Contacts of the strand formed by residues 159 - 165 (chain D) in PDB entry 5MYV
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 LEU 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ILE* 3.9 31.6 - - + +
140D LEU* 4.0 33.4 + - + +
141D LYS* 4.6 4.7 - - + -
144D ARG* 3.1 40.7 + - - +
157D VAL 4.0 2.6 + - - -
158D GLN* 1.3 71.1 + - - +
160D ILE* 1.3 59.3 + - - +
161D ASP 3.3 23.3 - - - +
162D ASP* 4.0 13.0 - - + +
175D MET* 3.7 27.6 - - + -
176D VAL 3.8 5.4 - - - +
177D PHE* 3.8 15.8 - - + -
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Residues in contact with ILE 160 (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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91D ARG* 5.9 3.4 - - - +
92D TYR* 4.7 7.2 - - + +
111D ASP* 5.8 3.4 - - - +
116D ARG* 3.9 30.1 - - - +
118D VAL* 4.2 11.9 - - + -
144D ARG* 4.2 8.7 + - - -
158D GLN* 4.2 5.8 - - + +
159D LEU* 1.3 74.2 - - - +
161D ASP* 1.3 64.7 + - + +
176D VAL* 2.8 19.5 + - + +
177D PHE 3.5 7.4 - - - +
178D GLU* 3.4 35.7 - - + +
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Residues in contact with ASP 161 (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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89D ASN* 3.2 25.5 + - - -
91D ARG* 3.9 10.8 + - - +
92D TYR* 2.8 30.4 + - - +
144D ARG* 5.3 2.0 - - - +
159D LEU* 3.3 12.8 - - - +
160D ILE* 1.3 81.3 - - + +
162D ASP* 1.3 85.3 + - - +
163D PHE* 4.6 1.3 - - - -
176D VAL* 2.9 34.6 + - + -
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Residues in contact with ASP 162 (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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89D ASN* 5.1 0.3 + - - -
137D ILE* 3.9 35.5 - - + +
141D LYS* 3.7 25.9 + - - -
144D ARG* 5.2 1.9 + - - -
159D LEU* 4.0 6.9 - - + +
161D ASP* 1.3 90.3 + - - +
163D PHE* 1.3 69.0 + - - +
173D VAL* 5.8 1.1 - - + -
174D CYS 3.3 13.0 - - - +
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Residues in contact with PHE 163 (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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88D PHE* 3.9 19.5 - + + -
89D ASN* 3.6 38.1 - - + +
92D TYR* 3.8 24.9 - + - -
120D MET* 3.8 19.3 - - - -
161D ASP* 4.6 0.2 - - - -
162D ASP* 1.3 83.7 - - - +
164D LYS* 1.3 73.6 + - - +
165D ILE* 3.7 16.8 - - + -
173D VAL* 3.8 4.3 - - - +
174D CYS* 2.8 54.5 + - + +
176D VAL* 3.8 13.2 - - + -
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Residues in contact with LYS 164 (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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130D THR* 5.5 1.0 - - - +
134D LEU* 4.3 32.8 - - - +
163D PHE* 1.3 84.2 - - - +
165D ILE* 1.3 70.4 + - - +
171D ILE* 4.0 35.6 - - + +
172D HIS 3.4 9.6 - - - +
173D VAL* 4.9 4.3 - - + -
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Residues in contact with ILE 165 (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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81D PRO* 4.5 6.1 - - + +
82D VAL* 4.1 21.1 - - + -
88D PHE* 3.7 33.4 - - + -
89D ASN 6.0 0.2 - - - +
120D MET* 5.9 0.2 - - + -
122D VAL* 4.5 3.1 - - + -
163D PHE* 3.7 24.5 - - + -
164D LYS* 1.3 80.4 - - - +
166D SER* 1.3 66.9 + - - +
171D ILE* 3.5 6.5 - - - +
172D HIS* 2.9 53.7 + - + +
174D CYS* 3.9 13.7 - - - -
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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