Contacts of the helix formed by residues 127 - 140 (chain E) in PDB entry 2F4V
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 ASN 127 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A C 3.2 32.5 + - - -
19A C 3.7 13.6 + - - +
87E SER* 3.8 1.4 + - - -
125E SER* 2.9 15.4 + - - +
126E ARG* 1.3 76.3 - - - +
128E PRO* 1.3 66.4 - - - +
129E ILE* 2.6 40.5 + - - +
130E ASN* 2.8 24.2 + - - +
131E ILE* 2.7 31.9 + - - +
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Residues in contact with PRO 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 5.1 8.3 - - - +
11E ILE* 6.0 1.8 - - + -
12E LEU* 4.5 23.6 - - + -
31E LEU* 4.5 4.0 - - + -
105E VAL* 4.1 24.7 - - + -
126E ARG 3.1 8.0 - - - +
127E ASN* 1.3 92.3 - - - +
129E ILE* 1.3 75.0 + - + +
130E ASN 2.9 0.2 + - - -
131E ILE* 2.9 0.8 + - + -
132E ALA* 2.6 29.4 + - - +
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Residues in contact with ILE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078A U 3.6 19.7 - - + +
1079A G 5.1 4.5 - - - -
12E LEU* 4.0 28.0 - - + -
14E ARG* 4.3 18.8 - - - +
31E LEU* 4.2 15.6 - - + +
45E PHE* 4.3 27.6 - - + -
127E ASN* 2.6 28.8 + - - +
128E PRO* 1.3 80.7 - - + +
130E ASN* 1.3 57.0 + - - +
132E ALA* 3.8 2.1 - - - +
133E TYR* 2.9 55.6 + - + -
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Residues in contact with ASN 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A C 4.1 2.4 + - - -
19A C 3.2 25.7 + - - -
1078A U 2.7 42.9 + - - +
84E PHE* 3.7 19.4 - - + +
85E GLY* 5.3 3.7 - - - -
87E SER* 3.0 21.3 + - - +
127E ASN* 2.8 23.5 + - - +
129E ILE* 1.3 76.6 - - - +
131E ILE* 1.3 54.2 + - - +
133E TYR* 3.3 5.9 - - - +
134E ALA* 2.5 38.5 + - - +
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Residues in contact with ILE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E SER* 3.6 17.3 - - - -
88E LYS 3.8 16.8 - - - +
89E ILE* 4.5 5.4 - - + +
105E VAL* 3.6 19.5 - - + -
106E PRO* 4.1 7.4 - - + -
122E GLU* 3.1 45.8 - - + +
125E SER 3.7 13.2 - - - +
126E ARG 3.5 20.6 - - - +
127E ASN 2.7 16.9 + - - +
128E PRO* 3.7 3.1 - - + +
130E ASN* 1.3 72.1 - - - +
132E ALA* 1.3 62.1 + - - +
134E ALA* 3.6 3.3 - - + +
135E THR* 3.0 24.1 + - - +
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Residues in contact with ALA 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ILE* 5.4 0.4 - - + -
31E LEU* 3.9 15.0 - - + -
43E LEU* 4.4 9.9 - - + -
105E VAL* 3.2 25.9 - - + +
109E ILE* 4.3 13.2 - - + -
128E PRO 2.6 15.2 + - - +
129E ILE 3.8 3.4 - - - +
131E ILE* 1.3 71.0 - - - +
133E TYR* 1.3 67.0 + - - +
135E THR* 2.7 21.2 + - - +
136E MET* 2.9 16.6 + - - +
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Residues in contact with TYR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078A U 4.4 4.5 - - - -
1079A G 3.9 20.0 + - - -
31E LEU* 5.5 1.1 - - + -
43E LEU* 4.5 21.5 - - + +
45E PHE* 4.6 17.8 + - + +
65E ASN* 5.9 4.3 - - - -
84E PHE* 3.3 43.6 - + + -
129E ILE* 2.9 49.1 + - + +
130E ASN 2.9 2.6 + - - +
132E ALA* 1.3 72.4 - - - +
134E ALA* 1.3 61.7 + - - +
136E MET* 3.5 10.8 - - + +
