Contacts of the helix formed by residues 108 - 121 (chain M) in PDB entry 3Q84
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 108 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104M ASN* 2.9 32.9 + - - +
107M ASN* 1.3 94.7 - - + +
109M ASP* 1.3 60.2 + - - +
110M LEU 3.6 0.2 - - - -
111M GLU* 3.9 0.7 - - - +
112M LYS* 2.9 31.5 + - - +
255M HIS* 4.4 15.7 - - + +
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Residues in contact with ASP 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M VAL* 4.9 4.9 - - + -
104M ASN 3.5 1.8 + - - -
105M LEU* 3.5 21.1 - - - +
108M GLU* 1.3 74.6 - - - +
110M LEU* 1.3 64.4 + - - +
112M LYS* 3.2 6.0 + - - +
113M VAL* 2.7 31.7 + - - +
248M VAL* 4.6 7.2 - - + +
251M ASP* 3.3 27.5 - - - +
252M ILE* 3.7 30.7 - - + +
255M HIS* 2.8 30.4 + - - -
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Residues in contact with LEU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M MSE 3.1 70.7 - - + +
46M VAL* 4.1 10.5 - - + +
47M GLN* 3.8 22.4 - - + +
105M LEU 3.3 6.2 + - - +
106M LEU* 3.5 34.7 + - + +
108M GLU 3.6 0.2 - - - -
109M ASP* 1.3 78.9 - - - +
111M GLU* 1.3 63.5 + - - +
113M VAL* 3.2 6.7 + - - -
114M LYS* 2.9 25.4 + - + -
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Residues in contact with GLU 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M LEU 3.6 15.3 + - - +
107M ASN* 3.6 28.5 + - - +
108M GLU 3.6 1.1 + - - +
110M LEU* 1.3 85.1 - - - +
112M LYS* 1.3 61.5 + - - +
114M LYS* 3.2 30.1 + - - +
115M ASN* 2.9 41.6 + - - +
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Residues in contact with LYS 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M GLU 2.9 20.6 + - - +
109M ASP* 3.5 8.3 - - - +
111M GLU* 1.3 78.3 - - - +
113M VAL* 1.3 65.0 + - - +
115M ASN* 3.2 7.3 + - - +
116M TRP* 3.1 17.2 + - - +
244M PHE* 3.6 28.8 - - + -
247M GLU* 2.9 29.2 + - - -
248M VAL* 4.3 11.4 - - + -
251M ASP* 3.1 27.5 + - - +
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Residues in contact with VAL 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M CYS* 4.1 22.1 - - + +
42M LEU* 4.4 15.3 - - + -
43M MSE 3.5 30.1 - - + -
46M VAL* 6.4 1.6 - - + -
109M ASP 2.7 21.5 + - - +
110M LEU* 3.9 3.4 - - - +
112M LYS* 1.3 75.4 - - - +
114M LYS* 1.3 62.8 + - - +
116M TRP* 3.3 3.1 + - - +
117M GLN* 3.0 22.2 + - - +
244M PHE* 3.8 17.4 - - + -
248M VAL* 4.1 23.1 - - + -
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Residues in contact with LYS 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M MSE 2.4 33.5 - - + +
110M LEU* 2.9 13.8 + - + +
111M GLU* 3.6 26.4 + - - +
113M VAL* 1.3 76.8 - - - +
115M ASN* 1.3 77.0 + - - +
117M GLN* 3.4 11.2 + - - +
118M LYS* 3.1 33.5 + - + +
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Residues in contact with ASN 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M GLU* 2.9 30.7 + - - +
112M LYS* 3.8 7.1 - - - +
113M VAL 3.2 0.2 - - - -
114M LYS* 1.3 90.5 - - - +
116M TRP* 1.3 59.1 + - - +
118M LYS* 3.3 8.6 + - - +
119M ASP* 2.6 33.3 + - - +
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Residues in contact with TRP 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M CYS* 4.0 22.0 - - - -
112M LYS 3.1 5.0 + - - +
113M VAL 3.6 2.7 - - - +
114M LYS 3.2 0.2 - - - -
115M ASN* 1.3 74.7 - - - +
117M GLN* 1.3 68.9 + - - +
119M ASP* 3.2 5.1 + - + +
120M ALA* 3.1 43.5 + - + +
121M TYR* 4.2 11.0 - + - -
237M PHE* 5.4 4.9 - + - -
240M LYS* 4.2 16.3 + - + +
241M ARG* 3.4 53.8 - - + -
244M PHE* 3.4 57.6 - + + +
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Residues in contact with GLN 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36M HIS* 3.4 51.3 + - + +
39M CYS* 3.5 21.8 - - + +
40M ASN* 2.8 28.7 + - - +
43M MSE 4.7 9.3 - - - +
113M VAL 3.0 17.3 + - - +
114M LYS* 3.6 11.7 - - - +
115M ASN 3.3 0.2 - - - -
116M TRP* 1.3 84.0 - - - +
118M LYS* 1.3 62.7 + - - +
121M TYR* 3.2 30.2 + - + +
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Residues in contact with LYS 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M LYS* 3.1 24.1 + - + +
115M ASN* 3.4 17.5 - - - +
116M TRP 3.1 0.4 - - - -
117M GLN* 1.3 81.0 + - - +
119M ASP* 1.3 64.4 + - - +
121M TYR 3.3 17.8 - - - +
122M HIS* 4.5 6.4 + - - -
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Residues in contact with ASP 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ASN* 2.6 27.7 - - - +
116M TRP* 3.2 7.7 + - + +
118M LYS* 1.3 85.6 - - - +
120M ALA* 1.3 58.5 + - - +
122M HIS* 3.9 14.9 + - - -
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Residues in contact with ALA 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M TRP* 3.1 37.9 + - + +
119M ASP* 1.3 78.1 - - - +
121M TYR* 1.3 78.9 + - + +
122M HIS* 4.0 4.4 - - - -
131M GLU* 3.3 15.6 - - - +
237M PHE* 3.4 27.4 - - + -
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Residues in contact with TYR 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M ILE* 3.4 27.7 + - + -
35M GLY* 3.5 9.3 - - - -
36M HIS* 3.4 43.7 + + + +
39M CYS* 5.3 0.7 - - - -
116M TRP* 4.2 14.7 - + - -
117M GLN* 3.2 20.8 + - + +
118M LYS* 3.3 17.2 - - - +
120M ALA* 1.3 95.3 - - + +
122M HIS* 1.3 63.2 + - - +
123M LYS 4.3 0.3 + - - -
129M PHE* 3.5 36.3 - + + -
131M GLU* 3.8 5.8 - - + -
237M PHE* 4.0 23.9 - + - -
241M ARG* 4.5 7.4 - - - +
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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