Contacts of the helix formed by residues 112 - 117 (chain G) in PDB entry 5IXM
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 ALA 112 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G TYR* 4.0 17.0 - - + +
84G ARG* 3.8 0.2 - - - -
110G ASP* 3.2 11.1 + - - +
111G PRO* 1.3 79.7 - - + +
113G TYR* 1.3 65.6 + - - +
114G PHE 3.6 0.9 - - - -
115G THR* 3.4 15.2 + - + -
116G ASP* 3.2 34.3 + - - +
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Residues in contact with TYR 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G GLN* 3.5 10.4 + - - -
64G ASP* 3.4 31.9 + - - +
84G ARG* 3.8 7.4 - - + +
85G TRP* 3.6 33.2 - - - -
86G LEU* 3.4 23.9 - - + +
108G VAL* 4.0 13.7 - - + -
109G SER* 4.0 10.8 - - - -
110G ASP* 3.2 21.5 + - - +
111G PRO 3.3 3.8 + - - -
112G ALA* 1.3 77.4 - - - +
114G PHE* 1.3 75.9 + + + +
116G ASP* 2.9 5.0 + - - +
117G LEU* 2.7 66.6 + - + +
118G THR 5.7 0.3 + - - -
119G SER* 4.5 7.1 - - - -
154G PHE* 6.3 0.2 - - + -
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Residues in contact with PHE 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G LEU* 3.6 13.9 - - + -
106G THR* 4.4 5.4 - - + -
108G VAL* 3.8 22.4 - - + -
111G PRO 4.9 1.2 + - - -
113G TYR* 1.3 85.5 - + + +
115G THR* 1.3 61.7 + - - +
117G LEU 3.6 15.1 - - - +
119G SER* 3.1 27.6 - - - -
121G TYR 3.4 17.0 - - - -
122G GLY* 3.4 18.4 - - - -
123G SER* 3.2 28.5 - - - +
124G THR* 3.3 19.1 + - - +
126G ASP* 4.6 4.7 - - + -
128G TYR 5.2 0.4 - - - -
129G ALA* 5.1 4.0 - - + -
154G PHE* 3.5 40.4 - + + -
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Residues in contact with THR 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ASN* 3.7 11.1 + - - -
111G PRO 4.7 2.6 + - - -
112G ALA* 3.5 22.7 + - + -
113G TYR 3.1 0.4 - - - -
114G PHE* 1.3 79.5 - - - +
116G ASP* 1.3 69.4 + - - +
124G THR* 4.2 15.6 + - - +
509G THR* 4.7 15.9 - - + +
521G ASP* 5.0 6.0 - - - +
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Residues in contact with ASP 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ASN* 3.4 10.6 + - - +
14G ASN* 2.9 28.1 + - - +
42G ARG* 3.6 23.0 + - - +
72G TYR* 4.3 3.3 - - - -
84G ARG* 2.3 39.9 + - - +
112G ALA* 3.2 19.2 + - - +
113G TYR 2.9 2.3 + - - +
115G THR* 1.3 94.3 - - - +
117G LEU* 1.3 63.4 + - + +
118G THR* 4.3 0.3 + - - -
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Residues in contact with LEU 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ASN* 4.9 0.4 - - - +
37G HIS* 5.9 0.4 - - + -
39G MET* 3.6 39.5 - - + -
42G ARG* 3.7 16.6 - - - -
45G GLN* 3.5 21.3 - - - +
66G LEU* 4.1 2.7 - - + -
84G ARG* 3.7 27.8 - - + +
113G TYR* 2.7 57.3 + - + +
114G PHE* 3.6 23.1 - - - +
116G ASP* 1.3 78.8 - - + +
118G THR* 1.3 64.0 + - - +
119G SER 3.8 1.6 + - - -
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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