Contacts of the helix formed by residues 108 - 123 (chain G) in PDB entry 3Q2K
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 ARG 108 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C LYS* 6.0 6.1 - - - +
87G TRP* 6.0 1.6 - - - +
106G ALA* 3.6 4.9 - - - +
107G THR* 1.3 90.5 + - - +
109G TRP* 1.3 67.6 + - - +
110G GLU* 4.4 4.9 - - + +
111G ASP* 3.0 35.1 + - - +
112G GLY 3.0 17.8 + - - -
178G TRP* 5.2 3.6 + - - +
179G GLU* 3.8 45.9 + - - +
329G LEU* 3.9 3.7 - - - +
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Residues in contact with TRP 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G THR 4.3 0.2 - - - -
108G ARG* 1.3 72.4 - - - +
110G GLU* 1.3 68.3 + - + +
112G GLY* 3.1 3.1 + - - -
113G LYS* 3.0 54.7 + - + +
326G LEU* 3.5 45.3 - - + -
329G LEU* 4.0 14.6 - - + +
330G ALA* 3.6 28.3 - - + -
333G THR* 3.6 25.1 + - + +
337G ARG* 4.1 19.1 - - - +
349G LEU* 3.8 30.0 - - + +
350G ASP 3.1 23.5 + - - -
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Residues in contact with GLU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ARG* 3.1 5.1 - - + +
109G TRP* 1.3 85.0 - - + +
111G ASP* 1.3 60.9 + - - +
113G LYS* 2.7 42.4 + - - +
114G ARG* 3.0 51.7 + - - +
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Residues in contact with ASP 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLY 5.2 1.2 - - - +
86G PRO* 3.8 26.8 - - + +
87G TRP* 3.4 31.5 + - + -
90G ILE* 5.3 0.3 - - - +
106G ALA* 4.3 0.9 - - + -
107G THR* 5.2 1.4 + - - -
108G ARG* 3.0 40.1 + - - +
110G GLU* 1.3 78.1 - - - +
112G GLY* 1.3 58.8 + - - +
114G ARG* 3.2 24.1 + - - +
115G MET* 2.8 30.1 + - - +
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Residues in contact with GLY 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G MET* 4.7 1.1 - - - -
106G ALA* 3.7 18.4 - - - +
108G ARG 3.0 9.5 + - - -
109G TRP 3.1 4.0 + - - -
111G ASP* 1.3 75.9 - - - +
113G LYS* 1.3 64.6 + - - +
115G MET* 3.2 13.1 - - - +
116G VAL* 3.1 23.9 + - - +
326G LEU* 3.8 7.6 - - - -
329G LEU* 3.8 10.5 - - - -
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Residues in contact with LYS 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ARG* 5.0 15.0 - - - +
109G TRP* 3.0 59.8 + - + +
110G GLU* 2.7 32.9 + - - +
111G ASP 3.4 0.2 - - - -
112G GLY* 1.3 74.8 - - - +
114G ARG* 1.3 61.5 + - - +
116G VAL* 3.0 14.9 + - - +
117G LYS* 3.0 15.6 + - - +
326G LEU* 4.0 18.3 - - + +
350G ASP* 3.2 20.9 + - - -
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Residues in contact with ARG 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G TRP* 3.5 31.1 - - - -
90G ILE* 4.1 13.2 - - + +
110G GLU* 3.0 43.3 + - - +
111G ASP* 3.3 30.4 + - - +
112G GLY 3.1 0.2 - - - -
113G LYS* 1.3 74.9 - - - +
115G MET* 1.3 66.8 + - - +
116G VAL 3.1 0.2 + - - -
117G LYS* 3.2 27.1 + - - +
118G ALA* 3.1 23.8 + - + +
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Residues in contact with MET 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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85G HIS 3.7 8.7 - - - +
86G PRO* 3.5 35.9 - - + +
89G ALA* 3.7 16.1 - - + -
90G ILE* 3.9 12.9 - - + +
101G SER* 4.3 12.3 - - - +
105G MET* 3.2 58.1 - - + +
111G ASP 2.8 9.6 + - - +
112G GLY* 3.2 20.0 - - - +
114G ARG* 1.3 78.1 - - - +
116G VAL* 1.3 64.3 + - - +
118G ALA* 3.5 1.0 + - - +
