Contacts of the helix formed by residues 10 - 31 (chain A) in PDB entry 1EQ1
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ALA* 2.8 37.7 - - + +
9A PHE* 1.3 79.9 + - - +
11A GLU* 1.3 64.0 + - - +
12A MET 2.9 7.6 + - - -
13A GLU* 3.0 16.6 + - - +
14A LYS* 3.6 25.4 + - + +
123A ALA* 3.9 12.8 - - + +
124A LYS* 3.9 30.6 - - - +
127A ALA* 3.4 27.1 - - - +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN 4.5 11.3 - - - +
8A ALA 4.5 2.9 + - - +
9A PHE* 3.2 0.6 - - - +
10A GLU* 1.3 79.2 - - - +
12A MET* 1.3 69.8 + - + +
13A GLU 3.2 0.4 - - - -
14A LYS* 3.5 24.1 - - + +
15A HIS* 3.0 26.8 + - + +
145A TYR* 5.0 2.9 - - + -
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Residues in contact with MET 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA 4.9 0.7 - - - +
9A PHE* 3.0 39.9 - - + +
10A GLU 2.9 0.6 + - - -
11A GLU* 1.3 85.9 - - + +
13A GLU* 1.3 57.1 + - - +
15A HIS* 2.4 33.2 + - + -
16A ALA* 3.0 10.8 + - - +
119A SER* 4.1 8.0 + - - +
123A ALA* 6.0 0.9 - - + -
141A ILE* 3.8 21.1 - - + +
142A LYS* 3.8 32.3 - - + -
145A TYR* 3.9 29.2 - - + +
148A PHE* 4.8 2.9 - - + -
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE 4.5 0.2 + - - -
10A GLU 3.0 9.8 + - - +
12A MET* 1.3 79.0 - - - +
14A LYS* 1.3 61.5 + - + +
16A ALA* 4.3 1.3 - - - -
17A LYS* 2.9 28.2 + - + +
116A VAL* 3.9 15.1 - - + +
117A GLN* 5.1 1.4 + - - -
119A SER* 3.7 29.6 + - - +
120A GLN* 3.1 53.8 + - - +
123A ALA* 3.9 8.4 - - + +
124A LYS* 4.8 6.6 + - - -
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Residues in contact with LYS 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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10A GLU* 3.6 22.7 + - - +
11A GLU* 3.1 35.1 + - + +
13A GLU* 1.3 80.8 + - + +
15A HIS* 1.3 65.3 + - - +
17A LYS* 4.0 5.2 - - - +
18A GLU* 3.0 28.1 + - - +
124A LYS* 5.3 5.9 - - - +
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Residues in contact with HIS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.0 10.0 + - + +
12A MET* 2.4 41.3 + - + -
14A LYS* 1.3 77.4 - - - +
16A ALA* 1.3 70.8 + - + +
18A GLU* 2.7 35.2 - - - +
19A PHE* 3.1 16.3 - - + -
145A TYR* 2.4 77.2 + + + +
148A PHE* 4.0 3.6 - + - +
149A VAL* 3.2 27.9 - - + +
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Residues in contact with ALA 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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12A MET 3.0 18.3 + - - +
13A GLU* 4.2 4.5 - - - +
15A HIS* 1.3 84.7 + - + +
17A LYS* 1.3 65.7 + - - +
19A PHE* 3.0 14.7 + - - +
20A GLN* 3.2 10.9 + - - +
116A VAL* 4.5 7.7 - - + +
119A SER* 4.6 4.5 - - - +
148A PHE* 3.6 43.7 - - + -
152A ALA* 5.0 1.7 - - - +
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Residues in contact with LYS 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 GLU* 2.9 24.8 + - + +
14A LYS* 4.0 4.3 - - - +
16A ALA* 1.3 76.5 - - - +
18A GLU* 1.3 62.9 + - + +
20A GLN* 2.6 47.3 + - + +
21A LYS* 3.5 26.0 + - - +
116A VAL* 3.0 30.6 - - + +
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Residues in contact with GLU 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 LYS 3.0 14.4 + - - +
15A HIS* 2.7 45.1 - - - +
17A LYS* 1.3 85.9 - - + +
19A PHE* 1.3 78.9 + - + +
20A GLN 3.3 0.5 + - - -
21A LYS* 3.5 17.3 + - - +
22A THR* 4.0 4.2 + - - -
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Residues in contact with PHE 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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15A HIS* 3.1 19.7 - - + +
16A ALA* 3.0 10.7 + - - +
17A LYS 2.9 1.0 - - - -
18A GLU* 1.3 97.6 - - + +
20A GLN* 1.3 59.8 + - - +
21A LYS 3.3 0.2 - - - -
22A THR* 2.9 38.3 - - + +
23A PHE* 3.9 1.0 - - - -
148A PHE 4.4 0.7 - - - +
149A VAL* 3.1 57.7 - - + -
152A ALA* 3.3 22.1 - - + +
153A GLU* 4.7 9.2 - - + -
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 3.2 3.1 + - - +
17A LYS* 2.6 39.0 + - + +
19A PHE* 1.3 70.6 - - - +
21A LYS* 1.3 87.4 + - + +
22A THR 3.1 5.2 - - - -
