Contacts of the strand formed by residues 153 - 158 (chain D) in PDB entry 3M4D
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 153 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE* 3.5 22.6 - - + +
81D PRO 3.8 18.8 - - - -
82D SER 4.6 1.3 - - - -
84D PHE* 3.8 19.7 - + - -
151D PRO* 3.3 20.3 - - - +
152D ASP* 1.3 88.4 - - + +
154D LYS* 1.3 63.6 + - - +
155D THR 4.2 0.2 + - - -
169D VAL* 3.8 27.4 - - + -
170D ILE 3.1 9.2 - - - +
171D PHE* 3.4 39.0 - + - -
172D ASN* 4.1 0.9 - - - +
217D SER* 3.5 27.1 - - - -
219D LEU* 4.0 21.1 - - + -
220D LEU* 3.9 14.6 - - + -
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Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASP* 5.0 10.7 + - - -
151D PRO* 4.3 14.1 - - + -
153D PHE* 1.3 75.3 - - - +
155D THR* 1.3 61.3 + - - +
156D ILE* 3.9 18.8 - - + +
168D LYS 3.6 1.4 - - - +
169D VAL* 3.2 5.1 - - - -
170D ILE* 2.9 42.6 + - + +
172D ASN* 3.5 34.1 - - + +
214E ASN 3.1 25.0 + - - +
215E LYS* 4.4 3.6 - - - +
216E ALA 3.6 20.4 + - - +
218E SER* 5.5 3.4 - - - +
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE* 3.8 20.4 - - - +
103D PRO* 4.4 16.4 - - + -
104D ARG 5.0 5.9 - - - +
105D ASN* 4.4 4.3 - - - +
154D LYS* 1.3 73.7 - - - +
156D ILE* 1.3 63.6 + - - +
167D TRP* 4.7 5.2 - - + -
168D LYS 3.8 2.2 - - - -
169D VAL* 3.9 15.2 - - + +
224D PHE* 5.1 2.5 - - + -
228D PHE* 4.1 25.6 - - + -
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Residues in contact with ILE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ASN* 3.4 12.6 - - - +
154D LYS* 4.3 18.8 - - + +
155D THR* 1.3 79.9 - - - +
157D LEU* 1.3 64.6 + - - +
158D GLU 3.5 0.5 + - - -
167D TRP* 3.1 10.2 - - - +
168D LYS* 2.9 59.8 + - + +
170D ILE* 3.8 30.7 - - + -
214E ASN* 5.0 5.2 - - - +
218E SER* 4.3 20.6 - - - -
222E SER* 3.3 30.3 - - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 3.7 26.0 - - + -
103D PRO 3.9 4.9 - - - +
104D ARG* 3.9 24.8 - - - -
105D ASN* 2.9 35.7 + - - +
156D ILE* 1.3 72.1 - - - +
158D GLU* 1.3 67.9 + - - +
160D PRO* 4.4 4.0 - - + -
165D VAL* 3.8 23.1 - - + -
166D GLY 3.6 15.7 - - - +
167D TRP* 3.7 22.1 - - + +
60E THR* 4.0 7.4 - - + +
222E SER* 3.2 8.7 - - - +
225E SER* 3.8 19.5 - - - +
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LYS* 2.8 34.6 + - - +
87D GLN* 3.1 32.2 + - - +
157D LEU* 1.3 78.3 - - - +
159D SER* 1.3 67.4 + - - +
160D PRO* 2.9 13.1 - - - +
166D GLY* 2.7 36.8 + - - +
167D TRP* 3.8 12.9 + - - +
168D LYS* 3.9 17.7 + - + +
222E SER* 4.0 8.1 - - - +
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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