Contacts of the helix formed by residues 156 - 163 (chain A) in PDB entry 4MYF
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 THR 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASN* 5.5 9.6 - - - +
115A ASP* 4.9 1.3 - - - -
142A ASP* 3.1 25.6 - - - -
143A VAL* 3.0 16.3 - - - +
144A ARG* 2.7 48.8 + - + +
155A GLY* 1.3 74.1 - - - -
157A PRO* 1.3 73.2 - - + +
159A ARG* 3.3 4.8 + - - +
160A GLN* 3.3 18.9 + - - +
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Residues in contact with PRO 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 3.3 22.9 - - + +
115A ASP* 3.8 19.5 - - - +
117A SER* 4.0 6.1 - - - -
118A ALA* 3.6 35.1 - - + +
142A ASP* 3.9 15.3 - - - +
155A GLY 3.5 0.4 - - - +
156A THR* 1.3 89.8 - - + +
158A PHE* 1.3 75.9 + - + +
160A GLN* 3.4 6.4 - - - +
161A LEU* 3.2 29.9 + - - +
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 5.9 0.9 - - + -
117A SER* 3.7 14.8 - - - -
134A VAL* 3.8 20.9 - - + -
136A ASN* 3.3 39.5 - - + -
141A LEU 4.5 0.7 - - - +
142A ASP* 3.4 26.3 + - + +
143A VAL* 4.1 6.7 - - + -
156A THR 3.3 0.6 - - - -
157A PRO* 1.3 86.4 - - + +
159A ARG* 1.3 60.3 + - - +
161A LEU* 3.8 24.3 - - + +
162A LEU* 3.0 32.7 + - - +
172A PHE* 3.7 31.2 - + + -
224A PHE* 4.6 1.3 - + - -
226A SER* 3.5 25.8 - - - -
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ASP 3.7 4.0 + - - -
143A VAL* 2.9 32.5 + - + +
144A ARG 3.5 10.5 - - - +
145A PRO* 3.6 35.7 - - - +
156A THR* 3.3 19.4 + - - +
158A PHE* 1.3 76.3 - - - +
160A GLN* 1.3 66.2 + - + +
162A LEU* 3.4 1.1 + - - +
163A GLU* 3.0 45.1 + - - +
186A HIS* 5.4 1.0 - - - -
189A TYR* 3.4 51.6 + - + +
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Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP* 5.5 1.6 - - - +
118A ALA* 3.6 18.7 - - + +
122A ARG* 3.0 32.8 - - - +
155A GLY* 3.0 32.6 + - - +
156A THR 3.3 10.2 + - - +
157A PRO* 3.4 7.9 - - - +
159A ARG* 1.3 81.9 - - + +
161A LEU* 1.3 61.4 + - + +
163A GLU* 3.5 16.2 + - - +
164A GLU* 3.5 17.1 + - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A SER 3.6 19.5 - - - +
118A ALA* 3.4 23.3 - - + +
121A GLY* 3.7 21.1 - - - -
122A ARG* 3.7 16.4 - - + +
125A LEU* 4.4 9.2 - - + -
134A VAL* 5.0 9.0 - - + -
157A PRO 3.2 17.0 + - - +
158A PHE* 3.6 27.6 + - + +
159A ARG 3.2 0.2 - - - -
160A GLN* 1.3 78.1 - - - +
162A LEU* 1.3 64.1 + - - +
163A GLU 3.1 1.6 - - - -
164A GLU* 3.1 21.1 + - + +
167A PHE* 3.4 24.3 - - + +
224A PHE* 4.7 3.8 - - + -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A VAL* 4.2 7.0 - - + -
158A PHE 3.0 21.5 + - - +
159A ARG 3.4 0.9 + - - +
161A LEU* 1.3 76.0 - - - +
163A GLU* 1.3 59.8 + - - +
164A GLU 3.2 6.0 + - - +
167A PHE* 3.9 26.7 - - + +
169A GLY* 4.1 18.4 - - - -
172A PHE* 3.9 34.5 - - + -
189A TYR* 3.6 37.2 - - + +
190A VAL* 4.4 10.1 - - + +
193A HIS* 3.7 29.0 - - + -
195A GLY* 5.8 0.4 - - - -
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG* 3.0 45.4 + - - +
160A GLN* 3.8 10.1 - - - +
161A LEU 3.1 0.8 - - - -
162A LEU* 1.3 77.7 - - - +
164A GLU* 1.3 60.6 + - - +
165A SER* 3.5 3.8 + - - -
189A TYR* 3.3 18.0 + - - +
193A HIS* 5.4 2.5 - - - +
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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