Contacts of the helix formed by residues 108 - 121 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ASN* 2.9 29.6 + - - +
107G ASN* 1.3 85.2 - - + +
109G ASP* 1.3 59.6 + - - +
110G LEU 3.8 0.2 - - - -
111G GLU* 3.7 12.7 - - - +
112G LYS* 2.8 30.8 + - - +
255G HIS* 3.8 18.1 + - + +
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Residues in contact with ASP 109 (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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46G VAL* 4.6 6.5 - - + -
104G ASN 3.2 3.2 + - - -
105G LEU* 3.2 30.1 - - - +
108G GLU* 1.3 74.7 - - - +
110G LEU* 1.3 68.2 + - - +
112G LYS* 3.1 11.0 + - - +
113G VAL* 3.0 23.8 + - - +
248G VAL* 4.7 4.9 - - + +
251G ASP* 3.3 20.3 - - - +
252G ILE* 4.0 23.3 - - + +
255G HIS* 2.5 37.6 + - - +
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Residues in contact with LEU 110 (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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43G MSE 3.2 36.4 - - + +
46G VAL* 4.6 11.3 - - + +
47G GLN* 3.9 23.1 - - + +
105G LEU 2.8 14.9 + - - +
106G LEU* 3.3 33.2 - - + +
109G ASP* 1.3 71.2 - - - +
111G GLU* 1.3 60.5 + - - +
113G VAL* 3.3 3.8 + - - -
114G LYS* 2.8 43.8 + - + -
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Residues in contact with GLU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LEU 3.4 5.1 + - - +
107G ASN* 2.8 29.1 - - - +
108G GLU* 3.7 18.5 - - - +
109G ASP 3.2 0.4 - - - -
110G LEU* 1.3 79.9 - - - +
112G LYS* 1.3 67.7 + - - +
114G LYS* 3.8 6.7 - - - +
115G ASN* 3.0 45.3 + - - +
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Residues in contact with LYS 112 (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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108G GLU 2.8 23.7 + - - +
109G ASP* 3.1 6.9 + - - +
111G GLU* 1.3 80.2 - - - +
113G VAL* 1.3 64.0 + - + +
115G ASN* 3.3 7.2 + - - +
116G TRP* 3.2 16.8 + - - +
244G PHE* 3.5 17.8 - - + -
247G GLU* 3.1 42.4 + - - +
248G VAL* 4.1 16.2 - - + +
251G ASP* 3.4 23.0 + - - +
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Residues in contact with VAL 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G CYS* 4.0 21.1 - - + +
42G LEU* 4.4 15.5 - - + -
43G MSE 3.1 31.0 - - + -
46G VAL* 6.2 2.2 - - + -
109G ASP 3.0 19.0 + - - +
110G LEU* 4.0 4.3 - - - +
112G LYS* 1.3 71.1 - - - +
114G LYS* 1.3 66.3 + - - +
115G ASN 3.1 1.1 - - - -
116G TRP* 3.2 1.4 + - - +
117G GLN* 3.0 24.4 + - - +
244G PHE* 3.5 21.3 - - + -
248G VAL* 3.9 23.3 - - + -
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Residues in contact with LYS 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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43G MSE 2.1 35.5 - - + +
110G LEU* 2.8 29.3 + - + +
111G GLU* 3.8 6.3 - - - +
113G VAL* 1.3 68.8 - - - +
115G ASN* 1.3 63.6 + - - +
117G GLN* 3.5 8.8 + - - +
118G LYS* 3.2 33.3 + - + +
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Residues in contact with ASN 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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111G GLU* 3.0 39.4 + - - +
112G LYS* 3.5 9.4 - - - +
113G VAL 3.1 0.2 - - - -
114G LYS* 1.3 76.2 - - - +
116G TRP* 1.3 65.3 + - - +
118G LYS* 2.9 31.5 + - - +
119G ASP* 3.2 9.8 + - - +
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Residues in contact with TRP 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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39G CYS* 4.0 17.9 - - - -
112G LYS 3.2 3.3 + - - +
113G VAL 3.2 2.0 + - - +
115G ASN* 1.3 79.4 - - - +
117G GLN* 1.3 68.2 + - + +
119G ASP* 2.9 19.5 + - + +
120G ALA* 3.1 29.1 + - + +
121G TYR* 3.9 26.5 - + - -
237G PHE* 5.5 4.5 - + - -
240G LYS* 4.2 11.4 + - + +
241G ARG* 3.6 44.4 - - + -
244G PHE* 3.4 62.7 - + + +
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Residues in contact with GLN 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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36G HIS* 3.2 49.5 + - + +
39G CYS* 3.7 17.8 - - + +
40G ASN* 2.8 29.1 + - - +
43G MSE 4.6 11.4 - - - +
113G VAL 3.0 17.1 + - - +
114G LYS* 3.7 7.5 - - - +
116G TRP* 1.3 86.1 - - + +
118G LYS* 1.3 62.6 + - - +
120G ALA 4.6 0.2 - - - +
121G TYR* 3.1 30.6 + - + +
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Residues in contact with LYS 118 (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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114G LYS* 3.2 25.1 + - + +
115G ASN* 2.9 24.6 + - - +
117G GLN* 1.3 78.4 + - - +
119G ASP* 1.3 64.4 + - - +
120G ALA 3.6 0.5 + - - -
121G TYR 3.6 12.7 - - - +
122G HIS* 3.9 11.4 + - - -
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Residues in contact with ASP 119 (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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115G ASN* 3.2 8.4 + - - +
116G TRP* 2.9 12.4 + - + +
118G LYS* 1.3 85.5 - - - +
120G ALA* 1.3 59.3 + - - +
122G HIS* 3.7 18.0 - - - -
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Residues in contact with ALA 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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116G TRP* 3.1 46.8 + - + +
117G GLN 3.3 0.2 + - - -
119G ASP* 1.3 80.1 - - - +
121G TYR* 1.3 68.6 - - + +
122G HIS* 4.1 2.4 - - - -
131G GLU* 3.2 26.4 - - - +
237G PHE* 3.6 19.7 - - + -
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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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32G ILE* 3.4 31.8 + - + -
35G GLY* 3.4 15.1 - - - -
36G HIS* 3.5 53.0 + + + +
39G CYS* 4.4 1.3 - - - -
116G TRP* 3.9 22.6 - + - -
117G GLN* 3.1 18.9 + - + +
118G LYS* 3.6 13.7 - - - +
120G ALA* 1.3 88.4 - - + +
122G HIS* 1.3 61.5 + - - +
123G LYS 4.1 1.7 + - - -
129G PHE* 3.8 19.3 - + + -
131G GLU* 3.7 9.9 - - + -
237G PHE* 3.8 27.7 - + - -
238G GLU* 5.6 0.2 + - - -
241G ARG* 4.1 10.9 - - - +
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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