Contacts of the strand formed by residues 85 - 89 (chain G) in PDB entry 4EMG
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 85 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 5.5 1.3 - - + -
81D ARG* 3.0 28.8 - - - +
24G VAL* 4.0 3.6 - - + -
26G LEU* 3.9 16.4 - - + -
27G ARG* 5.8 0.2 - - - -
43G LEU* 4.0 20.2 - - + +
45G MSE 3.4 26.5 - - + -
80G VAL* 4.3 2.0 - - + -
81G ARG 4.0 7.4 - - - +
82G GLY 3.0 14.5 + - - +
83G ASP 3.4 0.2 - - - -
84G SER* 1.3 76.1 - - - +
86G ILE* 1.3 61.3 + - - +
87G LEU 3.9 9.0 - - - +
88G ILE* 3.7 34.8 - - + -
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Residues in contact with ILE 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 4.1 12.1 - - + -
27D ARG 6.0 1.8 - - - +
30D ARG* 4.8 12.1 - - - +
79D PHE* 3.9 0.4 - - - +
81D ARG* 2.9 32.6 + - - +
84D SER* 3.8 24.5 - - - +
25G LYS* 2.8 24.1 + - + +
26G LEU 3.6 19.7 - - - +
27G ARG* 3.7 35.2 - - + +
28G GLY 4.9 0.7 - - - +
85G VAL* 1.3 78.4 - - - +
87G LEU* 1.3 78.4 + - + +
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Residues in contact with LEU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.3 7.9 - - + -
30D ARG* 4.6 4.3 - - - -
32D LEU* 4.4 2.5 - - + -
52D GLU* 3.9 33.4 - - + +
75D TYR* 4.3 5.4 - - - +
78D LEU* 4.0 33.4 - - + -
79D PHE* 3.2 11.7 - - - +
80D VAL* 4.2 15.0 - - + -
23G TYR* 4.4 3.6 - - + +
24G VAL* 3.4 5.4 - - - +
25G LYS* 3.0 43.7 + - + +
85G VAL* 3.9 0.2 - - - +
86G ILE* 1.3 98.8 - - + +
88G ILE* 1.3 71.6 + - - +
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Residues in contact with ILE 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D LEU* 3.8 3.0 - - - -
79D PHE* 2.8 48.6 + - + +
13G LEU* 4.1 4.6 - - + +
14G VAL* 3.8 33.2 - - + -
17G SER* 5.7 0.9 - - - +
22G VAL* 4.3 24.2 - - + -
23G TYR 3.3 8.3 - - - +
24G VAL* 4.4 6.5 - - + -
36G LEU* 6.0 0.7 - - + -
43G LEU* 4.3 13.2 - - + -
45G MSE 3.8 23.3 - - + -
85G VAL* 3.7 20.2 - - + -
87G LEU* 1.3 79.7 - - - +
89G ALA* 1.3 63.6 + - - +
90G PRO* 4.5 1.3 - - + -
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Residues in contact with ALA 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D TYR* 3.5 36.6 - - + -
77D MSE 3.7 10.3 - - - +
78D LEU* 4.2 2.7 - - + -
22G VAL* 3.4 3.8 - - - -
23G TYR* 2.8 47.0 + - + +
88G ILE* 1.3 78.3 - - - +
90G PRO* 1.3 71.8 - - + +
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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