Contacts of the strand formed by residues 45 - 54 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14K VAL* 5.2 2.5 - - + -
22K VAL* 5.1 1.6 - - - -
24K VAL* 3.8 29.4 - - + -
36K LEU* 3.8 28.0 - - + -
38K ALA 3.2 5.6 - - - +
39K TYR* 3.9 8.1 - - + -
43K LEU* 3.5 8.9 + - + +
44K ASN* 1.3 80.3 - - - +
46K VAL* 1.3 63.2 + - - +
47K LEU* 4.0 10.3 - - + -
78K LEU 3.6 0.2 - - - +
79K PHE* 3.4 5.4 - - - -
80K VAL* 2.7 51.5 + - + +
85K VAL* 3.3 34.3 - - + -
88K ILE* 3.8 25.8 - - + -
10N PRO* 4.6 2.5 - - - -
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Residues in contact with VAL 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K LEU* 3.9 0.3 - - - -
37K HIS* 2.9 34.3 + - + -
38K ALA* 2.9 19.5 + - + +
45K MSE 1.3 76.5 - - - +
47K LEU* 1.3 70.6 + - - +
77K MSE 3.9 28.9 - - + -
78K LEU 3.1 7.0 - - - +
79K PHE* 4.4 2.9 - - + -
9N GLU 5.1 0.7 - - - +
10N PRO* 3.4 35.2 - - + +
13N LEU* 3.9 25.8 - - + -
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Residues in contact with LEU 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K VAL* 4.1 11.4 - - + -
24K VAL* 4.2 11.2 - - + -
32K LEU* 3.9 39.5 - - + -
34K GLY* 4.0 21.3 - - - +
35K ARG 3.4 0.9 - - - -
36K LEU* 4.1 26.2 - - + -
45K MSE 4.0 10.9 - - + -
46K VAL* 1.3 82.6 - - - +
48K GLY* 1.3 60.5 + - - +
50K ALA* 3.9 16.3 - - + +
77K MSE 3.5 2.8 - - - -
78K LEU* 2.7 44.1 + - + +
80K VAL* 4.0 7.6 - - + -
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Residues in contact with GLY 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K GLY* 3.5 0.5 - - - -
35K ARG* 2.7 37.5 + - - +
37K HIS* 3.5 26.7 + - - -
47K LEU* 1.3 71.0 - - - +
49K ASP* 1.3 74.3 + - - +
50K ALA 3.3 3.0 + - - -
76K GLU 3.5 6.7 - - - -
77K MSE 4.0 2.9 - - - -
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Residues in contact with ASP 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K ASN 3.9 3.8 - - - +
34K GLY* 4.0 3.3 - - - -
35K ARG* 5.6 4.7 - - + +
48K GLY* 1.3 74.1 - - - +
50K ALA* 1.3 60.3 + - - +
51K GLU* 4.0 0.5 + - - +
74K HIS* 3.5 24.6 + - - -
75K TYR 3.3 8.3 + - - -
76K GLU* 2.8 20.7 + - - +
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Residues in contact with ALA 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K LEU* 5.6 0.2 - - + -
33K ASN 3.1 11.4 - - - +
34K GLY* 4.3 0.7 - - - -
47K LEU* 3.9 34.1 - - + +
48K GLY 4.0 0.7 - - - -
49K ASP* 1.3 75.1 - - - +
51K GLU* 1.3 62.5 + - - +
73K LYS 4.0 0.2 - - - +
74K HIS* 3.3 6.8 - - - -
75K TYR* 2.7 44.2 + - + +
78K LEU* 4.1 22.0 - - + -
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Residues in contact with GLU 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K GLU 3.8 0.2 - - - +
32K LEU* 3.2 8.7 - - - +
33K ASN* 2.8 48.5 + - + +
49K ASP 4.0 1.0 + - - +
50K ALA* 1.3 73.6 - - - +
52K GLU* 1.3 63.7 + - - +
53K ILE* 3.8 21.4 + - + +
72K ARG* 2.7 40.6 + - + +
73K LYS 3.4 9.2 - - - +
74K HIS* 4.5 9.2 - - + +
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Residues in contact with GLU 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 2.6 45.7 + - + -
31K GLU 3.4 3.6 - - - -
32K LEU* 3.6 18.6 - - + -
50K ALA 4.2 0.8 + - - -
51K GLU* 1.3 73.9 - - - +
53K ILE* 1.3 65.2 + - - +
54K VAL* 4.0 6.2 - - + +
71K ILE 3.8 0.7 - - - +
72K ARG* 3.3 5.7 - - - +
73K LYS* 2.7 46.3 + - + +
75K TYR* 2.7 39.0 + - + -
23N TYR* 4.6 2.0 + - - -
25N LYS* 5.0 1.2 - - - +
87N LEU* 3.9 13.3 - - - +
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Residues in contact with ILE 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K ASP 3.7 1.2 - - - +
30K ARG* 3.7 2.1 - - - -
31K GLU* 2.9 48.5 + - + +
33K ASN* 4.0 16.2 - - - +
51K GLU* 3.8 22.2 - - + +
52K GLU* 1.3 78.5 - - - +
54K VAL* 1.3 63.2 + - - +
55K THR* 3.9 22.0 + - + +
70K THR* 3.9 7.2 - - + +
71K ILE 3.8 2.2 - - - -
72K ARG* 3.2 50.9 - - + +
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Residues in contact with VAL 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K GLY 5.7 0.2 - - - +
29K ASP* 3.4 13.5 - - + +
30K ARG* 3.4 37.2 - - + +
52K GLU* 4.0 9.2 - - - +
53K ILE* 1.3 74.9 - - - +
55K THR* 1.3 69.5 + - - +
70K THR* 3.1 3.8 + - - -
71K ILE* 2.8 61.8 + - + +
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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