Contacts of the strand formed by residues 42 - 46 (chain F) 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 42 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F PRO* 3.6 6.1 - - - +
41F ASP* 1.3 94.2 - - + +
43F LEU* 1.3 65.1 + - - +
44F PHE* 3.5 25.8 - - + -
66F LEU* 3.9 24.2 - - + +
67F HIS 3.3 1.6 + - - -
68F ALA* 3.2 10.5 - - + -
69F LEU 2.9 23.3 + - - -
95F PRO* 4.3 1.8 - - - -
97F VAL* 3.3 22.4 - - + +
99F VAL* 5.1 1.6 - - + -
213F ILE* 4.5 13.9 - - + -
217F LEU* 4.4 15.9 - - + -
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F PRO* 5.2 2.5 - - + -
42F VAL* 1.3 76.8 - - - +
44F PHE* 1.3 76.1 + - - +
45F VAL* 3.7 20.4 - - + -
69F LEU* 3.6 20.4 - - + +
71F PHE* 3.8 28.9 - - + -
89F GLU 4.7 0.9 - - - +
90F LEU* 4.5 14.4 - - + -
93F ILE* 4.7 11.9 - - + -
95F PRO* 4.0 22.0 - - + -
97F VAL 3.0 7.5 + - - +
98F ILE* 3.3 26.5 - - + +
99F VAL 2.8 25.1 + - - -
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Residues in contact with PHE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F VAL* 3.5 23.8 - - + -
43F LEU* 1.3 78.5 - - - +
45F VAL* 1.3 57.5 + - - +
50F VAL* 3.5 21.6 - - + +
53F MET* 3.9 23.6 - - - -
59F TRP* 3.9 20.9 - + - -
63F PHE* 3.8 30.3 - + - -
68F ALA* 4.2 7.9 - - + -
69F LEU 2.8 19.6 + - - +
70F ASN* 4.0 4.3 - - - +
71F PHE* 2.7 34.7 + - - +
99F VAL* 3.6 23.1 - - + +
101F TRP* 6.6 0.2 - + - -
137F LEU* 6.0 0.2 - - + -
209F LEU* 4.2 14.4 - - + -
213F ILE* 4.2 11.4 - - + -
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Residues in contact with VAL 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU* 3.7 26.4 + - + -
44F PHE* 1.3 78.9 - - - +
46F GLY* 1.3 59.2 + - - +
50F VAL* 3.6 8.9 - - - +
71F PHE* 4.1 17.9 - - + +
81F VAL* 5.0 10.8 - - + -
84F ARG* 6.0 1.1 - - - +
85F LEU* 4.1 24.7 - - + -
89F GLU* 5.4 0.4 - - - +
98F ILE* 4.5 5.2 - - + -
99F VAL 2.9 14.0 + - - +
100F VAL* 3.5 25.1 - - + -
101F TRP* 3.1 18.7 + - - +
125F ILE* 5.1 2.2 - - + -
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Residues in contact with GLY 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F VAL* 1.3 77.6 - - - +
47F ASP* 1.3 62.8 + - - -
50F VAL* 3.5 3.7 - - - +
71F PHE 4.0 5.9 + - - -
72F GLY* 3.3 1.7 - - - -
73F ILE 3.1 20.4 + - - +
76F ASP* 4.4 0.2 - - - +
81F VAL* 3.9 22.1 - - - +
84F ARG* 3.3 10.4 + - - +
101F TRP 3.3 13.0 - - - -
102F VAL* 4.3 2.5 - - - -
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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