Contacts of the strand formed by residues 42 - 46 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R PRO* 3.5 5.7 - - - +
41R ASP* 1.3 84.0 - - + +
43R LEU* 1.3 61.5 + - - +
44R PHE* 4.5 13.0 - - + -
66R LEU* 3.6 37.0 - - + +
67R HIS 3.3 2.6 + - - +
68R ALA* 3.1 14.6 - - + -
69R LEU 2.9 24.3 + - - -
95R PRO* 4.4 2.0 - - - -
97R VAL* 3.3 36.6 - - + +
99R VAL* 4.9 2.7 - - + -
213R ILE* 4.0 21.3 - - + -
217R LEU* 4.7 4.9 - - + -
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Residues in contact with LEU 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R PRO* 5.2 1.8 - - + -
42R VAL* 1.3 76.7 - - - +
44R PHE* 1.3 61.5 + - - +
45R VAL* 3.8 25.4 - - + -
69R LEU* 3.6 27.4 - - + +
71R PHE* 3.9 28.7 - - + -
85R LEU* 5.3 0.4 - - + -
89R GLU 5.0 0.4 - - - +
90R LEU* 5.0 7.9 - - + -
93R ILE* 4.1 20.4 - - + -
95R PRO* 4.0 8.3 - - + -
97R VAL 3.0 5.7 + - - -
98R ILE* 3.2 36.5 - - + +
99R VAL* 2.7 32.3 + - - -
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Residues in contact with PHE 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R VAL* 4.5 10.3 - - + -
43R LEU* 1.3 74.9 - - - +
45R VAL* 1.3 57.2 + - - +
50R VAL* 3.5 22.5 - - + +
53R MET* 4.4 10.1 - - + -
59R TRP* 3.5 33.7 - + - -
63R PHE* 4.0 26.7 - + + -
68R ALA* 3.9 17.9 - - + -
69R LEU 2.8 15.8 + - - +
70R ASN* 3.9 5.2 - - - +
71R PHE* 2.7 35.2 + - - +
99R VAL* 3.5 31.0 - - + -
209R LEU* 3.8 26.0 - - + -
213R ILE* 4.4 4.9 - - + -
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Residues in contact with VAL 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R LEU* 3.8 19.1 - - + -
44R PHE* 1.3 75.1 - - - +
46R GLY* 1.3 58.2 + - - +
50R VAL* 3.5 8.9 - - - +
71R PHE* 3.9 19.1 - - + +
81R VAL* 5.0 8.1 - - + -
84R ARG* 4.8 5.2 - - - +
85R LEU* 3.8 26.0 - - + -
98R ILE* 3.8 14.4 - - + -
99R VAL 2.9 17.7 + - - +
100R VAL* 3.5 22.7 - - + -
101R TRP 3.1 22.3 + - - -
102R VAL* 4.9 1.1 - - - -
125R ILE* 5.0 4.5 - - + -
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Residues in contact with GLY 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45R VAL* 1.3 77.4 - - - +
47R ASP* 1.3 61.8 + - - -
50R VAL* 3.7 5.0 - - - +
71R PHE 3.9 5.1 + - - -
72R GLY* 3.3 1.1 - - - -
73R ILE 3.1 21.8 + - - +
81R VAL* 4.0 12.5 - - - +
84R ARG* 3.3 10.6 + - - +
101R TRP 3.3 10.8 - - - -
102R VAL* 3.7 13.5 - - - -
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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