Contacts of the helix formed by residues 1016 - 1029 (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 HIS1016 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014C GLY 3.0 7.8 + - - +
1015C GLU* 1.3 82.8 - - - +
1017C PHE* 1.3 55.0 + - - +
1018C ARG* 2.9 26.4 + - + -
1019C GLU* 2.8 44.6 + - + +
1020C VAL 3.8 0.7 + - - -
1056C TYR* 3.2 62.0 + + - +
1058C VAL* 4.9 0.6 - - - +
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Residues in contact with PHE1017 (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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1015C GLU* 4.6 0.7 - - - -
1016C HIS* 1.3 70.9 - - - +
1018C ARG* 1.3 57.5 + - - +
1019C GLU 3.2 0.2 - - - -
1020C VAL* 3.0 32.6 - - + +
1021C MET* 3.0 50.9 + - + +
1040C PHE* 3.7 32.1 - + + -
1051C ILE* 3.7 39.0 - - + -
1052C ASN 4.4 3.8 - - - -
1053C GLU* 4.1 16.2 - - - +
1056C TYR* 3.6 27.2 - - - +
1057C GLU 4.4 1.6 - - - +
1058C VAL* 3.5 26.4 - - + +
1063C PHE* 6.3 2.5 - + - -
1077C LEU* 4.9 9.9 - - + -
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Residues in contact with ARG1018 (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 HIS* 2.9 26.3 + - + -
1017C PHE* 1.3 73.8 - - - +
1019C GLU* 1.3 60.6 + - - +
1021C MET* 3.3 29.7 - - + +
1022C LYS* 2.9 27.2 + - - +
1053C GLU* 4.2 21.0 + - - +
1054C ASP* 4.4 19.3 + - - +
1056C TYR* 3.6 30.4 + - + -
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Residues in contact with GLU1019 (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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1015C GLU* 3.3 29.6 - - - +
1016C HIS* 2.8 24.1 + - + +
1018C ARG* 1.3 78.3 - - - +
1020C VAL* 1.3 59.6 + - - +
1022C LYS* 3.1 6.6 + - + +
1023C ARG* 2.9 40.1 + - - +
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Residues in contact with VAL1020 (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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1009C LEU* 4.0 19.1 - - + -
1010C ARG 4.0 5.6 - - - +
1011C ILE* 4.4 10.1 - - + -
1015C GLU* 3.6 25.8 - - + +
1016C HIS 3.8 1.0 + - - -
1017C PHE* 3.0 47.0 + - + +
1019C GLU* 1.3 78.7 - - - +
1021C MET* 1.3 59.7 + - - +
1023C ARG* 3.1 29.5 + - - +
1024C ILE* 2.9 37.2 + - + +
1058C VAL* 5.3 1.1 - - + -
1077C LEU* 6.0 0.7 - - + -
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Residues in contact with MET1021 (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* 3.0 41.9 + - + +
1018C ARG* 3.3 36.1 - - + +
1019C GLU 3.1 0.4 - - - -
1020C VAL* 1.3 79.2 - - + +
1022C LYS* 1.3 60.6 + - + +
1023C ARG 3.1 0.4 - - - -
1024C ILE* 3.7 9.5 - - - +
1025C GLN* 2.9 28.5 + - - +
1033C LYS* 5.7 7.2 - - - -
1040C PHE* 3.8 33.5 - - + -
1053C GLU* 3.9 28.9 - - + +
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Residues in contact with LYS1022 (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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1018C ARG 2.9 17.0 + - - +
1019C GLU* 3.1 7.4 + - + +
1021C MET* 1.3 76.7 - - + +
1023C ARG* 1.3 60.5 + - - +
1025C GLN* 3.9 27.6 - - + +
1026C SER* 2.9 27.6 + - - -
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Residues in contact with ARG1023 (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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978C ASP* 4.8 8.1 - - - -
1009C LEU* 3.7 21.5 - - + -
1010C ARG* 3.0 47.4 + - - +
1012C HIS* 5.6 2.2 - - - +
1015C GLU* 3.3 20.6 + - - -
1019C GLU* 2.9 25.4 + - - +
1020C VAL* 3.1 50.7 - - - +
1022C LYS* 1.3 77.0 - - - +
1024C ILE* 1.3 65.2 + - - +
1026C SER* 3.0 10.0 + - - -
1027C LEU* 3.0 21.1 + - - +
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Residues in contact with ILE1024 (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 PHE* 4.0 20.0 - - + -
1009C LEU* 3.5 30.9 - - + +
1020C VAL* 2.9 23.4 + - + +
1021C MET* 3.7 9.2 - - - +
1023C ARG* 1.3 76.5 - - - +
1025C GLN* 1.3 57.0 + - - +
1027C LEU* 2.9 10.8 + - - +
1028C LEU* 2.9 47.0 + - + +
1038C PHE* 5.5 3.8 - - + -
1040C PHE* 4.2 23.8 - - + -
1077C LEU* 3.9 20.4 - - + -
1079C LEU* 4.3 10.3 - - + -
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Residues in contact with GLN1025 (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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1021C MET* 2.9 20.2 + - - +
1022C LYS* 3.8 29.4 - - + +
1024C ILE* 1.3 77.5 - - - +
1026C SER* 1.3 65.0 + - - +
1028C LEU* 4.5 3.4 - - - +
1029C ASP* 3.1 27.1 + - - +
1032C GLU* 4.2 14.8 + - - -
1033C LYS* 4.4 14.5 + - - +
1035C PHE* 3.1 49.4 - - + +
1038C PHE* 5.9 2.0 - - + -
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Residues in contact with SER1026 (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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1022C LYS* 2.9 20.9 + - - -
1023C ARG* 3.0 12.5 + - - -
1025C GLN* 1.3 77.9 - - - +
1027C LEU* 1.3 61.4 + - - +
1029C ASP* 4.6 7.7 - - - +
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Residues in contact with LEU1027 (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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903C PHE* 3.9 47.2 - - + +
1007C PHE* 3.5 45.3 - - + -
1023C ARG 3.0 9.6 + - - +
1024C ILE* 2.9 11.4 + - - +
1026C SER* 1.3 79.6 - - - +
1028C LEU* 1.3 69.4 + - + +
1029C ASP* 4.3 1.7 - - - +
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Residues in contact with LEU1028 (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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903C PHE* 4.2 26.2 - - + -
994C HIS* 4.1 29.2 - - + +
1007C PHE* 4.4 10.5 - - + -
1024C ILE* 2.9 40.1 + - + +
1025C GLN* 4.3 0.9 - - - +
1027C LEU* 1.3 80.0 - - + +
1029C ASP* 1.3 73.1 + - - +
1030C ILE* 3.7 11.5 - - + +
1035C PHE* 4.3 9.4 - - + -
1038C PHE* 3.9 29.2 - - + -
1079C LEU* 4.6 5.2 - - + -
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Residues in contact with ASP1029 (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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1025C GLN* 3.1 15.0 + - - +
1026C SER* 4.6 5.8 - - - +
1027C LEU 4.3 4.3 - - - +
1028C LEU* 1.3 84.9 - - - +
1030C ILE* 1.3 59.9 + - - +
1032C GLU* 4.1 16.1 - - - +
1035C PHE* 3.4 10.4 - - - -
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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