Contacts of the strand formed by residues 30 - 39 (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 ARG 30 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25J LYS* 3.5 5.6 - - - +
26J LEU* 2.9 53.7 + - + +
27J ARG 4.6 5.0 + - - +
28J GLY 3.2 11.7 + - - +
29J ASP* 1.3 81.5 - - - +
31J GLU* 1.3 69.7 + - - +
32J LEU* 4.9 0.7 - - + -
52J GLU* 2.6 49.4 + - + +
53J ILE 3.7 1.6 - - - +
54J VAL* 3.4 25.6 - - + +
23K TYR* 5.9 0.2 + - - -
25K LYS* 3.2 40.2 - - - +
28K GLY 6.0 0.6 - - - +
29K ASP 5.7 0.2 - - - +
86K ILE* 5.2 10.8 - - - +
87K LEU* 4.5 8.3 - - - -
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Residues in contact with GLU 31 (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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73I LYS* 4.3 10.2 - - - +
23J TYR* 2.7 43.2 + - + +
24J VAL 3.3 6.1 - - - +
25J LYS* 4.0 9.6 - - + +
26J LEU 4.6 0.4 - - - +
29J ASP 5.7 0.4 - - - -
30J ARG* 1.3 80.7 - - - +
32J LEU* 1.3 75.3 + - - +
33J ASN* 5.3 0.7 - - - +
52J GLU* 3.4 0.9 - - - +
53J ILE* 2.9 48.7 + - + +
55J THR* 4.0 20.9 - - + +
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Residues in contact with LEU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J VAL 4.5 0.2 - - - -
23J TYR* 3.5 2.8 - - - -
24J VAL* 2.8 36.5 + - + +
26J LEU* 3.9 30.7 - - + -
30J ARG* 4.9 0.7 - - + -
31J GLU* 1.3 85.2 - - - +
33J ASN* 1.3 72.7 + - - +
47J LEU* 3.9 19.1 - - + -
50J ALA* 5.7 0.2 - - + -
51J GLU 3.2 7.2 - - - +
52J GLU* 3.7 29.2 - - + -
78J LEU* 3.9 16.6 - - + -
80J VAL* 3.5 35.7 - - + -
87K LEU* 4.4 4.0 - - + -
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Residues in contact with ASN 33 (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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21J ILE* 5.0 8.5 - - + +
22J VAL 3.3 7.3 - - - +
23J TYR* 3.8 27.5 + - - +
31J GLU* 5.3 0.4 - - - +
32J LEU* 1.3 82.8 + - - +
34J GLY* 1.3 58.2 + - - +
47J LEU* 4.7 2.7 - - - -
49J ASP 4.0 1.1 - - - +
50J ALA* 3.0 5.9 - - - +
51J GLU* 2.8 48.2 + - + +
53J ILE* 4.0 24.5 - - - +
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Residues in contact with GLY 34 (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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21J ILE* 3.2 12.5 - - - +
22J VAL* 2.8 34.1 + - - +
33J ASN* 1.3 76.4 - - - +
35J ARG* 1.3 61.4 + - - -
36J LEU 3.6 0.5 + - - -
47J LEU* 4.0 15.9 - - - +
48J GLY 3.5 11.0 - - - -
49J ASP 4.0 4.9 - - - -
50J ALA* 4.1 1.3 - - - -
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Residues in contact with ARG 35 (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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19J ASP* 2.9 48.7 + - - +
20J GLU* 3.3 5.9 + - - +
21J ILE* 3.8 31.8 - - + +
34J GLY* 1.3 71.4 - - - -
36J LEU* 1.3 58.9 + - - +
37J HIS* 3.1 34.2 + - + +
47J LEU* 3.4 2.4 - - - -
48J GLY 2.7 40.8 + - - +
49J ASP* 5.6 3.7 - - + +
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Residues in contact with LEU 36 (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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14J VAL* 3.3 39.5 - - + +
17J SER* 3.7 26.7 - - - +
18J LEU* 3.7 14.4 - - + +
19J ASP* 2.7 31.4 + - - -
20J GLU 3.0 10.5 + - - +
22J VAL* 4.3 14.1 - - + -
34J GLY 3.6 3.0 + - - -
35J ARG* 1.3 66.8 - - - +
37J HIS* 1.3 61.3 + - - +
38J ALA 3.5 25.4 - - - +
39J TYR* 4.5 2.0 - - + -
45J MSE 3.8 24.2 - - + -
46J VAL 3.9 1.3 - - - -
47J LEU* 3.9 13.9 - - + -
88J ILE* 6.0 1.1 - - + -
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Residues in contact with HIS 37 (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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18J LEU* 4.0 9.2 - - - +
19J ASP* 4.2 20.5 + - - +
35J ARG* 3.1 26.1 + - + -
36J LEU* 1.3 73.0 - - - +
38J ALA* 1.3 64.0 + - + +
46J VAL* 2.9 21.3 + - + +
47J LEU 4.4 0.2 - - - -
48J GLY* 3.5 35.8 + - - -
77J MSE 3.7 22.5 - - + -
9K GLU* 4.7 4.7 - - - +
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Residues in contact with ALA 38 (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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18J LEU* 4.1 6.4 - - - +
36J LEU* 3.5 8.0 - - - +
37J HIS* 1.3 83.4 - - + +
39J TYR* 1.3 64.2 + - - +
45J MSE 3.2 4.9 - - - -
46J VAL* 2.9 30.7 + - + -
9K GLU* 3.4 31.4 - - + +
10K PRO* 3.9 18.4 - - + -
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Residues in contact with TYR 39 (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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11J LEU* 4.7 12.7 + - + +
14J VAL* 3.8 26.0 - - + -
15J ARG* 3.1 43.0 - - + +
18J LEU* 3.5 34.9 - - + +
36J LEU* 4.5 3.4 - - + -
38J ALA* 1.3 79.4 - - - +
40J ASP* 1.3 76.9 + - - +
41J GLU* 6.1 0.2 - - - -
43J LEU* 5.0 6.1 - - + -
44J ASN 3.0 14.1 - - - +
45J MSE 3.9 12.1 - - + -
9K GLU* 4.9 3.0 - - - +
10K PRO* 3.2 13.4 - - - +
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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