Contacts of the helix formed by residues 12 - 29 (chain A) in PDB entry 1EQB
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 ASP 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ILE* 2.7 25.0 + - + +
11A TYR* 1.3 87.0 - - + +
13A ALA* 1.3 64.9 + - - +
14A GLU* 3.0 7.4 + - - +
15A LEU* 2.8 30.3 + - - +
16A TRP* 2.9 20.8 + - - +
81B ARG* 2.4 39.9 + - - -
274B VAL* 4.2 5.5 - - + +
277B LYS* 3.5 15.0 - - + +
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Residues in contact with ALA 13 (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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9A ALA 4.0 15.7 + - - +
10A ASP 5.4 0.6 - - - -
11A TYR 3.9 1.2 - - - -
12A ASP* 1.3 72.8 - - - +
14A GLU* 1.3 58.4 + - + +
16A TRP* 3.8 6.3 - - - +
17A GLN* 2.8 31.4 + - - +
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Residues in contact with GLU 14 (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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12A ASP* 3.0 6.3 + - - +
13A ALA* 1.3 76.2 - - + +
15A LEU* 1.3 65.9 + - - +
17A GLN* 3.2 7.5 + - - +
18A ALA* 3.1 23.0 + - - +
73B ILE* 5.1 2.0 - - + +
77B LEU* 3.6 24.8 - - + +
81B ARG* 3.4 20.6 + - - -
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Residues in contact with LEU 15 (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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8A ILE* 4.1 14.8 - - + -
12A ASP* 2.8 30.4 + - + +
14A GLU* 1.3 78.7 - - - +
16A TRP* 1.3 59.0 + - - +
18A ALA* 3.5 2.3 + - - +
19A MET* 3.0 49.4 + - + +
74B VAL* 4.1 28.5 - - + -
77B LEU* 3.7 18.5 - - + +
81B ARG* 4.3 0.2 - - - +
270B ALA* 3.4 27.6 - - + +
273B ALA* 4.5 4.0 - - + -
274B VAL* 3.5 21.8 - - + +
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Residues in contact with TRP 16 (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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8A ILE* 3.8 19.3 - - + +
9A ALA* 3.5 44.1 - - + +
12A ASP 2.9 15.8 + - - +
13A ALA* 3.8 6.7 - - - +
15A LEU* 1.3 75.5 - - - +
17A GLN* 1.3 63.7 + - - +
19A MET* 3.3 14.9 + - + +
20A GLU* 2.9 69.5 + - + +
45B GLN* 3.3 25.6 - - + -
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Residues in contact with GLN 17 (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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13A ALA 2.8 19.7 + - - +
14A GLU* 3.2 6.2 + - - +
16A TRP* 1.3 81.5 - - + +
18A ALA* 1.3 61.3 + - - +
20A GLU* 3.4 5.3 + - - +
21A GLN* 3.0 54.1 + - + +
73B ILE* 6.2 0.6 - - - +
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Residues in contact with ALA 18 (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 GLU 3.1 11.1 + - - +
15A LEU* 3.8 5.6 - - - +
17A GLN* 1.3 76.3 - - - +
19A MET* 1.3 66.3 + - - +
21A GLN* 3.3 14.7 + - - +
22A GLU* 3.1 18.4 + - - +
70B TYR* 3.6 18.1 - - - +
73B ILE* 3.5 37.7 - - + -
74B VAL* 4.0 9.9 - - + -
77B LEU* 5.4 0.2 - - + -
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Residues in contact with MET 19 (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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8A ILE* 3.7 24.9 - - + -
15A LEU* 3.0 44.9 + - + +
16A TRP* 3.6 18.4 - - + +
18A ALA* 1.3 74.6 - - - +
20A GLU* 1.3 66.2 + - - +
22A GLU* 3.0 20.0 + - - +
23A LYS* 3.0 11.9 + - - +
45B GLN* 4.8 2.0 - - + +
46B ALA* 4.0 16.6 - - + -
49B SER* 3.4 36.6 - - - +
51B LEU* 4.2 22.5 - - + +
74B VAL* 4.9 1.8 - - + -
270B ALA* 4.6 2.5 - - - -
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Residues in contact with GLU 20 (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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16A TRP* 2.9 67.7 + - + +
17A GLN* 3.8 5.8 - - - +
19A MET* 1.3 73.8 - - - +
21A GLN* 1.3 62.8 + - + +
23A LYS* 3.1 51.0 + - - +
24A VAL* 3.1 14.6 + - + +
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Residues in contact with GLN 21 (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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17A GLN* 3.0 46.6 + - + +
