Contacts of the strand formed by residues 30 - 34 (chain C) in PDB entry 1EV2
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 PHE 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 4.6 0.2 - - - -
25C CYS* 2.8 32.7 + - + +
27C ASN 3.4 13.9 + - - -
28C GLY* 3.8 13.5 - - - -
29C GLY* 1.3 78.2 - - - +
31C PHE* 1.3 63.6 + - - +
32C LEU 3.8 0.2 + - - -
42C GLY* 3.9 8.3 - - - -
43C VAL* 3.5 23.3 - - - +
44C ARG* 2.9 47.8 - - + -
118C LEU* 4.2 9.6 - - + -
119C LYS 3.5 15.7 - - - -
120C ARG 3.3 27.8 - - - -
121C THR 3.6 5.8 - - - -
122C GLY* 3.5 23.6 - - - -
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Residues in contact with PHE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 4.0 29.4 - - + -
23C LEU 3.5 2.2 - - - +
24C TYR* 3.7 33.4 - + + -
29C GLY 5.2 0.9 - - - -
30C PHE* 1.3 73.9 - - - +
32C LEU* 1.3 64.6 + - - +
33C ARG* 3.2 4.3 + - - +
42C GLY* 3.3 2.3 - - - -
43C VAL 2.7 41.7 + - - +
44C ARG* 3.7 21.3 - - - -
45C GLU 4.5 0.7 - - - -
46C LYS* 3.8 27.1 - - + -
51C ILE* 3.9 26.4 - - + +
118C LEU* 4.7 0.2 - - - -
142C MET* 3.9 16.2 - - + -
166G LEU* 3.5 28.5 - - + -
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 2.9 46.2 + - + +
30C PHE 3.8 1.2 + - - -
31C PHE* 1.3 71.6 - - - +
33C ARG* 1.3 64.0 + - - +
34C ILE* 5.1 3.6 - - + -
40C VAL* 3.8 25.8 - - + -
41C ASP 3.9 6.3 - - - +
51C ILE* 3.5 22.3 - - - +
53C LEU* 4.1 15.6 - - + +
65C ILE* 5.1 1.3 - - + -
74C LEU* 4.2 25.6 - - + -
82C LEU* 5.4 1.1 - - + -
116C VAL* 4.5 15.7 - - + -
118C LEU* 4.2 22.5 - - + +
139C PHE* 4.4 10.1 - - + -
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Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C PHE 4.1 3.6 - - - +
32C LEU* 1.3 74.7 - - - +
34C ILE* 1.3 68.7 + - - +
35C HIS* 4.5 6.3 - - + +
39C ARG 3.9 0.5 - - - +
40C VAL* 3.5 10.4 - - - +
41C ASP* 2.7 71.3 + - - +
43C VAL* 2.9 30.4 - - + +
48C ASP* 2.7 43.6 + - - -
50C HIS* 3.5 23.1 - - + +
51C ILE* 4.0 7.4 - - + -
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 5.1 5.2 - - + -
33C ARG* 1.3 76.3 - - - +
35C HIS* 1.3 64.0 + - - +
39C ARG 3.9 2.7 - - - +
40C VAL* 4.5 10.1 - - + -
50C HIS* 2.9 28.3 + - - +
53C LEU* 3.6 26.0 - - + -
65C ILE* 4.3 7.0 - - + +
67C GLY* 3.7 22.7 - - - +
70C ALA* 3.4 24.5 + - + +
72C ARG* 4.5 2.7 - - + +
74C LEU* 4.3 29.8 - - + +
84C ALA* 3.3 29.4 - - + -
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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