Contacts of the helix formed by residues 109 - 119 (chain C) in PDB entry 3E5X
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 GLU 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C THR 4.5 1.6 + - - -
87C LEU* 3.7 21.5 - - + +
88C TYR* 2.8 33.2 + - + +
108C SER* 1.3 72.9 - - - +
110C LYS* 1.3 60.0 + - + +
112C LEU* 3.1 6.0 + - - +
113C ARG* 3.0 60.1 + - - +
9D ASP* 5.1 1.9 - - - +
124D PHE* 3.7 22.8 - - + +
128D LYS* 5.0 3.6 + - - -
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Residues in contact with LYS 110 (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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108C SER* 3.2 7.9 + - - +
109C GLU* 1.3 79.5 - - + +
111C SER* 1.3 65.1 + - - +
113C ARG* 3.4 20.8 + - - +
114C THR* 3.2 23.7 + - - -
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Residues in contact with SER 111 (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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31C MET* 3.0 31.3 - - - +
32C GLY* 4.4 2.5 - - - -
107C PHE* 3.0 14.5 - - - +
108C SER* 2.8 42.0 + - - -
110C LYS* 1.3 76.3 - - - +
112C LEU* 1.3 55.1 + - - +
114C THR* 3.1 10.5 + - - -
115C VAL* 2.9 30.3 + - - +
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Residues in contact with LEU 112 (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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25C LEU* 5.4 4.3 - - + -
53C MET* 3.9 26.5 - - + -
87C LEU* 3.6 32.3 - - + -
107C PHE* 3.6 30.5 - - + +
108C SER 3.0 17.0 + - - +
109C GLU 3.1 5.8 + - - +
111C SER* 1.3 72.6 + - - +
113C ARG* 1.3 66.4 + - - +
115C VAL* 2.9 9.4 + - + +
116C PHE* 2.8 54.5 + - + -
126C ILE* 4.4 12.1 - - + -
124D PHE* 4.1 7.2 - - + -
127D PHE* 4.5 2.9 - - + -
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Residues in contact with ARG 113 (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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109C GLU* 3.0 49.3 + - - +
110C LYS* 3.6 18.1 - - - +
111C SER 3.4 0.2 - - - -
112C LEU* 1.3 74.3 - - - +
114C THR* 1.3 62.7 + - - +
116C PHE* 3.3 4.2 + - - +
117C ARG* 3.0 52.4 + - - +
120D GLU* 2.9 36.8 + - - +
121D ASP* 3.0 29.1 + - - -
124D PHE* 3.7 26.3 - - + +
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Residues in contact with THR 114 (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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31C MET* 4.1 24.2 - - + -
110C LYS 3.2 11.3 + - - -
111C SER* 3.1 13.6 + - - -
113C ARG* 1.3 79.5 - - - +
115C VAL* 1.3 61.3 + - - +
117C ARG* 3.6 15.8 + - - +
118C THR* 3.3 20.5 + - - +
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Residues in contact with VAL 115 (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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25C LEU* 4.6 6.3 - - + -
28C TYR* 4.1 17.5 - - + -
31C MET* 3.9 21.8 - - + -
107C PHE* 4.0 28.3 - - + -
111C SER 2.9 19.5 + - - +
112C LEU* 2.9 13.0 + - + +
114C THR* 1.3 74.6 - - - +
116C PHE* 1.3 72.8 + - + +
118C THR* 3.0 7.8 + - - -
119C ASP* 2.8 23.6 + - - +
122C MET* 4.0 23.1 - - + -
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Residues in contact with PHE 116 (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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112C LEU* 2.8 36.5 + - + +
113C ARG* 4.0 3.4 - - - +
115C VAL* 1.3 79.2 - - + +
117C ARG* 1.3 63.9 + - - +
118C THR 3.1 2.0 + - - -
119C ASP 3.6 5.8 - - - -
120C GLU* 3.4 20.1 + - - +
122C MET* 4.0 7.9 - - + -
123C ILE* 3.7 35.4 - - + +
126C ILE* 3.8 22.4 - - + -
120D GLU* 5.6 2.7 - - + +
123D ILE* 3.8 42.0 - - + -
124D PHE* 3.8 15.9 - + - -
127D PHE* 3.7 27.1 - + - -
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Residues in contact with ARG 117 (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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113C ARG* 3.0 41.1 + - - +
114C THR* 3.8 12.6 + - - +
116C PHE* 1.3 76.1 - - - +
118C THR* 1.3 59.7 + - - +
120D GLU* 2.8 43.0 + - - +
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Residues in contact with THR 118 (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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28C TYR* 4.1 20.0 - - + +
31C MET* 3.7 19.8 - - + +
114C THR* 3.3 12.3 + - - +
115C VAL 3.0 9.1 + - - -
117C ARG* 1.3 80.7 - - - +
119C ASP* 1.4 57.9 + - + +
120C GLU 4.1 0.8 + - - -
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Residues in contact with ASP 119 (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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24C LYS* 5.6 1.9 - - - +
28C TYR* 2.6 42.2 + - + +
115C VAL 2.8 11.7 + - - +
116C PHE* 3.6 13.2 - - - -
118C THR* 1.4 74.4 - - + +
120C GLU* 1.3 63.8 + - - +
121C ASP* 3.0 33.0 + - - +
122C MET* 3.2 35.6 + - + +
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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