Contacts of the helix formed by residues 117 - 130 (chain G) in PDB entry 6CM9
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 PHE 117 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79G PHE* 3.9 12.6 - - + -
83G ARG* 5.3 0.5 + - - -
115G THR* 3.1 19.4 - - + -
116G GLN* 1.3 106.1 - - + +
118G VAL* 1.3 62.9 + - - +
119G GLN 3.4 1.1 - - - -
120G GLY* 3.6 3.1 + - - +
121G LEU* 3.4 22.2 + - - +
152G TYR* 4.7 18.0 + + - -
134S ALA* 3.9 24.2 - - + -
137S ASP* 4.1 23.6 - - + -
138S SER* 3.7 28.9 - - - -
141S LEU* 3.9 14.4 - - + -
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Residues in contact with VAL 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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79G PHE* 3.6 29.8 - - + -
82G LYS* 3.7 27.6 - - + -
86G TYR* 5.1 4.2 - - + -
110G ASP* 4.3 11.9 - - + +
113G HIS* 3.8 37.9 - - + +
115G THR* 3.5 21.8 + - + +
117G PHE* 1.3 75.3 - - - +
119G GLN* 1.3 59.8 + - - +
120G GLY 3.2 0.2 - - - -
121G LEU* 3.0 7.7 + - + +
122G ALA* 2.9 24.3 + - - +
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Residues in contact with GLN 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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110G ASP 3.5 20.0 - - - +
111G LEU* 2.7 27.4 + - - +
112G ASN* 3.5 3.4 - - - +
113G HIS* 2.5 33.0 + - + +
114G SER 5.5 0.7 - - - -
115G THR 3.3 15.4 + - - +
116G GLN* 4.6 1.6 - - - -
118G VAL* 1.3 74.1 - - - +
120G GLY* 1.3 59.7 + - - +
122G ALA* 3.7 2.0 - - - +
123G LEU* 2.9 36.6 + - + +
145G LEU* 3.7 8.7 - - + +
153G LEU* 3.2 37.3 - - + +
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Residues in contact with GLY 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 GLN 3.7 7.1 + - - -
117G PHE 3.6 7.5 + - - -
118G VAL 3.2 1.2 - - - -
119G GLN* 1.3 78.3 - - - +
121G LEU* 1.3 57.4 + - - +
124G CYS* 2.9 31.1 + - - +
152G TYR* 4.0 11.9 - - - -
153G LEU* 4.4 1.1 - - - +
156G LYS* 3.7 31.4 - - - +
116S GLU* 5.7 1.8 - - - -
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Residues in contact with LEU 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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79G PHE* 3.7 22.7 - - + -
82G LYS* 4.4 2.2 - - + -
83G ARG* 3.5 55.6 - - - +
86G TYR* 3.7 31.0 - - + -
90G MET* 5.5 5.6 - - + -
117G PHE 3.4 8.6 + - - +
118G VAL* 3.0 10.1 + - + +
120G GLY* 1.3 76.0 - - - +
122G ALA* 1.3 58.5 + - - +
124G CYS* 3.8 7.7 - - + +
125G THR* 2.9 35.2 + - - -
112S PHE* 5.9 1.3 - - + -
115S ASP* 6.1 4.0 - - + -
116S GLU* 5.4 7.2 - - - +
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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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86G TYR* 4.2 12.3 - - - +
107G ILE* 3.5 17.8 - - + +
110G ASP* 3.6 39.0 - - + +
111G LEU* 3.7 17.3 - - + +
118G VAL 2.9 10.8 + - - +
119G GLN 3.4 1.3 + - - +
120G GLY 3.4 0.2 - - - -
121G LEU* 1.3 76.3 - - - +
123G LEU* 1.3 58.7 + - - +
125G THR* 4.3 0.8 - - - -
126G LEU* 3.5 20.3 + - - +
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Residues in contact with LEU 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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111G LEU* 3.7 20.0 - - + -
119G GLN* 2.9 21.7 + - + +
120G GLY 4.0 1.3 - - - +
122G ALA* 1.3 78.4 - - - +
124G CYS* 1.3 59.3 + - - +
126G LEU* 3.9 2.1 - - + +
127G GLY* 3.0 24.6 + - - -
142G VAL* 4.5 11.7 - - + -
145G LEU* 4.2 19.7 - - + -
153G LEU* 3.9 24.9 - - + +
156G LYS* 3.9 28.9 - - + +
157G ALA* 4.3 12.1 - - - +
