Contacts of the strand formed by residues 1014 - 1019 (chain C) in PDB entry 4DAJ
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 ARG1014 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012C GLY 5.5 0.4 - - - -
1013C LEU* 1.3 83.5 - - - +
1015C LEU* 1.3 65.9 + - - +
1016C LYS 3.1 14.8 + - - +
1018C TYR* 3.3 58.1 - - + +
1019C LYS 4.8 4.6 + - - +
1028C GLY* 3.3 30.8 + - - -
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Residues in contact with LEU1015 (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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1013C LEU* 4.2 24.0 - - + -
1014C ARG* 1.3 71.7 - - - +
1016C LYS* 1.3 59.1 + - + +
1027C ILE* 4.1 2.4 - - - +
1057C VAL* 4.2 6.6 - - + +
1058C ILE* 3.5 43.1 + - - +
1059C THR* 5.0 0.4 - - - -
1060C LYS* 3.8 39.5 - - + -
1063C ALA* 5.4 5.6 - - + -
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Residues in contact with LYS1016 (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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1014C ARG* 3.1 20.5 - - - +
1015C LEU* 1.3 79.8 - - + +
1017C ILE* 1.3 71.6 + - - +
1018C TYR* 3.5 3.6 + - - +
1027C ILE* 4.1 4.7 - - - +
1056C GLY 3.8 11.2 - - - +
1057C VAL* 4.5 11.9 - - + -
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Residues in contact with ILE1017 (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 LYS* 1.3 80.3 - - - +
1018C TYR* 1.3 65.4 + - - +
1025C TYR* 3.9 26.2 - - + -
1026C THR 3.6 13.7 - - - +
1027C ILE* 4.0 8.9 - - + +
1033C LEU* 4.7 10.5 - - + -
1039C LEU 5.7 0.9 - - - +
1042C ALA* 5.0 3.6 - - + -
1043C LYS* 5.0 15.7 - - + +
1046C LEU* 4.0 25.8 - - + -
1056C GLY* 3.7 24.8 + - - +
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Residues in contact with TYR1018 (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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1011C GLU* 3.0 34.3 + - - +
1012C GLY 5.7 1.1 - - - -
1014C ARG* 3.3 67.8 - - + +
1016C LYS 4.0 2.0 - - - -
1017C ILE* 1.3 78.0 - - - +
1019C LYS* 1.3 85.2 + - - +
1020C ASP* 4.7 6.1 - - - -
1025C TYR* 3.6 1.3 - - - -
1026C THR* 2.7 87.9 + - + +
1027C ILE* 4.2 2.0 - - - -
1028C GLY 3.9 16.6 + - - -
1030C GLY 4.2 2.9 + - - -
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Residues in contact with LYS1019 (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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1014C ARG* 4.8 5.0 + - - +
1018C TYR* 1.3 89.1 - - - +
1020C ASP* 1.3 71.7 + - - +
1023C GLY* 2.9 34.8 + - - +
1024C TYR 3.7 4.0 - - - +
1025C TYR* 4.2 16.5 - - + +
1036C SER 4.8 1.8 + - - -
1037C PRO* 4.4 24.5 + - - +
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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