Contacts of the strand formed by residues 172 - 178 (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 HIS 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D PRO* 4.2 23.1 - - + +
122D VAL* 4.0 15.9 - - + +
123D VAL 2.7 27.1 + - - +
124D LYS* 4.2 5.2 - - + -
125D SER* 3.0 32.4 + - - -
164D LYS* 3.4 3.6 - - - -
165D ILE* 2.9 45.1 + - + -
166D SER 3.7 21.1 - - - -
167D GLY* 3.9 12.9 - - - -
168D MET 5.2 0.4 + - - -
171D ILE* 1.3 75.0 - - - +
173D VAL* 1.3 61.9 + - - +
174D CYS* 3.7 2.1 + - - -
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Residues in contact with VAL 173 (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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122D VAL* 3.6 1.7 - - - -
123D VAL* 3.0 35.9 + - + +
130D THR* 4.0 21.6 + - + +
133D ALA* 3.9 30.5 - - + -
134D LEU* 4.3 16.8 - - + -
137D ILE* 4.5 14.4 - - + -
162D ASP* 5.8 0.7 - - + -
163D PHE 3.9 5.8 - - - +
164D LYS* 4.7 4.9 - - - +
171D ILE* 4.0 18.8 + - + -
172D HIS* 1.3 71.4 - - - +
174D CYS* 1.3 70.8 + - - +
175D MET* 4.4 9.4 - - + -
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Residues in contact with CYS 174 (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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120D MET* 4.6 7.4 - - + -
121D LYS 3.2 5.8 - - - +
122D VAL* 4.1 17.3 - - - -
162D ASP* 3.3 8.2 - - - +
163D PHE* 2.8 70.1 + - + +
165D ILE* 3.9 28.5 - - - -
172D HIS 3.9 6.5 - - - -
173D VAL* 1.3 80.2 - - - +
175D MET* 1.3 63.0 + - - +
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Residues in contact with MET 175 (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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119D ALA 3.8 0.7 - - - +
120D MET* 3.4 2.1 - - - -
121D LYS* 2.8 53.9 + - + +
123D VAL* 4.1 10.3 - - + -
133D ALA* 3.9 31.2 - - + +
136D GLU* 3.5 38.4 - - - +
137D ILE* 3.4 29.2 - - + -
140D LEU* 4.3 2.7 - - - -
159D LEU* 3.7 4.5 - - + -
161D ASP 3.7 4.9 - - - -
173D VAL* 4.4 2.2 - - + -
174D CYS* 1.3 75.2 - - - +
176D VAL* 1.3 63.9 + - - +
177D PHE* 3.6 31.1 - - + -
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Residues in contact with VAL 176 (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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92D TYR* 3.9 23.3 - - + -
118D VAL* 3.7 37.9 - - + -
119D ALA 3.5 4.3 - - - +
120D MET* 4.4 10.5 - - + -
159D LEU* 3.7 4.3 - - - +
160D ILE* 2.8 40.6 + - + +
161D ASP* 2.9 26.1 + - + +
163D PHE* 3.8 27.8 - - + -
175D MET* 1.3 75.0 - - - +
177D PHE* 1.3 59.1 + - - +
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Residues in contact with PHE 177 (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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118D VAL* 3.5 8.1 - - - +
119D ALA* 2.9 37.4 + - + +
121D LYS* 4.1 20.2 - - + -
136D GLU* 5.3 2.5 - - - -
140D LEU* 3.9 16.2 - - + -
157D VAL* 3.3 34.3 - - + -
158D GLN 3.5 14.6 - - - +
159D LEU* 3.8 17.5 - - + -
160D ILE* 3.5 6.1 - - - -
175D MET* 3.6 46.2 - - + -
176D VAL* 1.3 76.2 - - - +
178D GLU* 1.3 68.5 + - - +
180D LEU* 5.5 2.7 - - + -
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Residues in contact with GLU 178 (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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116D ARG* 3.6 29.6 + - - +
117D PHE 4.8 1.6 - - - +
118D VAL* 4.7 3.8 - - - +
119D ALA* 4.3 2.9 - - - +
158D GLN* 4.5 12.3 + - + +
160D ILE* 3.4 11.3 - - + +
177D PHE* 1.3 82.4 - - - +
179D VAL* 1.3 65.6 + - - +
180D LEU* 3.4 32.5 + - + +
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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