Contacts of the helix formed by residues 156 - 167 (chain R) in PDB entry 4M8B
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 ARG 156 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R TYR* 3.4 24.5 - - + +
12R ASP* 3.7 21.5 + - - +
13R ASP* 2.8 35.8 + - - -
15R GLN* 5.3 0.2 - - - +
16R ASP* 2.8 21.3 + - - +
154R LEU 3.9 2.8 + - - +
155R ARG* 1.3 74.8 - - - +
157R PRO* 1.3 70.8 - - + +
158R SER* 3.2 18.9 + - - +
159R GLU* 3.0 48.0 + - + +
160R ASN* 3.3 12.6 + - - +
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Residues in contact with PRO 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R TYR 5.6 1.3 - - - +
9R GLY* 5.2 0.2 - - - -
10R TYR 3.3 16.6 - - - +
11R ILE* 3.8 20.4 - - + -
16R ASP* 3.4 24.5 - - + +
19R LEU* 3.7 7.4 - - + +
20R VAL* 3.9 11.4 - - + -
50R ILE* 5.1 3.4 - - + -
155R ARG 3.7 4.0 - - - +
156R ARG* 1.3 82.8 - - - +
158R SER* 1.3 56.5 + - - +
160R ASN* 3.0 27.2 + - + +
163R PHE* 3.4 46.1 - - + +
164R HIS* 5.3 0.7 - - - -
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Residues in contact with SER 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R GLN* 4.0 19.5 - - - -
16R ASP* 2.6 22.8 + - - -
19R LEU* 3.4 19.3 - - - +
156R ARG* 3.2 23.0 + - - -
157R PRO* 1.3 76.5 - - - +
159R GLU* 1.3 62.6 + - - +
160R ASN 3.4 1.3 - - - -
164R HIS* 4.6 11.3 + - - -
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Residues in contact with GLU 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155R ARG* 3.1 19.3 + - + -
156R ARG* 3.0 48.4 + - + +
158R SER* 1.3 87.7 + - - +
160R ASN* 1.3 58.8 + - - +
161R PRO* 3.7 4.3 - - - +
164R HIS* 5.3 2.2 - - - -
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Residues in contact with ASN 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R TYR 4.8 5.7 + - - -
155R ARG* 3.5 36.4 + - + +
156R ARG 3.4 14.6 - - - +
157R PRO* 3.0 12.3 + - + +
158R SER 3.4 1.0 - - - -
159R GLU* 1.3 76.9 - - - +
161R PRO* 1.3 59.8 - - - +
162R PHE* 3.0 19.7 + - - +
163R PHE* 2.8 53.3 + - + +
164R HIS* 3.8 6.8 + - - -
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Residues in contact with PRO 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R ARG* 3.2 20.0 - - - +
159R GLU 3.7 3.6 - - - +
160R ASN* 1.3 86.0 - - - +
162R PHE* 1.3 63.1 + - - +
163R PHE 3.2 0.4 - - - -
164R HIS* 3.2 45.3 + - + +
165R LYS* 4.7 1.7 + - - -
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Residues in contact with PHE 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R CYS* 5.9 0.4 - - + -
28R ASN* 5.4 4.9 - - + -
29R LEU* 3.8 20.4 - - + -
160R ASN* 2.8 19.0 + - - +
161R PRO* 1.3 78.9 - - - +
163R PHE* 1.3 79.2 + + - +
164R HIS 3.6 0.3 + - - -
165R LYS* 2.7 43.1 + - - +
166R PHE* 3.6 30.2 - + - -
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Residues in contact with PHE 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R CYS* 3.9 27.1 - - + -
8R TYR 4.2 13.5 - - - -
19R LEU* 3.4 24.5 - - + +
20R VAL* 4.3 3.6 - - + -
29R LEU* 3.9 22.9 - - + -
157R PRO* 3.4 42.6 - - + +
160R ASN* 2.8 37.9 + - + -
162R PHE* 1.3 91.8 - + - +
164R HIS* 1.3 55.6 + - - +
165R LYS 3.2 2.9 - - - -
166R PHE* 2.8 49.3 + + + +
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Residues in contact with HIS 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R LEU* 5.0 4.8 - - + +
157R PRO 5.3 1.3 - - - -
158R SER* 4.6 14.6 + - - -
159R GLU 5.3 0.8 - - - -
160R ASN 4.0 6.4 + - - -
161R PRO* 3.2 44.5 + - + +
162R PHE 3.3 0.2 - - - -
163R PHE* 1.3 77.2 - - - +
165R LYS* 1.3 57.6 + - - +
166R PHE 3.1 4.0 + - - -
167R ARG* 3.3 18.2 + - - +
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Residues in contact with LYS 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R ASN* 4.2 9.2 + - - -
28R ASN* 4.0 14.8 - - - +
161R PRO 4.7 1.6 + - - -
162R PHE* 2.7 52.6 + - - +
164R HIS* 1.3 77.3 - - - +
166R PHE* 1.3 83.3 + - + +
167R ARG* 3.2 7.1 + - - +
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Residues in contact with PHE 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R LEU* 3.2 28.0 - - - +
22R GLN* 3.2 17.9 - - - +
23R GLY* 3.4 22.2 - - - +
26R ASN* 4.1 8.7 - - - -
28R ASN* 3.3 47.6 - - + -
29R LEU* 4.2 6.7 - - + -
162R PHE* 3.6 34.5 - + - -
163R PHE* 2.8 39.3 + + - +
165R LYS* 1.3 100.7 - - + +
167R ARG* 1.3 65.9 + - - +
168R PRO* 3.2 3.5 - - - +
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Residues in contact with ARG 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R LEU* 4.0 3.6 - - - -
22R GLN* 3.5 9.5 - - - +
164R HIS 3.3 13.8 + - - +
165R LYS 3.2 5.8 + - - +
166R PHE* 1.3 75.4 - - - +
168R PRO* 1.3 98.7 + - + +
169R SER* 3.7 6.1 + - - +
170R GLN 5.6 0.6 - - - +
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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