Contacts of the helix formed by residues 107 - 129 (chain G) in PDB entry 6C3P
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 TYR 107 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G ILE* 4.2 19.0 - - + +
92G GLY* 4.3 2.5 - - - -
93G ILE* 4.1 40.2 - - + +
96G ASP* 5.1 9.6 - - + -
102G HIS* 5.1 2.0 + - - +
103G HIS 4.6 2.7 - - - -
104G LEU* 3.3 41.9 - - + +
106G LEU* 1.3 82.7 - - + +
108G MET* 1.3 82.6 + - + +
109G PRO* 3.2 3.4 - - - -
110G ALA* 2.7 29.0 + - - +
111G GLY* 2.8 12.4 + - - -
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Residues in contact with MET 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G PHE* 5.9 4.9 - - + -
33G VAL* 5.6 5.8 - - + -
104G LEU* 3.0 47.3 + - + +
105G HIS* 4.8 0.9 - - - -
107G TYR* 1.3 91.2 - - + +
109G PRO* 1.3 66.7 - - + +
111G GLY* 3.2 4.0 + - - +
112G MET* 2.9 50.6 + - + +
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Residues in contact with PRO 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G PHE* 5.6 2.0 - - + -
29G ASP* 3.2 17.5 - - - +
32G ASN* 4.6 11.7 - - + +
33G VAL* 3.6 30.0 - - + -
36G HIS* 3.7 5.2 + - - -
88G GLU* 5.4 4.7 - - - +
105G HIS* 3.0 27.6 - - - +
106G LEU 4.0 7.4 - - - +
107G TYR 3.4 0.4 - - - -
108G MET* 1.3 94.2 - - + +
110G ALA* 1.3 57.8 + - - +
112G MET* 3.3 5.4 + - + +
113G ALA* 2.9 27.6 + - - +
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LEU* 3.8 9.2 - - + +
88G GLU* 3.8 34.0 + - + +
89G ILE* 3.5 24.2 - - + +
106G LEU 4.9 0.4 - - - +
107G TYR* 2.7 18.1 + - - +
109G PRO* 1.3 77.8 - - - +
111G GLY* 1.3 55.3 + - - +
113G ALA* 3.3 9.7 + - - +
114G PHE* 2.9 27.4 + - - +
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Residues in contact with GLY 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ILE* 4.1 14.0 - - - +
107G TYR* 2.8 12.7 + - - -
108G MET* 3.2 5.1 + - - -
110G ALA* 1.3 75.2 - - - +
112G MET* 1.3 71.2 + - - +
114G PHE* 3.2 6.6 + - - +
115G MET* 3.0 23.9 + - - +
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Residues in contact with MET 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G VAL* 4.0 21.8 - - + -
36G HIS* 3.7 19.7 - - + +
37G VAL* 5.2 8.3 - - + -
40G LEU* 4.5 19.2 - - + +
41G PHE* 6.4 1.8 - - - -
108G MET* 2.9 38.0 + - + +
109G PRO 3.7 7.4 - - - +
111G GLY* 1.3 79.1 - - - +
113G ALA* 1.3 57.0 + - - +
115G MET* 3.4 8.9 + - + +
116G ALA* 2.8 31.0 + - - +
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Residues in contact with ALA 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G HIS* 3.3 30.0 + - + -
81G LEU* 5.1 0.8 - - + +
85G LEU* 3.5 25.5 - - + +
109G PRO 2.9 11.3 + - - +
110G ALA* 3.4 9.4 - - - +
111G GLY 3.2 0.2 - - - -
112G MET* 1.3 74.0 - - - +
114G PHE* 1.3 59.5 + - - +
116G ALA* 3.8 1.2 - - - +
117G ALA* 2.8 33.3 + - - +
179G TYR* 4.7 5.8 - - - +
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Residues in contact with PHE 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G LEU* 3.4 37.2 - - + -
85G LEU* 4.5 10.2 - - + +
86G VAL* 5.5 6.5 - - + -
89G ILE* 4.2 18.6 - - + -
110G ALA 2.9 16.3 + - - +
111G GLY* 3.2 10.3 + - - +
113G ALA* 1.3 73.1 - - - +
