Contacts of the strand formed by residues 1039 - 1044 (chain C) in PDB entry 4YOC
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 LYS1039 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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995C PHE* 4.7 1.0 - - - -
1037C LYS* 3.6 15.9 - - + +
1038C PHE* 1.3 74.1 - - - +
1040C PHE* 1.3 60.3 + - - +
1041C ALA 3.9 0.2 + - - -
1050C TYR* 3.5 34.8 - - + -
1053C GLU* 5.5 0.2 - - - -
1078C GLY 3.3 7.1 - - - +
1079C LEU* 3.4 1.7 - - - -
1080C ASP* 2.9 49.1 + - + +
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Residues in contact with PHE1040 (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 PHE* 3.7 30.3 - + + -
1021C MET* 3.8 45.8 - - + -
1024C ILE* 4.2 15.7 - - + -
1035C PHE 5.3 0.9 - - - -
1038C PHE* 3.5 42.4 - + + -
1039C LYS* 1.3 71.7 - - - +
1041C ALA* 1.3 60.0 + - - +
1050C TYR* 3.3 8.3 - - - -
1051C ILE* 2.9 35.3 + - + +
1053C GLU* 4.2 20.4 + - + +
1077C LEU* 4.7 3.4 - - + -
1078C GLY 3.4 4.7 - - - -
1079C LEU* 3.7 24.7 - - + -
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Residues in contact with ALA1041 (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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995C PHE* 4.4 13.7 - - + -
1040C PHE* 1.3 76.9 - - - +
1042C ILE* 1.3 64.1 + - - +
1043C VAL* 4.7 1.8 - - + -
1048C HIS* 4.4 14.8 - - + -
1049C GLN 3.5 10.3 - - - +
1050C TYR* 4.0 21.5 - - + -
1051C ILE* 4.1 2.4 - - - +
1077C LEU* 3.4 8.7 - - - +
1078C GLY* 2.8 36.4 + - - +
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Residues in contact with ILE1042 (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 ALA* 1.3 72.2 - - - +
1043C VAL* 1.3 66.7 + - - +
1044C MET* 4.1 27.3 + - + +
1047C ARG 3.7 0.5 - - - +
1048C HIS* 3.0 5.0 - - - -
1049C GLN* 2.9 37.1 + - + +
1051C ILE* 3.7 28.9 - - + -
1057C GLU 6.1 0.9 - - - +
1062C ASP* 4.1 28.9 - - + +
1063C PHE* 3.6 36.3 - - + -
1075C PRO* 4.8 3.1 - - + -
1076C TRP 3.8 3.8 - - - +
1077C LEU* 5.2 1.1 - - + -
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Residues in contact with VAL1043 (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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995C PHE* 5.4 0.4 - - + -
999C VAL* 4.4 28.7 - - + -
1041C ALA* 4.5 2.9 - - + +
1042C ILE* 1.3 75.1 - - - +
1044C MET* 1.3 64.6 + - - +
1045C MET 5.3 0.2 - - - +
1046C GLY* 4.6 10.5 - - - +
1047C ARG 3.3 11.0 - - - +
1048C HIS* 4.4 4.0 - - + -
1075C PRO* 3.2 7.3 - - - +
1076C TRP* 2.9 91.9 + - + +
1078C GLY* 4.4 10.5 - - - +
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Residues in contact with MET1044 (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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1042C ILE* 4.1 24.0 - - + +
1043C VAL* 1.3 78.0 - - - +
1045C MET* 1.3 77.5 + - + +
1046C GLY 3.1 0.9 - - - -
1047C ARG* 2.8 51.8 + - + +
1049C GLN* 4.0 34.5 - - + +
1062C ASP 5.5 3.1 - - - +
1073C PRO 6.1 0.4 - - - -
1074C ARG 5.8 0.2 - - - -
1075C PRO* 4.2 23.8 - - + -
1076C TRP* 5.7 0.9 - - - -
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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