Contacts of the strand formed by residues 21 - 26 (chain L) 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 ILE 21 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L GLU* 1.3 76.2 + - - +
22L VAL* 1.3 67.3 + - - +
23L TYR 4.3 0.2 + - - -
33L ASN* 5.0 8.1 - - + +
34L GLY* 3.2 20.2 - - - +
35L ARG* 3.7 36.1 - - + +
90L PRO 4.2 0.2 - - - -
91L PRO* 3.2 30.4 - - + +
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Residues in contact with VAL 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L SER* 3.6 32.8 - - - +
20L GLU 4.3 6.3 - - - +
21L ILE* 1.3 79.0 - - - +
23L TYR* 1.3 61.3 + - - +
24L VAL* 3.9 19.6 - - + +
32L LEU 4.0 0.3 - - - +
33L ASN* 3.3 8.4 - - - +
34L GLY 2.7 38.1 + - - +
36L LEU* 4.3 16.2 - - + -
45L MSE 5.2 1.3 - - - -
47L LEU* 4.1 17.0 - - + -
88L ILE* 4.3 15.3 - - + -
89L ALA 3.4 11.2 - - - +
90L PRO* 4.3 3.1 - - + -
91L PRO* 4.7 0.2 - - + -
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Residues in contact with TYR 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L VAL* 1.3 73.2 - - - +
24L VAL* 1.3 66.3 + - - +
25L LYS* 3.5 29.8 - - + +
31L GLU* 2.7 48.0 + - + +
32L LEU 3.5 10.3 - - - -
33L ASN* 3.9 17.5 - - - +
87L LEU* 4.8 6.3 - - + -
88L ILE* 3.2 6.2 - - - +
89L ALA* 2.8 44.7 + - + +
52M GLU* 4.6 4.0 + - - -
73M LYS* 3.8 16.2 + - - +
75M TYR* 3.1 41.1 + + + -
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Residues in contact with VAL 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L VAL* 3.9 21.3 - - + +
23L TYR* 1.3 83.6 - - - +
25L LYS* 1.3 63.8 + - - +
26L LEU* 3.6 26.6 + - + -
31L GLU* 3.3 5.2 - - - +
32L LEU* 2.7 47.6 + - + +
45L MSE 3.8 31.6 - - + -
47L LEU* 4.2 14.1 - - + -
85L VAL* 4.1 4.7 - - + -
87L LEU 3.3 10.3 - - - +
88L ILE* 4.5 4.0 - - + -
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Residues in contact with LYS 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 3.5 18.7 - - - +
24L VAL* 1.3 73.0 - - - +
26L LEU* 1.3 77.7 + - - +
28L GLY 4.3 1.0 - - - +
29L ASP* 3.1 33.9 + - - +
30L ARG 3.4 16.1 + - - +
31L GLU* 4.0 12.0 - - + +
85L VAL 3.9 0.9 - - - -
86L ILE* 2.9 32.1 + - + -
87L LEU* 3.0 40.2 + - + +
30M ARG* 3.0 41.9 - - - +
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Residues in contact with LEU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I ILE* 4.1 21.3 - - + -
87I LEU* 4.4 2.7 - - + -
24L VAL* 3.6 24.5 - - + +
25L LYS* 1.3 99.4 + - - +
27L ARG* 1.3 70.3 + - - +
30L ARG* 3.0 40.0 + - + +
32L LEU* 4.0 25.4 - - + -
80L VAL* 3.9 18.8 - - + -
84L SER* 3.1 19.7 - - - +
85L VAL* 3.9 9.0 - - + -
86L ILE* 3.6 4.7 - - - +
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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