160G CYS* 4.1 29.5 - - + +
119S ILE* 4.6 4.0 - - - +
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Residues in contact with CYS 124 (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 MET* 3.7 11.7 - - + -
120G GLY 2.9 20.2 + - - +
121G LEU* 3.2 8.5 + - + +
123G LEU* 1.3 78.5 - - - +
125G THR* 1.3 56.3 + - - +
127G GLY* 3.3 0.7 + - - -
128G CYS* 2.9 30.2 + - - -
156G LYS* 4.5 5.8 - - - +
115S ASP* 3.6 41.7 - - + +
119S ILE* 3.6 30.1 - - + +
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Residues in contact with THR 125 (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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86G TYR* 3.2 48.4 + - + +
89G ALA* 4.1 11.0 - - + -
90G MET* 3.6 19.3 - - + +
103G MET* 4.6 1.3 - - - -
107G ILE* 4.3 12.3 - - + -
121G LEU 2.9 11.7 + - - -
122G ALA 4.8 1.8 - - - -
124G CYS* 1.3 75.7 - - - +
126G LEU* 1.3 58.5 + - - +
129G MET* 3.0 52.2 + - - +
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Residues in contact with LEU 126 (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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107G ILE* 4.4 12.9 - - + +
111G LEU* 4.6 2.5 - - + -
122G ALA 3.5 16.8 + - - +
123G LEU* 3.6 4.4 + - + +
124G CYS 3.4 0.2 - - - -
125G THR* 1.3 78.2 - - - +
127G GLY* 1.3 61.0 + - - +
130G GLY* 3.2 23.4 + - - +
134G MET* 3.8 31.2 - - + -
135G CYS* 5.0 6.3 - - - -
138G LEU* 3.7 37.5 - - + -
142G VAL* 3.7 16.2 - - + -
160G CYS* 3.6 23.0 - - - -
163G HIS* 3.5 10.9 - - - -
164G VAL* 5.2 3.8 - - + -
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Residues in contact with GLY 127 (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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123G LEU 3.0 16.4 + - - -
124G CYS 3.7 2.2 - - - -
125G THR 3.2 0.2 - - - -
126G LEU* 1.3 77.0 - - - +
128G CYS* 1.3 61.9 + - - +
159G LEU 5.3 0.4 - - - -
160G CYS* 4.1 6.5 - - - -
163G HIS* 3.0 37.2 + - - -
119S ILE* 4.6 12.1 - - - -
120S GLY* 3.6 13.7 - - - -
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Residues in contact with CYS 128 (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 MET* 3.7 28.0 - - + +
124G CYS* 2.9 34.2 + - - +
127G GLY* 1.3 77.1 - - - +
129G MET* 1.3 61.7 - - + +
163G HIS* 4.6 4.0 - - - -
18S LYS* 4.0 20.9 - - - +
19S TRP 4.4 5.1 - - - +
20S TYR* 4.1 28.1 - - + +
22S THR* 5.4 2.9 - - - +
115S ASP* 4.1 1.3 - - - -
119S ILE* 4.0 5.6 - - - -
120S GLY* 3.6 25.0 - - - +
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Residues in contact with MET 129 (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 3.3 17.9 - - - +
90G MET* 3.7 28.5 - - + +
93G LEU* 3.5 34.5 - - + +
94G ASP* 4.0 18.3 - - - +
95G GLU* 4.9 1.7 + - - +
100G HIS* 4.5 0.2 - - - +
103G MET* 3.7 23.3 - - + +
125G THR* 3.0 30.6 + - - +
128G CYS* 1.3 82.5 - - + +
130G GLY* 1.3 67.0 + - - +
131G SER* 3.6 1.4 + - - -
134G MET* 4.6 3.6 - - - +
163G HIS* 4.9 0.9 - - - -
19S TRP 5.9 0.9 - - - +
22S THR* 5.2 8.3 - - + -
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Residues in contact with GLY 130 (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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95G GLU* 4.5 1.0 - - - +
125G THR 3.8 1.4 + - - -
126G LEU* 3.2 30.2 + - - -
129G MET* 1.3 79.4 - - - +
131G SER* 1.3 61.5 + - - -
134G MET* 3.9 15.0 - - - -
135G CYS* 4.7 0.9 - - - -
163G HIS* 2.9 24.6 + - - -
167G LYS* 3.3 12.1 + - - -
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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