Contacts of the helix formed by residues 103 - 121 (chain F) in PDB entry 3TGX
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 PRO 103 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F PRO* 5.2 2.9 - - + +
30F GLU 3.9 4.7 - - - +
31F PHE* 3.6 38.1 - - + -
102F LYS* 1.3 95.2 - - + +
104F PRO* 1.3 78.9 - - + +
105F LYS* 3.1 3.6 + - + +
106F GLU* 2.8 33.9 + - - +
107F PHE* 3.0 18.3 + - - -
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Residues in contact with PRO 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F VAL* 3.8 18.8 - - + +
27F LEU* 4.3 22.4 - - + +
28F VAL 3.5 22.2 - - - +
29F PRO* 4.0 12.8 - - + -
30F GLU 3.3 15.7 - - - +
32F LEU* 4.8 3.6 - - + -
55F LEU* 4.5 13.2 - - + -
103F PRO* 1.3 87.9 - - + +
105F LYS* 1.3 62.3 + - - +
107F PHE* 3.5 7.1 - - + +
108F LEU* 3.1 30.6 + - - +
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Residues in contact with LYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LYS* 5.1 8.1 + - + +
24F VAL* 3.7 35.4 - - + +
103F PRO* 3.1 3.0 + - + +
104F PRO* 1.3 80.3 - - - +
106F GLU* 1.3 75.3 + - - +
108F LEU* 3.5 5.8 + - - +
109F GLU* 3.2 34.4 + - - +
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Residues in contact with GLU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LYS* 3.8 34.1 - - + +
103F PRO* 2.8 35.1 - - - +
105F LYS* 1.3 84.7 - - - +
107F PHE* 1.3 66.2 + - - +
109F GLU* 3.3 20.8 + - + +
110F ARG* 3.0 33.6 + - + +
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Residues in contact with PHE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 3.7 25.1 - - + -
33F PRO 3.5 22.9 - - - -
34F ALA* 3.8 17.9 - - + -
50F PHE* 3.6 34.7 - + + -
53F ALA* 3.6 29.2 - - + -
55F LEU* 4.2 20.4 - - + -
102F LYS* 4.1 7.4 - - - +
103F PRO 3.0 19.4 + - - +
104F PRO* 3.5 7.9 - - + +
106F GLU* 1.3 77.3 - - - +
108F LEU* 1.3 80.0 + - + +
110F ARG* 3.6 0.5 + - - +
111F PHE* 3.1 31.7 + + - +
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 3.4 34.1 - - + +
20F LEU* 3.6 43.3 - - + +
21F LYS* 3.8 15.0 - - + +
24F VAL* 5.4 1.8 - - + -
27F LEU* 4.8 10.8 - - + -
55F LEU* 4.1 15.5 - - + -
74F LEU* 5.5 0.4 - - + -
104F PRO* 3.1 22.6 + - + +
105F LYS* 3.8 6.3 - - - +
106F GLU 3.2 0.4 - - - -
107F PHE* 1.3 96.9 - - + +
109F GLU* 1.3 60.5 + - - +
111F PHE* 3.0 9.1 + - + +
112F LYS 3.0 22.7 + - - -
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Residues in contact with GLU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LYS* 3.7 28.1 + - - +
105F LYS* 3.2 26.2 - - - +
106F GLU* 3.3 33.1 + - + +
108F LEU* 1.3 76.9 - - - +
110F ARG* 1.3 59.5 + - + +
112F LYS* 3.5 6.7 + - + +
113F SER* 3.0 29.2 + - - -
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Residues in contact with ARG 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ALA* 3.1 31.2 + - + -
35F PRO 4.1 14.5 - - - +
36F GLU* 2.9 42.1 + - - +
50F PHE* 3.6 14.9 - - + -
100F GLU* 3.3 29.1 + - - +
102F LYS* 3.0 44.2 - - - +
106F GLU* 3.0 22.4 + - + +
107F PHE 3.9 4.7 - - - +
109F GLU* 1.3 75.6 - - + +
111F PHE* 1.3 64.6 + - - +
113F SER* 3.5 9.3 + - - +
114F LEU* 3.2 17.2 + - - +
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Residues in contact with PHE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 5.6 3.1 - - + -
17F VAL* 3.7 22.7 - - + -
47F PHE* 4.2 20.2 - + - -
50F PHE* 3.4 54.7 - + + -
51F GLN* 4.6 7.6 - - + -
74F LEU* 4.4 24.5 - - + -
107F PHE* 3.1 25.2 + + - +
108F LEU* 3.0 14.7 + - + +
110F ARG* 1.3 75.1 - - - +
112F LYS* 1.3 65.1 + - - +
113F SER 3.3 0.2 + - - -
114F LEU* 3.3 4.3 + - + +
115F LEU* 3.0 47.1 + - + +
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Residues in contact with LYS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 4.2 20.9 - - + -