119G CYS* 3.2 26.9 + - - -
126G LEU* 4.2 9.8 - - + +
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Residues in contact with VAL 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G MET* 3.8 11.9 - - + -
112G GLY 3.1 15.4 + - - +
113G LYS* 3.0 8.8 + - - +
114G ARG 3.0 1.0 - - - -
115G MET* 1.3 79.4 - - - +
117G LYS* 1.3 62.5 + - - +
119G CYS* 3.4 2.4 + - - +
120G ASP* 3.1 24.5 + - - +
126G LEU* 3.9 11.2 - - + -
322G GLY* 3.8 28.0 - - - +
323G ARG* 3.5 38.6 - - + +
326G LEU* 3.9 17.3 - - + -
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Residues in contact with LYS 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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87F TRP* 5.5 15.7 - - + -
113G LYS 3.0 11.4 + - - +
114G ARG* 3.8 31.6 - - - +
116G VAL* 1.3 76.2 - - - +
118G ALA* 1.3 57.6 + - - +
120G ASP* 3.2 12.8 - - + +
121G GLU* 2.9 53.0 + - - +
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Residues in contact with ALA 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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90G ILE* 4.0 35.7 - - + +
93G ALA* 3.8 6.2 - - + +
94G GLN* 4.8 5.8 - - - +
114G ARG 3.1 15.6 + - - +
115G MET 4.0 2.7 - - - +
117G LYS* 1.3 79.2 - - - +
119G CYS* 1.3 57.6 + - - +
121G GLU* 3.9 5.7 - - - +
122G ALA* 2.9 31.5 + - - +
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Residues in contact with CYS 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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89G ALA* 4.4 6.3 - - - -
93G ALA* 3.9 15.3 - - - -
99G VAL* 3.7 26.7 - - - -
115G MET 3.2 19.2 + - - +
116G VAL 4.1 2.5 - - - +
118G ALA* 1.3 73.6 - - - +
120G ASP* 1.3 69.3 + - - +
123G GLY 3.1 15.1 + - - -
124G VAL* 3.1 30.0 + - - +
126G LEU* 3.7 34.8 - - + -
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Residues in contact with ASP 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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180F TRP* 5.3 2.1 - - - -
116G VAL* 3.1 19.9 + - - +
117G LYS* 3.2 15.6 - - + +
119G CYS* 1.3 76.2 - - - +
121G GLU* 1.3 59.2 + - - +
123G GLY* 3.0 19.8 + - - -
124G VAL 5.0 1.3 - - - -
323G ARG* 3.2 39.5 + - - -
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Residues in contact with GLU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G LYS* 2.9 39.0 + - - +
118G ALA* 3.9 5.6 - - - +
120G ASP* 1.3 77.0 - - - +
122G ALA* 1.3 65.4 + - - +
123G GLY 3.2 0.5 + - - -
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Residues in contact with ALA 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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93G ALA* 3.2 36.8 - - + +
94G GLN* 5.0 2.2 - - - -
96G GLY* 5.3 2.9 - - - -
118G ALA 2.9 18.9 + - - +
119G CYS 4.2 1.8 - - - +
121G GLU* 1.3 75.9 - - - +
123G GLY* 1.3 57.7 + - - +
124G VAL* 3.2 9.8 + - + +
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Residues in contact with GLY 123 (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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98G HIS* 4.9 4.3 - - - -
119G CYS 3.1 0.2 + - - -
120G ASP 3.0 17.9 + - - -
121G GLU 3.1 1.6 + - - -
122G ALA* 1.3 76.6 - - - +
124G VAL* 1.3 62.8 + - - +
125G ARG* 5.8 0.5 - - - -
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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