Contacts of the strand formed by residues 133 - 137 (chain M) 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 LYS 133 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96M LYS 3.0 13.9 + - - +
97M VAL* 3.3 10.8 - - + +
98M ILE 3.0 22.0 + - - -
131M GLN 4.6 5.4 - - - +
132M ALA* 1.3 73.2 - - - +
134M ILE* 1.3 59.7 + - - +
169M ASN* 4.1 25.1 - - + +
216M LEU* 3.8 46.0 - - + +
219M GLU* 4.6 15.4 - - - +
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Residues in contact with ILE 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M ILE* 3.4 13.0 - - + +
100M VAL* 4.6 10.8 - - + -
122M VAL* 4.4 11.9 - - + +
125M ILE* 4.2 23.3 - - + -
126M ASN* 3.8 34.5 - - + +
132M ALA 3.9 9.2 - - - +
133M LYS* 1.3 77.6 - - - +
135M ILE* 1.3 70.8 + - - +
136M VAL* 4.2 8.1 - - + -
168M ALA 4.2 1.6 - - - +
169M ASN 2.9 22.0 + - - +
170M VAL* 3.3 22.7 - - + -
171M GLN* 3.0 28.9 + - - +
216M LEU* 5.8 0.2 - - - -
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Residues in contact with ILE 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M VAL* 3.9 9.6 - - + -
98M ILE 2.8 11.2 + - - +
99M VAL* 3.3 7.5 - - + -
100M VAL* 2.7 33.3 + - - +
134M ILE* 1.3 77.4 - - - +
136M VAL* 1.3 57.6 + - - +
137M LEU* 4.0 13.8 + - + -
171M GLN* 3.5 6.3 - - + +
173M LEU* 4.1 14.8 - - + -
209M LEU* 4.0 22.9 - - + -
212M LEU* 3.9 17.3 - - + -
213M ILE* 3.5 32.8 - - + -
216M LEU* 3.7 27.8 - - + -
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Residues in contact with VAL 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100M VAL* 3.4 20.6 - - + +
101M TRP* 5.6 0.2 - - - -
102M VAL 6.0 0.2 - - - +
118M ILE* 4.0 23.3 - - + -
122M VAL* 3.9 28.0 - - + -
134M ILE* 4.2 7.2 - - + -
135M ILE* 1.3 77.9 - - - +
137M LEU* 1.3 74.7 + - - +
138M GLY 3.5 0.5 + - - -
160M LEU* 4.4 13.2 - - + -
164M LEU* 4.0 20.2 - - + -
170M VAL* 4.2 3.1 - - + -
171M GLN 2.9 10.4 + - - +
172M LEU* 3.3 3.9 - - + +
173M LEU 2.8 26.4 + - - -
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Residues in contact with LEU 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M PHE* 6.2 0.2 - - + -
53M MET* 5.0 2.5 - - + -
99M VAL* 4.3 12.1 - - + -
100M VAL 3.0 9.6 + - - +
101M TRP* 3.1 70.1 - - + +
102M VAL 5.1 1.2 + - - +
118M ILE* 5.7 1.2 - - - +
135M ILE* 4.0 3.8 - - + -
136M VAL* 1.3 82.3 - - - +
138M GLY* 1.3 60.9 + - - +
139M LEU* 3.9 2.6 + - - +
160M LEU* 5.5 0.7 - - - +
173M LEU* 3.4 24.5 - - + +
175M THR* 5.0 5.2 - - - +
205M ILE* 4.5 11.0 - - + -
209M LEU* 3.6 42.0 - - + -
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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