17F VAL* 4.4 10.7 - - + +
18F ASP* 3.5 32.1 + - - +
21F LYS* 4.3 13.4 - - - +
108F LEU 3.0 11.0 + - - +
109F GLU* 3.7 11.2 - - + +
111F PHE* 1.3 75.8 - - - +
113F SER* 1.3 57.6 + - - +
115F LEU* 3.4 11.2 + - - +
116F GLN* 2.9 61.3 + - - +
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Residues in contact with SER 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLU 5.8 3.8 - - - -
109F GLU 3.0 18.0 + - - -
110F ARG* 3.7 10.7 - - - -
112F LYS* 1.3 75.0 - - - +
114F LEU* 1.3 67.1 + - - +
116F GLN* 3.2 13.5 + - - +
117F LYS* 3.0 36.7 + - - +
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PRO 5.8 0.9 - - - +
38F VAL* 4.2 23.6 - - + -
43F GLU* 4.2 15.9 - - + +
46F ALA* 3.8 1.3 - - + -
47F PHE* 3.4 43.3 - - + +
50F PHE* 3.4 24.2 - - + -
110F ARG 3.2 10.6 + - - +
111F PHE* 3.3 8.9 + - + +
113F SER* 1.3 77.9 - - - +
115F LEU* 1.3 58.3 + - + +
117F LYS* 3.2 17.3 + - + +
118F MET* 2.9 51.8 + - + +
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Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F MET* 4.2 19.6 - - - +
13F LEU* 3.5 42.6 - - + +
14F ILE* 3.7 17.9 - - + +
17F VAL* 4.4 4.9 - - + -
47F PHE* 3.8 33.4 - - + -
111F PHE* 3.0 38.3 + - + +
112F LYS* 3.6 4.9 - - - +
114F LEU* 1.3 76.5 - - + +
116F GLN* 1.3 62.9 + - - +
118F MET* 3.2 7.1 + - - +
119F ILE* 3.0 30.5 + - + +
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Residues in contact with GLN 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 3.7 20.5 - - + +
112F LYS* 2.9 54.8 + - - +
113F SER* 3.6 11.2 + - - +
115F LEU* 1.3 73.7 - - - +
117F LYS* 1.3 67.3 + - + +
119F ILE* 3.5 4.8 + - - +
120F HIS* 3.1 22.0 + - - +
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Residues in contact with LYS 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLU 4.2 5.7 + - - -
37F ASP* 2.5 52.7 + - - +
38F VAL* 4.5 3.9 - - + +
43F GLU* 5.0 4.5 - - - +
113F SER* 3.0 28.5 + - - +
114F LEU* 3.4 17.9 - - + +
116F GLN* 1.3 76.5 - - + +
118F MET* 1.3 66.0 + - + +
119F ILE 2.9 1.6 + - - -
120F HIS* 3.0 6.9 + - - +
121F GLN* 3.0 42.0 + - - +
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Residues in contact with MET 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F HIS* 5.7 3.3 - - + -
10F MET* 4.9 14.7 - - - +
43F GLU* 3.8 24.9 - - + +
44F TRP* 3.6 55.0 - - + +
47F PHE* 4.0 24.2 - - + -
114F LEU* 2.9 42.7 + - + +
115F LEU* 3.2 8.7 + - - +
117F LYS* 1.3 76.4 - - + +
119F ILE* 1.3 60.8 + - - +
121F GLN* 4.0 9.2 + - - +
122F HIS* 4.3 20.3 + - - -
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Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F MET* 4.0 30.8 - - + +
10F MET* 3.8 20.4 - - + +
11F ARG* 3.9 28.3 - - + +
14F ILE* 3.7 30.5 - - + -
115F LEU* 3.0 15.2 + - + +
116F GLN* 3.8 5.2 - - - +
117F LYS 2.9 0.2 + - - -
118F MET* 1.3 76.4 - - - +
120F HIS* 1.3 69.5 + - - +
121F GLN 3.4 0.5 + - - -
122F HIS* 3.5 12.6 + - - +
123F LEU 4.5 1.0 + - - -
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Residues in contact with HIS 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F GLN 3.1 13.9 + - - +
117F LYS* 3.0 6.0 + - - +
119F ILE* 1.3 81.5 - - - +
121F GLN* 1.3 54.7 + - + +
122F HIS 3.2 0.2 - - - -
123F LEU* 2.7 53.4 + - + +
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Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F GLU* 3.1 36.3 + - - +
117F LYS* 3.0 32.0 + - - +
118F MET* 4.5 5.8 - - - +
119F ILE 3.2 0.8 - - - -
120F HIS* 1.3 79.8 - - + +
122F HIS* 1.3 68.6 + - + +
123F LEU* 3.4 11.7 - - + +
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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