Contacts of the helix formed by residues 147 - 159 (chain C) in PDB entry 4I6J
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 GLU 147 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C PHE 3.3 3.0 + - - -
146C THR* 1.3 83.2 + - - +
148C GLU* 1.3 64.1 + - - +
149C GLU 3.3 0.8 - - - +
150C GLU* 3.6 16.8 - - - +
151C ALA* 2.8 37.9 + - + +
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C THR* 3.5 5.1 + - - +
147C GLU* 1.3 77.7 - - - +
149C GLU* 1.3 71.8 + - + +
150C GLU 3.1 0.2 + - - -
151C ALA* 3.1 3.5 + - - -
152C GLN* 2.8 48.9 + - + +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 2.5 38.5 + - - -
145C PHE* 3.6 17.4 - - + -
146C THR* 2.9 44.9 + - - +
148C GLU* 1.3 86.3 - - + +
150C GLU* 1.3 57.8 + - - +
152C GLN* 3.8 8.0 - - - +
153C VAL* 3.1 29.4 + - - +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.6 18.4 + - + +
136C ARG* 2.9 27.0 + - - -
143C ASN* 3.0 26.1 + - - -
145C PHE* 3.7 28.9 - - + +
146C THR 5.1 0.2 - - - +
147C GLU* 3.4 19.1 + - - +
148C GLU 3.1 0.6 - - - -
149C GLU* 1.3 78.9 - - - +
151C ALA* 1.3 58.1 + - - +
153C VAL* 3.3 5.8 + - - +
154C ARG* 3.1 26.9 + - + +
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLU* 2.8 34.4 + - - +
148C GLU* 4.0 3.6 - - - +
150C GLU* 1.3 68.5 - - - +
152C GLN* 1.3 66.4 + - - +
153C VAL 3.1 1.8 - - - -
154C ARG* 3.2 18.0 - - + +
155C LYS* 3.1 23.9 + - - +
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Residues in contact with GLN 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C GLU* 2.8 40.3 + - + +
149C GLU* 3.8 7.6 - - - +
151C ALA* 1.3 77.8 - - - +
153C VAL* 1.3 61.6 + - + +
155C LYS* 3.7 17.3 - - - +
156C GLU* 3.3 39.9 + - - +
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.5 24.2 - - + -
67B ASN* 3.9 33.7 - - - +
145C PHE* 4.6 9.6 - - + -
149C GLU 3.1 16.5 + - - +
150C GLU* 3.3 10.2 + - - +
151C ALA 3.1 0.6 - - - -
152C GLN* 1.3 76.9 - - + +
154C ARG* 1.3 60.5 + - - +
155C LYS 3.1 1.6 - - - -
156C GLU* 3.4 10.4 + - - +
157C ASN* 2.8 54.4 + - - +
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Residues in contact with ARG 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.9 21.7 - - - +
150C GLU* 3.1 14.7 + - - +
151C ALA* 3.2 23.1 - - - +
153C VAL* 1.3 77.3 - - - +
155C LYS* 1.3 61.4 + - + +
157C ASN* 3.7 8.2 - - - +
158C GLN* 3.2 36.8 + - - +
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Residues in contact with LYS 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ALA 3.1 16.9 + - - +
152C GLN* 3.7 18.8 - - - +
153C VAL 3.1 0.4 - - - -
154C ARG* 1.3 76.0 - - - +
156C GLU* 1.3 70.2 + - - +
158C GLN* 3.1 37.8 - - - +
159C TRP* 3.7 24.2 + - + +
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Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B HIS* 4.7 3.8 + - - -
101B GLN* 4.1 19.0 + - - +
105B ARG* 4.5 10.3 + - - -
152C GLN* 3.3 32.6 + - + +
153C VAL* 3.9 9.2 - - - +
155C LYS* 1.3 81.9 - - + +
157C ASN* 1.3 64.6 + - - +
159C TRP* 3.1 57.9 - - + +
160C CYS* 4.1 5.6 + - - -
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Residues in contact with ASN 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 3.9 9.9 - - - +
57B ALA* 3.2 46.6 + - + +
58B HIS* 5.3 8.1 - - + +
60B SER* 3.7 4.6 + - - -
61B GLN* 3.8 11.7 + - - +
70B PHE* 4.6 5.9 - - - -
153C VAL* 2.8 47.9 + - - +
154C ARG* 3.7 7.4 - - - +
155C LYS 3.1 0.6 - - - -
156C GLU* 1.3 77.0 - - - +
158C GLN* 1.3 56.9 + - - +
159C TRP 3.0 5.2 - - - -
160C CYS* 3.0 26.0 + - - +
161C GLU* 5.1 0.2 - - - -
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Residues in contact with GLN 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B HIS* 4.2 9.0 + - - +
154C ARG* 3.2 24.8 + - - +
155C LYS* 3.1 35.9 + - - +
157C ASN* 1.3 72.9 - - - +
159C TRP* 1.3 70.4 + - + +
160C CYS 3.0 6.6 + - - -
161C GLU* 3.1 43.1 + - - +
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Residues in contact with TRP 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B HIS* 3.1 49.2 + + + +
97B GLU* 3.2 47.3 - - + +
98B LEU* 3.6 22.9 - - + +
101B GLN* 3.5 32.1 - - + -
155C LYS* 3.7 30.4 + - + +
156C GLU* 3.1 50.0 - - + +
157C ASN 3.0 0.6 - - - -
158C GLN* 1.3 83.9 - - + +
160C CYS* 1.3 56.8 + - - +
161C GLU 3.2 5.8 + - - +
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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