Contacts of the strand formed by residues 85 - 89 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24I VAL* 4.1 2.0 - - + -
26I LEU* 3.8 18.2 - - + -
27I ARG* 5.5 0.4 + - - -
43I LEU* 4.1 15.7 - - + +
45I MSE 3.3 26.2 - - + -
80I VAL* 4.2 2.2 - - + -
81I ARG 4.0 9.0 - - - +
82I GLY* 3.0 15.2 + - - +
84I SER* 1.3 76.4 - - - +
86I ILE* 1.3 63.3 + - - +
87I LEU 4.0 8.5 - - - +
88I ILE* 3.7 33.4 - - + -
79L PHE* 5.4 0.9 - - + -
81L ARG* 2.9 33.9 - - + +
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Residues in contact with ILE 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LYS* 2.9 23.5 + - + +
26I LEU 3.6 20.4 - - - +
27I ARG* 3.6 36.6 - - + +
28I GLY 4.9 0.7 - - - +
85I VAL* 1.3 79.2 - - - +
87I LEU* 1.3 76.5 + - + +
26L LEU* 4.1 11.7 - - + -
27L ARG 6.1 0.9 - - - +
30L ARG* 4.9 11.4 - - - +
79L PHE* 4.9 0.4 - - - -
80L VAL* 4.5 0.2 - - - +
81L ARG* 2.9 32.8 + - - +
84L SER* 3.7 24.7 - - - +
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I TYR* 4.4 4.0 - - + -
24I VAL* 3.3 5.5 - - - +
25I LYS* 3.0 44.2 + - + -
86I ILE* 1.3 100.7 - - + +
88I ILE* 1.3 70.1 + - - +
26L LEU* 4.4 7.4 - - + -
30L ARG* 4.6 5.4 - - - -
32L LEU* 4.4 2.0 - - + -
52L GLU* 3.9 32.8 - - + +
75L TYR* 4.2 7.9 - - - +
78L LEU* 4.1 23.1 - - + -
79L PHE 3.3 11.0 - - - +
80L VAL* 4.2 22.4 - - + -
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Residues in contact with ILE 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LEU* 4.1 4.3 - - + +
14I VAL* 3.9 31.9 - - + -
17I SER* 5.6 1.6 - - - +
22I VAL* 4.3 23.3 - - + -
23I TYR 3.3 8.5 - - - +
24I VAL* 4.4 7.0 - - + -
36I LEU* 6.1 0.4 - - + -
43I LEU* 4.3 9.9 - - + -
45I MSE 3.8 24.9 - - + -
85I VAL* 3.7 20.2 - - + -
87I LEU* 1.3 80.4 - - - +
89I ALA* 1.3 62.5 + - - +
90I PRO* 5.0 0.9 - - + -
78L LEU* 4.0 2.6 - - - -
79L PHE* 2.7 55.9 + - + +
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Residues in contact with ALA 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I VAL* 3.4 3.8 - - - -
23I TYR* 2.9 44.8 + - + +
88I ILE* 1.3 78.1 - - - +
90I PRO* 1.3 71.3 - - + +
75L TYR* 3.5 37.2 - - + -
77L MSE 3.8 9.2 - - - +
78L LEU* 4.2 2.2 - - + -
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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