115G MET* 1.3 68.3 + - + +
117G ALA* 3.3 4.8 + - - +
118G VAL* 3.0 38.6 + - + +
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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
----------------------------------------------------------
40G LEU* 3.9 20.2 - - + -
111G GLY 3.0 15.4 + - - +
112G MET* 3.8 10.1 - - + +
114G PHE* 1.3 81.8 - - + +
116G ALA* 1.3 57.9 + - - +
118G VAL* 3.3 6.5 + - - +
119G THR* 2.9 34.0 + - - +
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Residues in contact with ALA 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G HIS* 3.9 21.5 - - + +
39G LEU* 3.9 8.0 - - + +
40G LEU* 5.0 6.3 - - + -
112G MET 2.8 23.0 + - - +
113G ALA 3.3 3.1 + - - +
115G MET* 1.3 70.4 - - - +
117G ALA* 1.3 62.2 + - - +
119G THR* 3.3 7.1 + - - -
120G SER* 2.8 29.1 + - - -
142G TYR* 3.3 27.4 - - + +
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Residues in contact with ALA 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G THR* 5.2 8.3 - - + +
81G LEU* 3.6 29.4 - - + -
82G LEU* 5.7 6.3 - - + +
113G ALA 2.8 17.0 + - - +
114G PHE* 3.7 4.9 - - - +
116G ALA* 1.3 75.3 - - - +
118G VAL* 1.3 65.6 + - + +
120G SER* 2.4 26.7 + - - -
121G VAL* 2.9 14.6 + - - +
143G TRP* 5.4 7.2 - - + -
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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
----------------------------------------------------------
82G LEU* 4.9 9.0 - - + -
114G PHE* 3.0 39.1 + - + +
115G MET* 3.6 8.5 - - - +
117G ALA* 1.3 76.1 - - + +
119G THR* 1.3 60.2 + - - +
121G VAL* 3.2 10.0 + - + +
122G VAL* 3.0 38.5 + - + +
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Residues in contact with THR 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G LEU* 5.0 3.8 - - + -
40G LEU* 4.9 6.7 - - - +
43G THR* 3.5 26.5 - - - +
44G PHE* 3.6 34.3 - - + -
47G LEU* 6.0 4.5 - - + -
115G MET* 2.9 19.1 + - - +
116G ALA* 3.7 8.0 - - - -
117G ALA 3.2 0.2 - - - -
118G VAL* 1.3 75.6 - - - +
120G SER* 1.3 59.9 + - - +
122G VAL* 3.9 5.0 - - + +
123G TYR* 2.8 37.3 + - + +
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Residues in contact with SER 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G LEU* 4.3 10.9 - - - +
78G THR* 5.1 2.9 - - - +
116G ALA 2.8 13.1 + - - -
117G ALA* 2.4 33.7 + - - -
119G THR* 1.3 76.3 - - - +
121G VAL* 1.3 64.6 + - - +
123G TYR* 3.8 5.3 - - - +
124G TYR* 2.9 27.5 + - - +
139G LEU* 4.2 23.4 - - - +
142G TYR* 5.4 0.4 - - - -
143G TRP* 4.2 17.2 - - - -
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Residues in contact with VAL 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G TRP* 3.5 35.7 - - + -
78G THR* 3.5 29.6 - - + -
79G PHE* 6.2 1.6 - - + -
117G ALA 2.9 14.3 + - - +
118G VAL* 3.2 12.5 + - + +
120G SER* 1.3 84.1 + - - +
122G VAL* 1.3 71.0 + - + +
124G TYR* 3.3 3.0 + - - +
125G HIS* 2.9 23.3 + - + +
223G ASN* 6.1 0.4 - - - +
225G LEU* 5.6 7.9 - - + -
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Residues in contact with VAL 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G LEU* 4.6 14.8 - - + -
51G TRP* 5.8 5.8 - - + -
118G VAL* 3.0 29.5 + - + +
119G THR* 4.1 4.5 - - - +
