Contacts of the helix formed by residues 113 - 122 (chain G) in PDB entry 40ER
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 LYS 113 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54G SER* 3.2 30.5 + - - +
55G LEU 4.0 5.2 - - - +
56G GLN* 3.9 23.1 - - + +
57G VAL* 3.5 5.8 - - - +
111G GLU 4.2 7.9 - - - +
112G HIS* 1.3 80.2 - - - +
114G ILE* 1.3 61.5 + - - +
115G GLU* 3.4 14.9 + - + +
116G THR* 3.1 22.5 + - - +
117G TRP* 2.8 30.0 + - - +
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Residues in contact with ILE 114 (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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51G PHE* 3.9 21.3 - - + -
52G ASP 3.5 19.3 - - - +
53G THR* 3.6 15.5 - - + +
55G LEU* 3.0 24.2 + - + +
56G GLN 4.3 2.9 - - - +
57G VAL* 3.5 19.8 - - + +
60G ALA* 4.1 10.1 - - + -
74G LEU* 3.9 21.8 - - + -
86G LEU* 4.1 19.3 - - + -
113G LYS* 1.3 70.2 - - - +
115G GLU* 1.3 54.2 + - - +
117G TRP* 3.1 5.9 + - + +
118G ARG* 2.8 51.4 + - + +
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Residues in contact with GLU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G THR* 3.1 41.5 + - + +
54G SER* 4.4 9.2 - - - -
76G ASP* 5.4 1.8 - - - +
78G LYS* 5.7 5.2 - - - -
113G LYS* 4.8 14.5 + - + +
114G ILE* 1.3 77.0 - - - +
116G THR* 1.3 66.4 + - - +
118G ARG* 3.6 10.2 - - - +
119G GLU* 3.1 25.6 + - - +
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Residues in contact with THR 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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112G HIS* 3.5 22.0 - - + +
113G LYS* 3.1 34.0 + - - +
115G GLU* 1.3 85.1 + - - +
117G TRP* 1.3 60.9 + - - +
119G GLU* 3.3 28.3 - - - +
120G VAL* 3.4 13.1 + - + +
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Residues in contact with TRP 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G VAL* 4.1 11.9 - - + -
61G PHE* 6.3 1.8 - + - -
86G LEU* 6.0 1.6 - - + -
90G ASP* 3.1 59.7 - - + -
93G ASN* 3.8 9.2 - - + -
94G ILE* 3.5 33.7 - - + +
97G ARG* 5.5 3.8 - - - +
98G TYR* 4.0 4.9 - + - -
112G HIS* 3.4 30.7 - + - +
113G LYS 2.8 13.8 + - - +
114G ILE* 3.7 5.4 - - + +
116G THR* 1.3 72.5 - - - +
118G ARG* 1.3 71.7 + - + +
119G GLU 3.1 1.6 - - - -
120G VAL* 3.1 14.1 - - + +
121G TYR* 2.8 75.1 + + + +
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Residues in contact with ARG 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G THR* 6.0 2.2 - - + -
74G LEU* 3.7 29.7 - - - +
83G VAL* 3.3 37.4 + - - +
84G GLY* 3.7 11.1 - - - -
85G MET 4.3 5.1 + - - +
114G ILE* 2.8 40.9 + - + +
115G GLU* 3.6 10.3 - - - +
116G THR 3.3 0.2 - - - -
117G TRP* 1.3 82.2 - - + +
119G GLU* 1.3 56.3 + - - +
121G TYR* 4.1 7.9 - - - -
122G LEU* 2.8 65.5 + - + +
127G LYS 5.2 7.6 + - - -
128G PRO* 6.1 0.2 - - - +
401G AMP 4.8 10.1 + - - -
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Residues in contact with GLU 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G GLU 3.1 12.2 + - - +
116G THR* 3.3 22.4 - - - +
117G TRP 3.1 0.6 - - - -
118G ARG* 1.3 77.8 - - - +
120G VAL* 1.3 60.1 + - + +
122G LEU* 3.8 3.5 - - - +
123G GLN* 3.0 31.8 + - + +
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Residues in contact with VAL 120 (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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97G ARG* 4.3 12.9 + - + +
98G TYR* 3.3 28.0 - - + +
112G HIS* 4.1 4.7 - - + +
116G THR* 3.4 10.5 + - + +
117G TRP* 3.1 33.9 - - + +
119G GLU* 1.3 77.1 - - + +
121G TYR* 1.3 63.7 + - + +
123G GLN* 3.3 23.7 - - + +
124G ASP* 4.0 6.9 - - - +
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Residues in contact with TYR 121 (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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89G THR* 5.0 1.0 - - - +
90G ASP* 4.4 0.4 - - - -
93G ASN* 2.7 34.6 + - + -
97G ARG* 5.2 15.7 - - - +
117G TRP* 2.8 57.6 + + + +
118G ARG* 3.7 9.9 - - - +
120G VAL* 1.3 80.1 - - + +
122G LEU* 1.3 70.5 + - + +
123G GLN 3.2 2.0 + - - -
124G ASP* 3.9 11.4 + - - +
125G SER* 4.0 7.8 + - - +
401G AMP 3.3 32.8 + + - -
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Residues in contact with LEU 122 (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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118G ARG* 2.8 53.2 + - + +
119G GLU* 3.8 4.5 - - - +
121G TYR* 1.3 89.3 - - + +
123G GLN* 1.3 64.7 + - - +
124G ASP 3.1 2.4 - - - -
125G SER* 3.1 29.1 + - - +
126G PHE* 3.6 50.5 - - + -
127G LYS 4.8 10.3 - - - +
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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