +
1021C SER* 5.1 6.5 - - - +
1022C VAL* 1.3 85.7 - - - +
1024C LEU* 1.3 64.2 + - - +
1066C SER* 4.9 2.9 - - - -
1067C VAL 3.3 5.2 - - - -
1068C THR* 3.1 33.9 - - + -
2006D THR* 5.0 12.1 - - + -
2008D SER* 3.2 33.6 + - - +
2010D PHE* 3.2 19.9 - - - -
2027D PHE* 5.1 1.8 - - - -
2029D ASN* 5.8 1.1 - - - +
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Residues in contact with LEU1024 (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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1010C LEU 3.8 3.1 - - - -
1011C VAL* 4.3 1.1 - - - -
1012C PRO* 3.8 19.1 - - + -
1022C VAL* 4.6 3.4 - - + -
1023C THR* 1.3 78.6 - - - +
1025C GLY* 1.3 59.8 + - - +
1040C TRP* 4.8 0.2 - - + -
1066C SER* 3.6 5.0 - - - -
1067C VAL* 2.7 42.5 + - + +
1069C VAL* 4.9 3.1 - - + -
1074C TRP* 3.6 53.2 - - + +
1079C ILE* 3.7 31.0 - - + -
1096C ILE* 3.5 30.1 - - + -
2010D PHE* 4.3 4.3 - - - -
2027D PHE* 4.1 4.2 - - - -
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Residues in contact with GLY1025 (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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1010C LEU* 2.8 45.6 + - - -
1024C LEU* 1.3 76.9 - - - +
1026C CYS* 1.3 57.3 + - - -
1040C TRP* 3.5 5.1 - - - -
1065C SER 3.4 10.1 - - - -
1096C ILE* 3.1 14.6 - - - +
2010D PHE* 4.4 0.4 - - - -
2027D PHE* 4.1 9.4 - - - -
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Residues in contact with CYS1026 (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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1007C VAL* 3.4 24.0 - - - -
1008C TYR 3.4 8.1 - - - -
1009C PRO* 4.7 1.6 - - - -
1010C LEU* 3.8 5.6 - - - +
1025C GLY* 1.3 73.9 - - - +
1027C LEU* 1.3 60.2 + - - +
1028C VAL* 4.1 2.0 - - - -
1038C LEU* 4.4 9.0 - - + +
1040C TRP* 3.7 7.9 - - + -
1064C SER* 3.3 8.1 - - - -
1065C SER 3.2 26.6 + - - +
1081C CYS* 2.0 53.8 - - + -
1083C VAL* 4.1 4.3 - - - -
1094C LYS* 5.4 0.7 - - - -
1096C ILE* 5.3 0.4 - - + -
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Residues in contact with LEU1027 (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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1006C SER 3.2 5.7 - - - +
1007C VAL* 3.4 0.6 - - - -
1008C TYR* 2.8 64.4 + - + +
1010C LEU* 4.1 14.6 - - + -
1026C CYS* 1.3 73.4 - - - +
1028C VAL* 1.3 59.5 + - - +
1029C LYS* 3.8 10.9 + - + -
1062C THR* 4.3 11.7 - - - +
1063C LEU 4.0 4.3 - - - +
1064C SER* 3.2 25.4 - - - +
2016D GLN* 4.1 8.1 - - - +
2023D SER* 4.0 26.5 - - - +
2025D VAL* 4.0 17.0 - - + -
2070D THR* 4.4 9.2 - - + -
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Residues in contact with VAL1028 (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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1005C PRO* 3.5 29.8 - - + -
1006C SER 3.4 4.0 - - - +
1007C VAL* 4.4 2.5 - - + -
1026C CYS* 4.5 2.2 - - - -
1027C LEU* 1.3 72.1 - - - +
1029C LYS* 1.3 57.1 + - - +
1031C TYR* 3.6 19.1 - - + -
1036C VAL* 4.9 5.2 - - + -
1038C LEU* 4.2 15.3 - - + -
1062C THR* 2.9 5.5 + - - -
1063C LEU* 2.8 48.0 + - + +
1083C VAL* 3.2 44.2 - - + -
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Residues in contact with LYS1029 (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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1005C PRO* 3.6 0.5 - - - +
1006C SER* 2.9 40.1 + - - +
1008C TYR* 4.5 16.6 - - + +
1027C LEU* 4.5 9.6 - - + -
1028C VAL* 1.3 76.1 - - - +
1030C GLY* 1.3 68.4 + - - +
1031C TYR* 3.6 2.9 - - - -
1057C GLN* 3.5 29.5 + - - +
1060C LEU* 6.1 1.2 - - - +
1061C TYR 3.8 0.4 - - - -
1062C THR* 3.4 12.6 - - - +
2016D GLN* 4.3 17.0 - - - +
2021D GLY* 6.3 2.2 - - - -
2023D SER* 4.3 5.4 - - - +
2072D THR* 4.2 23.2 - - - +
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Residues in contact with GLY1030 (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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1003C THR* 3.6 14.0 - - - +
1004C ALA 3.5 14.2 - - - +
1005C PRO 4.9 0.2 - - - -
1029C LYS* 1.3 82.8 - - - +
1031C TYR* 1.3 59.4 + - - +
1057C GLN* 3.3 14.1 - - - +
1060C LEU* 3.9 21.0 - - - +
1061C TYR 2.9 10.4 + - - -
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Residues in contact with TYR1031 (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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1003C THR 3.3 11.7 - - - +
1005C PRO* 3.6 22.0 - - + -
1028C VAL* 3.6 32.1 - - + -
1030C GLY* 1.3 79.4 - - - +
1032C PHE* 1.3 63.3 + - - +
1033C PRO 3.4 19.1 - - - -
1034C GLU* 4.1 10.2 + - + +
1036C VAL* 3.5 29.1 - - + +
1054C ALA* 3.0 26.9 - - - +
1060C LEU* 3.5 2.3 - - - -
1061C TYR* 2.6 75.7 + - + +
1062C THR* 3.8 7.6 - - - -
1063C LEU* 3.1 15.8 - - - +
1085C HIS* 3.8 2.7 - + + -
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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