121G VAL* 1.3 82.3 - - + +
123G TYR* 1.3 62.8 + - - +
125G HIS* 3.2 8.7 + - + +
126G ASN* 3.0 40.0 + - - +
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Residues in contact with TYR 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G LEU* 6.0 0.4 - - + -
43G THR* 4.0 28.2 - - + +
46G ILE* 3.3 42.4 - - + +
47G LEU* 4.5 19.5 - - + +
119G THR* 2.8 25.7 + - + +
120G SER* 3.8 4.0 - - - +
122G VAL* 1.3 77.5 - - - +
124G TYR* 1.3 66.6 + + - +
126G ASN* 3.1 3.6 + - - +
127G ILE* 2.9 56.8 + - + +
135G LEU* 3.5 24.7 + - - +
136G LEU* 5.1 2.7 - - - -
138G ALA* 5.2 2.5 - - + +
139G LEU* 3.6 33.4 - - + -
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Residues in contact with TYR 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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68G PHE* 3.1 39.3 + - + +
71G HIS* 5.8 3.1 - - - -
74G ARG* 3.1 39.6 + - - -
75G TRP* 4.9 17.9 - + + -
120G SER 2.9 18.5 + - - +
121G VAL* 4.0 2.7 - - - +
123G TYR* 1.3 82.0 - + + +
125G HIS* 1.3 59.1 + - - +
127G ILE* 4.3 11.7 - - + +
128G GLU* 2.8 44.8 + - + +
131G ASN* 5.8 4.5 - - + -
136G LEU* 5.2 14.8 - - + -
139G LEU* 5.8 9.6 - - + -
189G VAL* 5.3 3.3 - - + +
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Residues in contact with HIS 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G TRP* 5.2 10.7 - + + -
121G VAL* 2.9 14.9 + - + +
122G VAL* 3.5 13.3 - - - +
123G TYR 3.2 0.2 - - - -
124G TYR* 1.3 82.0 - - - +
126G ASN* 1.3 67.8 + - - +
127G ILE 3.3 0.2 + - - -
128G GLU* 3.3 17.4 + - + +
129G THR* 3.9 11.3 + - + +
221G PHE 5.6 2.8 + - - -
222G VAL* 6.2 0.4 - - - -
223G ASN* 3.9 36.5 + - + +
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Residues in contact with ASN 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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47G LEU* 3.4 32.2 - - + +
51G TRP* 4.7 15.6 - - - +
122G VAL* 3.0 30.3 + - - +
123G TYR 3.1 3.6 + - - +
125G HIS* 1.3 83.9 + - - +
127G ILE* 1.3 65.2 + - + +
129G THR* 3.3 22.1 + - - +
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Residues in contact with ILE 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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46G ILE 5.3 5.8 - - - +
47G LEU* 6.5 0.2 - - + -
123G TYR* 2.9 57.6 + - + +
124G TYR* 3.9 11.2 - - + +
126G ASN* 1.3 82.1 - - + +
128G GLU* 1.3 62.8 + - - +
129G THR 3.0 2.5 - - - -
130G SER 2.9 11.9 - - - +
131G ASN* 2.9 45.2 + - + -
132G PHE 4.4 4.9 - - - +
135G LEU* 5.5 6.7 - - + -
136G LEU* 4.8 20.0 - - + +
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G PHE* 5.4 11.7 - - + +
124G TYR* 2.8 40.3 + - + +
125G HIS* 3.3 13.2 + - + +
127G ILE* 1.3 76.9 - - - +
129G THR* 1.3 63.3 + - - +
131G ASN* 4.3 11.4 + - - +
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Residues in contact with THR 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLN* 5.1 1.0 - - - +
125G HIS* 4.1 14.8 - - + +
126G ASN* 3.3 19.4 + - - +
128G GLU* 1.3 81.1 - - + +
130G SER* 1.3 73.4 + - - -
131G ASN 3.8 1.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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