137E GLU* 3.5 19.2 + - - +
140E ARG* 5.1 0.2 + - - -
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Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E VAL* 3.2 25.5 - - + +
84E PHE* 3.7 25.9 - - + +
87E SER* 4.7 4.9 - - - +
89E ILE* 4.0 11.4 - - + -
130E ASN 2.5 19.5 + - - +
131E ILE* 3.6 7.4 - - - +
133E TYR* 1.3 71.8 - - - +
135E THR* 1.3 67.5 - - - +
137E GLU* 3.0 3.3 + - - -
138E ALA 2.7 20.6 + - - -
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Residues in contact with THR 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ILE* 3.7 13.3 - - - +
91E LEU* 5.0 5.3 - - + +
106E PRO* 3.4 28.8 - - + +
109E ILE* 3.5 37.2 - - + -
110E LEU* 4.9 4.7 - - + -
131E ILE 3.0 12.0 + - - -
132E ALA* 2.7 16.8 + - - -
134E ALA* 1.3 74.5 - - - +
136E MET* 1.3 60.2 + - - +
138E ALA* 2.6 29.7 - - - +
139E LEU* 2.9 12.8 + - + +
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Residues in contact with MET 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E VAL* 3.8 9.4 - - + +
42E GLY* 3.9 2.9 - - - -
43E LEU* 3.5 48.7 - - + +
65E ASN* 4.0 10.3 - - - +
67E VAL* 3.7 33.6 - - + +
109E ILE* 3.7 29.4 - - + -
132E ALA 2.9 13.7 + - - +
133E TYR* 3.5 13.2 - - + +
134E ALA 3.1 0.2 - - - -
135E THR* 1.3 71.5 - - - +
137E GLU* 1.3 51.7 + - - +
138E ALA 2.6 6.4 + - - -
139E LEU* 2.6 30.1 + - - +
140E ARG* 2.7 32.7 + - - +
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Residues in contact with GLU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E VAL* 4.0 10.1 - - + +
84E PHE* 5.5 11.0 - - + -
133E TYR 3.5 7.9 + - - +
134E ALA* 3.0 9.5 + - - +
136E MET* 1.3 74.9 - - - +
138E ALA* 1.3 50.7 + - - +
140E ARG* 3.1 45.2 - - - +
141E GLN* 2.7 54.1 + - - +
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Residues in contact with ALA 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ILE* 4.7 12.6 - - + +
82E VAL* 3.9 22.6 - - + +
89E ILE* 4.1 7.6 - - + -
91E LEU* 4.4 13.0 - - + -
134E ALA 2.7 11.2 + - - +
135E THR* 2.6 21.5 - - - +
136E MET 2.6 0.2 + - - -
137E GLU* 1.3 74.1 - - - +
139E LEU* 1.3 66.4 + - - +
141E GLN* 2.7 20.0 + - - +
142E LEU* 3.5 6.7 + - - +
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E VAL* 4.9 3.8 - - + -
67E VAL* 4.2 9.6 - - + -
69E VAL* 3.8 30.3 - - + -
70E PRO* 5.4 2.7 - - - +
76E ILE* 4.8 7.9 - - + -
91E LEU* 4.3 11.4 - - + -
109E ILE* 3.8 28.9 - - + +
110E LEU* 3.8 26.7 - - + -
113E ALA* 5.2 0.9 - - + -
135E THR* 3.5 11.0 - - + +
136E MET* 2.6 14.3 + - - +
138E ALA* 1.3 67.9 - - - +
140E ARG* 1.3 52.5 - - - +
141E GLN 2.2 20.8 + - - -
142E LEU* 2.6 41.4 + - + +
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Residues in contact with ARG 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ASN* 2.9 40.9 + - - +
66E MET 5.3 4.2 + - - -
67E VAL* 3.9 24.5 - - + +
133E TYR 5.1 0.4 + - - -
136E MET* 2.7 35.1 + - - +
137E GLU* 3.1 68.2 - - - +
139E LEU* 1.3 69.2 - - - +
141E GLN* 1.3 60.3 + - - +
142E LEU 3.6 0.6 - - - +
143E ARG* 3.6 15.8 + - - -
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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