Contacts of the helix formed by residues 108 - 121 (chain F) in PDB entry 2I2R
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 108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C PHE* 4.5 4.9 - + - -
37F GLU* 5.2 3.1 - - + -
42F LEU* 3.7 26.7 - - + -
53F LEU* 4.2 7.0 - - + -
56F LEU 4.0 1.8 - - - -
57F TYR* 3.4 61.9 - + + -
60F PHE* 3.4 52.7 - + + -
67F GLY 4.2 2.9 + - - +
107F LYS* 1.3 73.1 - - - +
109F GLU* 1.3 70.7 + - - +
111F PHE* 2.8 24.7 + + - +
112F VAL* 2.9 42.0 + - + +
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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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37F GLU* 3.6 34.3 + - - +
38F GLY 4.9 0.5 + - - -
42F LEU* 4.3 16.9 - - + +
45F GLN* 5.4 4.9 - - - +
107F LYS* 4.0 16.4 - - + +
108F PHE* 1.3 88.4 + - - +
110F ASP* 1.3 61.5 + - - +
112F VAL* 3.3 12.0 - - - +
113F THR* 2.6 34.7 + - - +
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Residues in contact with ASP 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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98F PHE* 4.2 21.2 - - + -
99F ASP* 5.7 1.9 + - - -
100F THR* 5.7 3.9 + - - -
101F THR* 3.2 29.6 + - - -
103F THR* 5.3 1.0 - - - +
105F SER 4.4 2.9 - - - +
106F VAL* 3.9 9.3 - - + +
107F LYS* 3.1 30.6 + - - +
109F GLU* 1.3 81.1 - - - +
111F PHE* 1.3 63.9 + - - +
113F THR* 3.2 5.5 + - - -
114F ALA* 3.0 24.6 + - - +
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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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7B ALA* 4.2 9.2 - - + -
8B TRP* 3.4 62.4 - + - -
11B PHE* 3.6 16.2 - + - -
56F LEU* 4.5 13.0 - - + -
60F PHE* 3.8 27.4 - + + -
98F PHE* 4.1 13.8 - + + -
106F VAL* 6.0 3.4 - - + -
107F LYS 3.3 3.2 + - - +
108F PHE* 2.8 22.6 + + - +
110F ASP* 1.3 80.0 - - - +
112F VAL* 1.3 66.3 + - + -
114F ALA* 3.5 3.3 - - - +
115F LEU* 3.2 48.4 + - + +
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Residues in contact with VAL 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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42F LEU* 4.0 20.9 - - + -
46F THR* 4.7 4.9 - - + -
48F PHE* 3.8 6.2 - - + -
53F LEU* 4.1 15.9 - - + -
56F LEU* 4.5 15.3 - - + -
108F PHE* 2.9 50.5 + - + +
109F GLU* 3.3 22.2 - - - +
111F PHE* 1.3 82.3 - - + +
113F THR* 1.3 55.1 + - - +
115F LEU* 3.4 5.0 + - - +
116F SER* 2.7 35.0 + - - -
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Residues in contact with THR 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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42F LEU* 5.8 0.7 - - - +
45F GLN* 5.2 8.0 + - - +
46F THR* 4.5 12.0 - - + +
109F GLU 2.6 24.9 + - - -
110F ASP* 3.7 6.1 + - - -
112F VAL* 1.3 73.1 - - - +
114F ALA* 1.3 68.6 + - - +
116F SER* 2.8 9.7 + - - -
117F ILE* 2.7 42.1 + - + +
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Residues in contact with ALA 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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11B PHE* 3.2 29.8 - - + -
98F PHE* 3.5 16.8 - - + -
110F ASP 3.0 16.9 + - - +
111F PHE 3.5 1.6 - - - +
113F THR* 1.3 77.4 - - - +
115F LEU* 1.3 56.3 + - - +
117F ILE* 3.1 7.9 + - - +
118F LEU* 2.8 31.2 + - - +
129F TRP* 4.3 18.2 - - - +
