Contacts of the strand formed by residues 30 - 39 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.5 5.7 - - - +
26A LEU* 2.9 56.0 + - + +
27A ARG 4.5 5.0 + - - +
28A GLY 3.2 11.1 + - - +
29A ASP* 1.3 80.8 - - - +
31A GLU* 1.3 71.6 + - - +
32A LEU* 5.0 0.7 - - + -
52A GLU* 2.6 48.8 + - + +
53A ILE 3.7 1.6 - - - +
54A VAL* 3.4 25.0 - - + +
25F LYS* 3.3 38.1 - - - +
28F GLY 5.7 1.8 - - - +
29F ASP 5.7 0.4 - - - +
86F ILE* 4.8 14.4 - - - +
87F LEU* 4.7 7.9 - - - -
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 2.7 44.4 + - + +
24A VAL 3.3 5.6 - - - +
25A LYS* 4.1 10.4 - - + +
26A LEU 4.7 0.4 - - - +
29A ASP 5.7 0.4 - - - -
30A ARG* 1.3 80.6 - - - +
32A LEU* 1.3 73.9 + - - +
33A ASN* 5.4 0.7 - - - +
52A GLU* 4.1 0.5 - - - +
53A ILE* 2.8 50.1 + - + +
55A THR* 4.0 21.9 - - + +
73G LYS* 4.5 9.4 - - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL 4.5 0.4 - - - -
23A TYR* 3.5 3.1 - - - -
24A VAL* 2.8 39.0 + - + +
26A LEU* 4.0 29.8 - - + -
30A ARG* 5.0 0.9 - - + -
31A GLU* 1.3 84.6 - - - +
33A ASN* 1.3 72.2 + - - +
47A LEU* 3.9 17.5 - - + -
50A ALA* 5.7 0.4 - - + -
51A GLU 3.2 5.8 - - - +
52A GLU* 3.7 28.3 - - + -
78A LEU* 3.9 17.0 - - + -
80A VAL* 3.4 36.1 - - + -
87F LEU* 4.4 3.8 - - + -
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Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.0 8.9 - - + +
22A VAL 3.3 7.1 - - - +
23A TYR* 3.7 28.0 + - - +
31A GLU* 5.4 0.6 - - - +
32A LEU* 1.3 82.1 + - - +
34A GLY* 1.3 58.8 + - - +
47A LEU* 4.6 3.1 - - - -
49A ASP 4.0 0.9 - - - +
50A ALA* 3.1 5.2 - - - +
51A GLU* 2.8 53.4 + - + +
53A ILE* 4.0 17.4 - - - +
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.2 11.9 - - - +
22A VAL* 2.8 34.8 + - - +
33A ASN* 1.3 77.1 - - - +
35A ARG* 1.3 61.4 + - - -
36A LEU 3.6 0.5 + - - -
47A LEU* 4.0 14.3 - - - +
48A GLY 3.5 10.3 - - - -
49A ASP 4.0 4.9 - - - -
50A ALA* 4.1 1.6 - - - -
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASP* 2.9 49.6 + - - +
20A GLU* 3.4 6.1 + - - +
21A ILE* 3.8 31.3 - - + +
34A GLY* 1.3 70.5 - - - -
36A LEU* 1.3 60.7 + - - +
37A HIS* 3.0 33.6 + - + +
47A LEU* 3.4 2.2 - - - -
48A GLY 2.8 41.3 + - - +
49A ASP* 5.6 4.5 - - + +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.4 40.4 - - + +
17A SER* 3.6 26.0 - - - +
18A LEU* 3.7 13.9 - - + +
19A ASP* 2.7 31.7 + - - -
20A GLU 3.0 10.5 + - - +
22A VAL* 4.3 14.6 - - + -
34A GLY 3.6 3.2 + - - -
35A ARG* 1.3 68.7 - - - +
37A HIS* 1.3 59.5 + - - +
38A ALA 3.5 24.5 - - - +
39A TYR* 4.5 2.0 - - + -
45A MSE 3.8 24.5 - - + -
46A VAL 3.9 1.6 - - - +
47A LEU* 4.0 13.7 - - + -
88A ILE* 6.0 0.9 - - + -
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Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.9 9.4 - - - +
19A ASP* 4.1 20.1 + - - +
35A ARG* 3.0 25.1 + - + -
36A LEU* 1.3 74.5 - - - +
38A ALA* 1.3 64.7 + - + +
46A VAL* 2.9 20.6 + - + +
47A LEU 4.4 0.2 - - - -
48A GLY* 3.6 36.0 + - - -
77A MSE 3.7 22.3 - - + -
9F GLU* 4.6 5.0 - - - +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.1 6.4 - - - +
36A LEU* 3.5 8.2 - - - +
37A HIS* 1.3 84.5 - - + +
39A TYR* 1.3 64.3 + - - +
45A MSE 3.2 4.3 - - - -
46A VAL* 3.0 31.3 + - + -
9F GLU* 3.3 32.5 - - + +
10F PRO* 3.7 18.6 - - + -
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.6 13.8 + - + +
14A VAL* 3.7 25.6 - - + -
15A ARG* 3.1 43.0 - - - +
18A LEU* 3.5 35.0 - - + -
36A LEU* 4.5 3.8 - - + -
38A ALA* 1.3 77.1 - - - +
40A ASP* 1.3 75.5 + - - +
41A GLU* 6.0 0.2 - - - -
43A LEU* 5.0 5.8 - - + -
44A ASN 3.0 14.6 - - - +
45A MSE 3.9 11.9 - - + -
9F GLU* 4.8 3.7 - - - +
10F PRO* 3.2 13.3 - - - +
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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