Contacts of the strand formed by residues 45 - 54 (chain J) 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 MSE 45 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J VAL* 5.2 3.6 - - + -
22J VAL* 5.1 1.3 - - - -
24J VAL* 3.8 29.6 - - + -
36J LEU* 3.8 26.9 - - + -
38J ALA 3.2 6.5 - - - +
39J TYR* 3.9 8.5 - - + -
43J LEU* 3.5 8.5 + - + +
44J ASN* 1.3 79.9 - - - +
46J VAL* 1.3 62.2 + - - +
47J LEU* 4.0 9.2 - - + -
78J LEU 3.6 0.2 - - - +
79J PHE* 3.4 4.7 - - - -
80J VAL* 2.7 52.3 + - + +
85J VAL* 3.3 33.7 - - + -
88J ILE* 3.9 26.2 - - + -
10K PRO* 4.5 3.1 - - - -
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Residues in contact with VAL 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J LEU 3.9 0.2 - - - -
37J HIS* 2.9 34.6 + - + -
38J ALA* 2.9 20.9 + - + +
45J MSE 1.3 75.5 - - - +
47J LEU* 1.3 71.5 + - - +
77J MSE 3.8 29.2 - - + -
78J LEU 3.1 7.0 - - - +
79J PHE* 4.4 2.7 - - + -
9K GLU 5.1 0.7 - - - +
10K PRO* 3.5 33.0 - - + +
13K LEU* 3.8 27.6 - - + +
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Residues in contact with LEU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J VAL* 4.2 11.7 - - + -
24J VAL* 4.2 12.6 - - + -
32J LEU* 3.9 39.7 - - + -
34J GLY* 4.0 21.3 - - - +
35J ARG 3.4 0.9 - - - -
36J LEU* 3.9 28.0 - - + -
45J MSE 4.0 10.7 - - + -
46J VAL* 1.3 81.9 - - - +
48J GLY* 1.3 59.9 + - - +
49J ASP 4.1 0.2 + - - -
50J ALA* 3.9 16.6 - - + +
77J MSE 3.6 1.9 - - - -
78J LEU* 2.7 44.6 + - + +
80J VAL* 4.1 7.2 - - + -
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Residues in contact with GLY 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J GLY* 3.5 0.3 - - - -
35J ARG* 2.7 37.6 + - - +
37J HIS* 3.5 27.1 + - - -
47J LEU* 1.3 71.3 - - - +
49J ASP* 1.3 74.9 + - - +
50J ALA 3.3 2.2 + - - -
76J GLU 3.5 7.2 - - - -
77J MSE 4.0 2.9 - - - -
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Residues in contact with ASP 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ASN 4.0 4.0 - - - +
34J GLY* 4.0 3.1 - - - -
35J ARG* 5.6 4.7 - - + +
48J GLY* 1.3 73.8 - - - +
50J ALA* 1.3 61.3 + - - +
51J GLU* 4.0 0.5 + - - +
74J HIS* 3.5 24.1 + - - -
75J TYR 3.3 8.1 - - - -
76J GLU* 2.7 21.0 + - - +
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Residues in contact with ALA 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J LEU* 5.7 0.2 - - + -
33J ASN 3.0 11.9 - - - +
34J GLY* 4.3 0.2 - - - -
47J LEU* 3.9 33.4 - - + +
48J GLY 4.0 0.4 - - - -
49J ASP* 1.3 75.7 - - - +
51J GLU* 1.3 61.3 + - - +
52J GLU 4.2 0.2 - - - -
74J HIS* 3.3 8.3 - - - -
75J TYR* 2.7 43.3 + - + +
78J LEU* 4.1 22.0 - - + -
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Residues in contact with GLU 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLU 3.8 0.2 - - - +
32J LEU* 3.2 9.2 - - - +
33J ASN* 2.8 48.2 + - + +
49J ASP 4.0 1.5 + - - +
50J ALA* 1.3 74.8 - - - +
52J GLU* 1.3 62.9 + - - +
53J ILE* 3.7 21.9 - - + +
72J ARG* 2.7 40.1 + - + +
73J LYS 3.4 9.6 - - - +
74J HIS* 4.5 7.6 - - + +
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Residues in contact with GLU 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ARG* 2.6 47.1 + - + -
31J GLU 3.4 3.4 - - - -
32J LEU* 3.7 18.4 - - + -
50J ALA 4.2 0.2 - - - -
51J GLU* 1.3 75.4 - - - +
53J ILE* 1.3 67.0 + - - +
54J VAL* 4.0 5.9 - - + +
71J ILE 3.8 0.3 - - - +
72J ARG* 3.3 6.6 - - - +
73J LYS* 2.7 45.0 + - + +
75J TYR* 2.7 41.5 + - + -
23K TYR* 4.7 3.4 + - - -
25K LYS* 5.2 0.2 - - - +
87K LEU* 4.0 11.5 - - - +
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Residues in contact with ILE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ASP 3.6 3.6 - - - +
30J ARG* 4.6 0.2 - - - -
31J GLU* 2.9 48.8 + - + +
33J ASN* 4.0 16.2 - - - +
51J GLU* 3.7 28.3 - - + +
52J GLU* 1.3 80.5 - - - +
54J VAL* 1.3 61.8 + - - +
55J THR* 3.8 21.6 + - + +
70J THR* 4.0 15.3 - - + +
71J ILE 3.8 2.7 - - - -
72J ARG* 3.4 36.3 - - + +
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Residues in contact with VAL 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ASP* 3.4 13.2 - - + +
30J ARG* 3.4 36.1 - - + +
52J GLU* 4.0 10.3 - - - +
53J ILE* 1.3 74.8 - - - +
55J THR* 1.3 70.9 + - - +
70J THR* 3.1 3.8 + - - -
71J ILE* 2.8 62.0 + - + +
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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