Contacts of the helix formed by residues 11 - 25 (chain H) in PDB entry 1EA4
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 GLU 11 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9H LEU 3.4 0.8 + - - -
10H SER* 1.3 70.0 - - - +
12H SER* 1.3 54.9 + - - +
14H LEU* 3.2 26.2 - - - +
15H GLU* 2.6 68.4 + - - +
1J MET* 3.1 38.1 + - + +
3J LYS* 3.5 24.5 + - - +
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Residues in contact with SER 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H SER* 2.9 18.6 + - - -
11H GLU* 1.3 80.5 - - - +
13H VAL* 1.3 70.6 + - - +
15H GLU* 2.9 13.3 - - - +
16H ASN* 2.8 23.4 + - - +
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Residues in contact with VAL 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LEU* 3.4 31.9 - - + -
10H SER* 2.8 24.3 + - - +
12H SER* 1.3 76.1 + - - +
14H LEU* 1.3 70.5 + - - +
16H ASN* 3.0 9.1 + - - +
17H LEU* 2.7 21.5 + - + +
20H MET* 5.5 0.2 - - - +
33J SER* 3.8 27.4 - - - +
36J LEU* 4.4 15.8 - - + +
37J GLU* 4.5 20.2 - - + -
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Residues in contact with LEU 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LEU* 4.5 13.5 - - + +
10H SER 2.7 15.1 + - - +
11H GLU* 3.2 25.6 - - - +
13H VAL* 1.3 77.1 - - - +
15H GLU* 1.3 62.2 + - - +
17H LEU* 2.7 32.2 + - + +
18H GLU* 2.3 51.2 - - - +
28H LYS* 5.3 0.7 - - + -
3J LYS* 3.7 29.8 - - + +
4J ARG 6.1 0.4 - - - +
5J LEU* 5.0 15.3 - - + -
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Residues in contact with GLU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H GLU* 2.6 51.7 + - - +
12H SER* 2.9 15.1 - - - +
14H LEU* 1.3 76.1 - - - +
16H ASN* 1.3 61.4 + - - +
18H GLU* 3.0 11.8 + - - +
19H LYS* 3.0 18.9 + - - +
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Residues in contact with ASN 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H SER 2.8 16.0 + - - +
13H VAL* 3.6 8.0 + - - +
15H GLU* 1.3 74.5 - - - +
17H LEU* 1.3 63.6 + - - +
19H LYS* 3.0 28.8 - - + +
20H MET* 2.7 62.0 + - - +
36J LEU* 5.1 2.0 + - - +
37J GLU* 5.0 5.1 + - - +
40J LYS* 3.9 22.0 - - - +
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Residues in contact with LEU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LEU* 4.7 7.9 - - + -
13H VAL 2.7 12.6 + - - +
14H LEU* 2.7 28.5 + - + +
16H ASN* 1.3 72.1 - - - +
18H GLU* 1.3 65.2 + - - +
20H MET* 2.9 10.5 + - - +
21H ALA* 2.8 22.3 + - + +
28H LYS* 3.7 33.9 - - + +
31H MET* 3.4 36.3 - - + -
32H ILE* 4.2 14.6 - - + -
5J LEU* 4.4 13.9 - - + -
36J LEU* 4.1 21.3 - - + -
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LEU* 2.3 69.3 + - - +
15H GLU* 3.2 9.2 + - - +
17H LEU* 1.3 78.2 - - - +
19H LYS* 1.3 64.9 + - - +
21H ALA* 3.4 1.4 + - - +
22H ARG* 2.8 45.0 + - - +
28H LYS* 2.9 39.4 + - - +
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Residues in contact with LYS 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H GLU 3.0 6.1 + - - +
16H ASN* 3.0 32.3 - - + +
17H LEU 2.9 0.2 + - - -
18H GLU* 1.3 80.9 - - - +
20H MET* 1.3 69.3 + - + +
22H ARG* 3.2 19.8 + - - +
23H GLU* 2.9 25.4 + - + +
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Residues in contact with MET 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASN* 2.7 55.5 + - - +
17H LEU* 2.9 14.3 + - + +
19H LYS* 1.3 75.9 - - + +
21H ALA* 1.3 57.3 + - - +
23H GLU* 3.2 7.1 + - - +
24H MET* 2.8 38.9 + - + +
31H MET* 4.0 14.4 - - + +
36J LEU* 3.8 29.8 - - + +
39J TYR* 4.0 25.8 - - - -
40J LYS* 4.2 14.4 - - + -
43J GLN* 6.0 0.7 - - - +
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Residues in contact with ALA 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU 2.8 20.2 + - - +
18H GLU* 3.6 6.1 - - - +
20H MET* 1.3 71.4 - - - +
22H ARG* 1.3 53.5 + - - +
24H MET 3.0 2.1 + - - -
25H GLY 2.8 31.5 + - - -
26H LEU* 2.9 28.7 + - - +
27H SER 4.2 6.1 - - - +
28H LYS* 4.4 11.2 - - + +
31H MET* 3.8 26.6 - - + -
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Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H GLU* 2.8 37.1 + - - +
19H LYS* 3.2 34.3 + - - +
21H ALA* 1.3 75.6 - - - +
23H GLU* 1.3 64.0 + - - +
25H GLY* 3.2 12.7 + - - -
26H LEU 4.9 0.9 - - - -
10L SER* 5.3 1.9 - - - -
12L SER* 4.7 5.5 + - - -
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Residues in contact with GLU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LYS* 2.9 14.9 + - + +
20H MET* 3.4 12.1 - - - +
22H ARG* 1.3 79.6 - - - +
24H MET* 1.3 62.2 + - + +
25H GLY 3.2 1.3 + - - -
37K GLU* 3.2 26.5 - - - +
40K LYS* 4.6 8.1 + - - -
41K LYS* 4.6 11.7 + - - +
12L SER* 4.5 9.2 + - - -
13L VAL* 4.9 1.7 - - - +
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Residues in contact with MET 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H MET* 2.8 25.6 + - - +
21H ALA 3.9 0.7 - - - +
23H GLU* 1.3 75.6 - - + +
25H GLY* 1.3 63.6 + - - +
26H LEU* 3.2 30.1 + - + +
31H MET* 3.9 21.1 - - + +
34H VAL* 5.3 2.9 - - + -
39J TYR* 3.8 28.5 - - - +
33K SER* 4.0 12.6 - - - +
34K VAL* 5.0 13.5 - - + +
37K GLU* 3.3 42.8 - - + +
38K ASN 5.8 0.2 - - - +
13L VAL* 4.1 6.1 - - - +
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Residues in contact with GLY 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ALA 2.8 8.0 + - - -
22H ARG* 3.2 8.6 + - - -
23H GLU 3.2 4.9 + - - -
24H MET* 1.3 79.9 - - - +
26H LEU* 1.3 59.9 + - - +
2K LYS* 4.0 11.0 + - - -
30K ALA* 5.7 0.5 - - - -
33K SER* 3.6 13.7 + - - -
10L SER* 2.8 32.5 + - - -
13L VAL* 4.1 5.6 - - - -
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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