18A ALA* 3.6 8.8 - - - +
19A MET 3.2 0.2 - - - -
20A GLU* 1.3 73.2 - - + +
22A GLU* 1.3 54.6 + - - +
24A VAL* 3.1 9.2 + - - +
25A ARG* 2.8 34.5 + - - +
70B TYR* 3.5 45.1 + - + -
73B ILE* 4.4 7.4 - - - +
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Residues in contact with GLU 22 (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 ALA 3.1 10.7 + - - +
19A MET 3.0 11.1 + - - +
21A GLN* 1.3 75.8 - - - +
23A LYS* 1.3 57.8 + - - +
25A ARG* 2.4 41.1 + - - -
26A GLN* 2.7 58.9 + - - +
50B GLN* 5.3 0.7 - - + -
51B LEU* 3.2 31.6 - - + -
54B LYS* 3.8 4.4 - - - +
67B GLY 4.2 1.7 - - - +
70B TYR* 3.9 20.1 - - + +
71B VAL* 4.2 15.1 + - + +
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Residues in contact with LYS 23 (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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16A TRP* 6.3 0.2 - - - -
19A MET 3.0 10.5 + - - +
20A GLU* 3.1 44.3 + - - +
22A GLU* 1.3 79.5 - - - +
24A VAL* 1.3 59.6 + - + +
26A GLN* 3.8 4.9 + - - +
27A GLU* 3.7 20.8 + - + +
4B ARG* 3.3 33.6 - - - +
50B GLN* 3.7 30.9 + - + +
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Residues in contact with VAL 24 (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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20A GLU* 3.1 12.7 + - + +
21A GLN* 3.1 9.9 + - - +
23A LYS* 1.3 78.8 - - + +
25A ARG* 1.3 59.7 + - - +
26A GLN 3.2 0.2 - - - -
27A GLU* 2.9 9.7 + - + +
28A GLU* 2.8 56.7 + - + +
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Residues in contact with ARG 25 (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 GLN 2.8 19.7 + - - +
22A GLU* 2.4 53.5 + - - +
24A VAL* 1.3 74.5 - - - +
26A GLN* 1.3 70.2 + - - +
28A GLU* 4.4 3.1 - - - +
29A HIS* 2.9 71.6 + - + +
31A GLU* 2.6 39.1 + - - +
36A GLU* 4.7 0.4 + - - -
54B LYS* 3.6 13.7 - - - +
67B GLY* 3.1 26.8 + - - -
69B GLU* 3.8 13.0 - - - +
70B TYR* 3.7 21.5 - - + -
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Residues in contact with GLN 26 (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 GLU* 2.7 46.7 + - - +
23A LYS 3.9 6.5 - - - +
24A VAL 3.2 0.2 - - - -
25A ARG* 1.3 90.7 - - - +
27A GLU* 1.3 59.0 + - + +
29A HIS* 4.0 3.2 - - - +
31A GLU* 5.6 0.9 - - - -
38A TYR* 3.7 23.8 + - + -
372A ARG* 3.8 3.8 + - - -
415A VAL* 3.4 20.2 - - + +
416A TYR* 4.3 2.1 - - - -
50B GLN* 2.8 52.4 + - - +
51B LEU* 4.5 1.2 - - - +
53B ASN* 3.1 28.8 + - - +
54B LYS* 4.7 3.2 - - - +
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Residues in contact with GLU 27 (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 LYS* 3.7 14.1 - - + +
24A VAL* 2.9 11.7 + - + +
26A GLN* 1.3 80.8 - - + +
28A GLU* 1.3 64.4 + - + +
29A HIS 3.3 0.7 - - - -
372A ARG* 2.4 28.1 + - - +
410A CYS* 3.5 8.8 - - - +
414A PRO* 3.2 17.6 - - - +
415A VAL* 3.0 37.9 + - - +
416A TYR* 3.0 26.1 + - - +
4B ARG* 5.4 2.8 + - - +
50B GLN* 5.7 1.0 + - - +
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Residues in contact with GLU 28 (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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24A VAL* 2.8 43.3 + - + +
25A ARG* 4.4 3.2 - - - +
27A GLU* 1.3 76.0 - - + +
29A HIS* 1.3 62.2 + - + +
341A ASN* 2.8 30.6 + - - +
406A VAL* 5.0 1.0 - - - +
407A LEU* 3.9 25.4 - - + +
410A CYS* 3.9 13.9 - - - -
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Residues in contact with HIS 29 (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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25A ARG* 2.9 46.6 + - + +
26A GLN 4.0 4.3 - - - +
27A GLU 3.3 0.2 - - - -
28A GLU* 1.3 83.2 - - + +
30A ILE* 1.3 64.5 + - - +
31A GLU* 3.4 17.7 + - + +
38A TYR* 4.2 1.7 + - - -
338A GLY* 4.8 6.7 - - - -
341A ASN* 3.2 45.9 + - - +
343A THR* 3.2 21.5 + - - +
372A ARG* 2.8 24.7 + - - -
410A CYS* 4.0 0.7 - - - -
67B GLY* 5.0 2.2 - - - -
69B GLU* 4.3 10.5 - - - -
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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