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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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7B ALA* 3.5 13.2 - - - +
10B PRO* 3.7 22.4 - - + -
11B PHE* 3.6 14.8 - - + -
48F PHE* 4.0 10.9 - - + -
56F LEU* 4.0 14.6 - - + -
111F PHE* 3.2 48.9 + - + +
112F VAL* 3.7 5.6 - - - +
113F THR 3.2 0.6 - - - -
114F ALA* 1.3 76.1 - - - +
116F SER* 1.3 61.1 + - - +
118F LEU* 4.2 3.4 - - + +
119F LEU* 2.8 67.1 + - + +
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Residues in contact with SER 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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46F THR* 3.5 18.5 - - - -
47F ASN* 3.0 35.1 + - - +
48F PHE* 3.8 15.4 - - - -
112F VAL 2.7 21.7 + - - -
113F THR* 3.2 9.4 - - - -
115F LEU* 1.3 72.8 - - - +
117F ILE* 1.3 58.2 + - - +
120F ARG* 3.1 13.3 + - - +
121F GLY 3.1 19.4 + - - -
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Residues in contact with ILE 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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47F ASN* 5.4 0.2 - - - -
113F THR* 2.7 34.5 + - + +
114F ALA* 3.5 6.3 - - - +
116F SER* 1.3 77.2 - - - +
118F LEU* 1.3 62.8 + - - +
121F GLY* 2.9 27.8 + - - +
125F GLU* 3.5 51.8 - - + +
126F LYS* 4.0 8.9 - - - +
129F TRP* 4.2 26.9 - - + -
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Residues in contact with LEU 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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10B PRO* 3.7 22.6 - - + +
11B PHE* 3.2 39.5 - - + -
14B ALA* 4.0 16.6 - - + -
114F ALA 2.8 12.5 + - - +
115F LEU* 4.0 4.7 - - - +
117F ILE* 1.3 80.7 - - + +
119F LEU* 1.3 66.6 + - + +
126F LYS* 4.5 16.3 - - + +
129F TRP* 3.5 46.0 - - + -
209F LEU* 5.2 7.3 - - - +
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Residues in contact with LEU 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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10B PRO* 3.7 33.0 - - + -
48F PHE* 4.2 13.2 - - + -
56F LEU* 6.0 0.4 - - + -
115F LEU* 2.8 39.1 + - + +
118F LEU* 1.3 75.1 - - - +
120F ARG* 1.3 77.9 + - + +
210F GLN 5.7 0.5 - - - +
212F PHE* 5.4 2.3 - - - -
213F GLN* 4.0 38.7 + - + +
214F ASN 5.5 0.2 - - - -
215F VAL* 4.3 22.0 - - + +
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Residues in contact with ARG 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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47F ASN* 3.0 50.5 + - + +
48F PHE* 3.6 20.4 - - + -
52F GLU* 2.8 35.0 + - - -
116F SER 3.1 12.5 + - - +
117F ILE 3.5 0.6 + - - -
119F LEU* 1.3 89.5 + - + +
121F GLY* 1.3 71.5 + - - +
212F PHE* 3.8 24.5 - - - -
213F GLN 4.1 6.1 + - - -
214F ASN* 4.6 2.0 + - - +
215F VAL 4.0 18.2 - - - +
210O GLN* 5.4 5.4 - - - +
212O PHE* 3.3 41.9 + - + +
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Residues in contact with GLY 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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47F ASN* 4.4 4.9 - - - -
116F SER 3.1 7.6 + - - -
117F ILE* 2.9 19.4 + - - +
120F ARG* 1.3 84.6 - - - +
122F THR* 1.3 68.5 + - - +
123F VAL 3.9 0.3 + - - -
125F GLU* 3.6 16.8 - - - -
126F LYS* 5.0 2.4 - - - +
210O GLN* 4.6 2.6 - - - +
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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