Contacts of the strand formed by residues 153 - 158 (chain D) in PDB entry 1VYH
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 VAL 153 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D THR* 2.9 27.2 + - - +
126D ALA* 3.8 14.2 - - + +
127D SER 2.8 20.9 + - - +
130D ALA* 3.3 11.0 - - + +
131D THR 3.1 31.6 - - - +
132D ILE* 3.9 18.8 - - + +
149D HIS* 3.4 27.4 - - + +
152D SER* 1.3 73.8 - - - +
154D GLN* 1.3 60.9 + - - +
155D ASP 3.8 2.2 - - - +
167D SER* 4.0 8.1 - - - +
168D CYS 3.1 9.4 - - - +
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Residues in contact with GLN 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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37B ASP* 6.1 2.2 - - - +
112D THR* 3.7 24.6 - - + +
113D ARG* 3.0 31.8 + - - +
126D ALA* 5.1 0.4 - - - -
128D GLU* 4.8 8.7 + - - -
152D SER* 3.6 22.3 + - - +
153D VAL* 1.3 75.2 - - - +
155D ASP* 1.3 57.0 + - - +
168D CYS 2.7 10.5 + - - -
169D SER 3.6 2.6 - - - -
170D ALA 3.3 24.4 + - - -
194D ASN* 3.7 18.0 + - - +
195D VAL 3.7 16.2 - - - +
196D SER* 3.9 21.8 - - - +
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Residues in contact with ASP 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ARG* 3.1 37.2 + - - +
126D ALA* 5.0 0.4 - - - -
153D VAL* 4.5 2.9 - - - +
154D GLN* 1.3 76.5 - - - +
156D ILE* 1.3 75.3 + - - +
167D SER* 3.5 4.5 - - - -
168D CYS* 3.1 30.8 + - - +
196D SER 4.1 0.9 - - - +
197D SER* 2.9 33.0 + - - -
198D VAL* 3.0 33.4 + - + +
241D ARG* 3.6 11.3 + - - -
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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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113D ARG* 3.7 18.6 - - + +
115D ILE* 3.1 38.6 - - + +
124D VAL* 3.8 14.6 - - + +
125D SER* 3.8 5.8 - - - -
126D ALA* 3.2 41.7 - - + +
132D ILE* 5.2 9.2 - - + -
155D ASP* 1.3 91.4 + - - +
157D SER* 1.3 66.9 + - - +
165D LEU* 3.5 26.0 - - + -
166D ALA 3.4 7.4 - - - +
167D SER* 5.3 1.6 - - - -
198D VAL* 4.3 3.3 - - - +
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Residues in contact with SER 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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115D ILE* 3.8 5.6 - - - -
156D ILE* 1.3 77.3 - - - +
158D PHE* 1.3 66.5 + - - +
165D LEU* 3.6 2.4 - - - -
166D ALA* 2.9 36.3 + - - -
198D VAL* 3.6 8.3 - - - -
199D SER* 3.5 25.1 - - - -
200D ILE* 3.1 27.9 + - - +
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Residues in contact with PHE 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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115D ILE* 3.6 36.5 - - + +
116D PHE 3.7 11.2 - - - +
117D HIS* 3.5 30.5 - + + -
118D PRO* 3.9 16.8 - - + -
124D VAL* 3.7 13.5 - - + -
157D SER* 1.3 82.2 + - - +
159D ASP* 1.3 67.9 + - - +
162D GLY* 4.6 5.6 - - - -
164D LEU 3.5 14.8 - - - -
165D LEU* 3.3 18.8 - - + -
179D PHE* 3.2 44.2 - + - -
200D ILE* 3.8 7.0 - - - +
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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