Contacts of the helix formed by residues 1021 - 1028 (chain C) in PDB entry 2E9X
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 SER1021 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008C VAL* 3.9 11.6 + - - +
1009C GLU 3.4 23.0 - - - -
1010C SER* 3.6 8.8 + - - -
1018C ASN* 3.0 17.4 + - - +
1019C PHE 3.4 0.2 - - - -
1020C LEU* 1.3 74.7 - - - +
1022C LEU* 1.3 62.3 + - - +
1023C ASP* 3.4 5.9 + - - +
1024C ASP* 2.9 32.8 + - - +
1025C ILE* 3.1 24.4 + - - +
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Residues in contact with LEU1022 (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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10A ILE* 3.8 38.4 - - + +
13A LEU* 4.1 17.7 - - + -
14A HIS* 4.3 23.3 - - + +
78A ALA* 4.1 26.2 - - + +
79A TYR* 4.5 2.0 - - - +
82A ASP* 3.6 33.4 - - + +
86A ARG* 4.6 4.3 - - - +
1005C TYR* 5.0 0.9 - - - +
1008C VAL 4.7 3.8 + - - -
1020C LEU 3.3 4.9 + - - +
1021C SER* 1.3 72.1 - - - +
1023C ASP* 1.3 62.2 + - - +
1025C ILE* 3.2 5.8 + - - +
1026C LEU* 3.0 28.2 + - - +
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Residues in contact with ASP1023 (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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14A HIS* 4.2 20.0 + - + +
1007C ARG* 6.1 2.9 - - - +
1008C VAL 5.8 0.2 + - - -
1010C SER* 4.1 20.0 + - - +
1021C SER* 3.2 6.2 + - - +
1022C LEU* 1.3 80.3 - - - +
1024C ASP* 1.3 57.6 + - - +
1026C LEU* 3.3 7.5 + - - +
1027C MET* 2.9 25.6 + - - +
1115C HIS* 2.6 36.8 + - - -
1170C GLU* 4.4 13.1 - - - +
1171C MET 5.8 0.2 + - - -
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Residues in contact with ASP1024 (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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74A ARG* 3.8 7.2 - - - +
1010C SER* 2.5 23.6 + - - -
1011C GLY 2.8 23.4 + - - -
1012C ALA* 3.3 10.1 - - - +
1017C GLU* 3.2 29.9 - - + +
1018C ASN 2.9 16.5 + - - -
1021C SER* 2.9 21.2 + - - +
1023C ASP* 1.3 75.7 - - - +
1025C ILE* 1.3 60.4 + - - +
1027C MET* 3.2 7.5 + - + +
1028C SER* 2.8 31.9 + - - -
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Residues in contact with ILE1025 (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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7A MET* 3.9 9.5 - - - +
10A ILE* 3.9 19.1 - - + -
71A ARG* 2.8 39.5 + - - +
74A ARG* 3.6 31.0 - - + +
75A CYS* 3.8 19.5 - - - -
78A ALA* 3.4 32.5 - - + -
1019C PHE 4.0 7.0 - - - +
1021C SER 3.1 15.3 + - - +
1022C LEU* 3.5 7.9 - - - +
1024C ASP* 1.3 78.0 - - - +
1026C LEU* 1.3 61.1 + - - +
1028C SER* 3.5 10.0 + - - -
1029C HIS* 3.5 3.5 + - - +
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Residues in contact with LEU1026 (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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7A MET* 3.5 24.2 - - + -
10A ILE* 4.0 9.6 - - + -
11A ARG* 3.8 26.5 - - + +
14A HIS* 3.5 46.4 - - + +
1022C LEU 3.0 18.6 + - - +
1023C ASP* 3.7 9.9 - - - +
1025C ILE* 1.3 73.9 - - - +
1027C MET* 1.3 66.3 + - - +
1029C HIS* 3.3 15.8 + - - +
1030C GLU* 3.7 9.5 - - - +
1115C HIS* 4.4 12.7 - - + +
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Residues in contact with MET1027 (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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1012C ALA* 3.6 19.7 - - + -
1017C GLU* 3.9 17.0 - - - +
1023C ASP 2.9 17.7 + - - +
1024C ASP* 3.4 9.0 - - - +
1026C LEU* 1.3 74.1 - - - +
1028C SER* 1.3 60.4 + - - +
1029C HIS 2.9 10.4 + - - -
1030C GLU* 3.1 29.9 + - - +
1070C LEU* 3.5 18.4 - - + -
1115C HIS* 3.6 40.4 - - + -
1118C GLY* 4.0 3.1 - - - +
1119C PHE* 3.7 21.5 - - - +
1122C GLN* 3.6 28.0 - - + -
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Residues in contact with SER1028 (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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71A ARG* 3.0 25.8 + - - -
74A ARG* 3.6 0.7 + - - -
1017C GLU* 3.0 26.2 + - - -
1024C ASP 2.8 23.5 + - - -
1025C ILE 3.5 0.6 + - - -
1027C MET* 1.3 77.0 - - - +
1029C HIS* 1.3 57.1 + - - +
1030C GLU 3.4 0.7 - - - -
1070C LEU* 3.3 20.0 + - - -
1071C TRP* 3.0 38.3 + - - -
1074C LYS* 5.6 0.2 - - - -
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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