23A PHE* 2.6 43.1 - - + -
24A SER* 3.4 6.6 + - - -
112A VAL* 5.2 0.7 - - + -
113A GLN* 3.7 41.3 + - - +
116A VAL* 3.3 30.6 - - + +
152A ALA* 4.8 2.0 - - - -
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Residues in contact with LYS 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 LYS* 3.7 28.5 - - - +
18A GLU* 3.5 11.7 + - - +
19A PHE 3.3 0.4 - - - -
20A GLN* 1.3 114.6 - - + +
22A THR* 1.3 63.4 + - - +
23A PHE 3.4 0.2 - - - -
24A SER* 4.0 8.5 - - - -
25A GLU* 3.5 23.9 + - - +
113A GLN* 6.1 0.2 - - - -
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Residues in contact with THR 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 GLU 4.0 3.0 + - - -
19A PHE* 2.9 35.5 + - + +
20A GLN 3.1 0.8 - - - -
21A LYS* 1.3 79.5 - - - +
23A PHE* 1.3 70.9 + - - +
25A GLU* 3.5 6.6 + - - +
26A GLN* 3.4 18.5 + - - +
153A GLU* 4.0 29.0 - - + +
156A GLN* 4.0 15.2 + - - +
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Residues in contact with PHE 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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19A PHE 3.9 3.8 - - - -
20A GLN* 2.6 43.7 - - + -
22A THR* 1.3 79.3 - - - +
24A SER* 1.3 96.6 + - - +
25A GLU 3.0 2.0 - - - -
26A GLN* 3.1 1.2 + - - +
27A PHE* 3.0 45.7 + + - -
109A GLN* 3.7 17.5 - - + -
112A VAL* 3.1 39.0 - - + -
113A GLN* 3.7 21.3 - - + -
152A ALA* 3.3 13.2 - - - +
155A VAL* 3.2 28.9 - - + -
156A GLN* 4.0 10.7 - - - +
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Residues in contact with SER 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 GLN* 3.4 15.6 + - - -
21A LYS* 4.1 8.7 - - - -
22A THR 3.4 0.4 - - - -
23A PHE* 1.3 99.9 - - - +
25A GLU* 1.3 61.4 + - - +
27A PHE* 4.1 6.6 + - - +
28A ASN* 3.4 15.4 - - - +
109A GLN* 3.1 31.4 + - - +
113A GLN* 3.9 11.6 + - - -
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Residues in contact with GLU 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 LYS 3.5 17.4 + - - +
22A THR* 3.8 6.4 - - - +
23A PHE 3.0 0.6 - - - -
24A SER* 1.3 80.9 - - - +
26A GLN* 1.3 65.0 + - - +
28A ASN* 3.5 19.1 - - + +
29A SER* 4.3 1.2 + - - -
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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 THR 3.4 2.7 + - - +
23A PHE 3.1 4.1 + - - +
25A GLU* 1.3 78.4 - - - +
27A PHE* 1.3 53.9 + - - +
28A ASN 2.8 4.9 - - - -
29A SER* 2.4 48.6 + - - +
30A LEU 3.7 1.2 + - - -
156A GLN* 3.2 58.8 - - + +
159A LEU* 3.9 2.9 - - + +
160A HIS* 3.0 53.9 + - - +
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Residues in contact with PHE 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 PHE* 3.0 50.8 + + - +
24A SER 4.2 3.4 - - - +
26A GLN* 1.3 76.9 - - - +
28A ASN* 1.3 62.2 + - - +
30A LEU* 3.0 20.4 + - + +
31A VAL 3.9 0.9 + - - -
47A SER* 4.1 9.9 - - - -
105A LYS* 3.4 27.0 + - + +
108A LEU* 4.2 12.6 - - + -
109A GLN* 3.5 46.2 - - + +
112A VAL* 5.0 0.9 - - + -
155A VAL* 3.5 29.8 - - + -
159A LEU* 3.2 42.2 - - + -
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Residues in contact with ASN 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 SER 3.4 17.8 - - - +
25A GLU* 3.5 13.9 + - - +
26A GLN 2.7 5.1 + - - -
27A PHE* 1.3 77.4 - - - +
29A SER* 1.3 51.4 + - - +
31A VAL* 2.7 36.9 - - - +
105A LYS* 4.9 3.1 - - - +
109A GLN* 5.2 3.8 + - - +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU 4.3 0.8 + - - -
26A GLN* 2.4 50.0 + - - -
28A ASN* 1.3 73.3 - - - +
30A LEU* 1.3 56.9 + - - -
31A VAL* 4.6 0.2 - - - -
32A ASN* 2.9 15.5 + - - +
160A HIS* 3.8 17.1 + - - -
163A ALA* 2.6 34.6 - - - +
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Residues in contact with LEU 30 (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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26A GLN 3.7 1.8 + - - -
27A PHE 3.0 13.3 + - - +
29A SER* 1.3 74.7 - - - +
31A VAL* 1.3 54.0 + - - +
32A ASN 2.5 17.2 + - - -
33A SER* 3.0 38.0 + - - +
39A PHE* 5.0 3.6 - - + +
40A ASN* 5.4 3.4 - - - +
43A LEU* 3.7 35.7 - - + -
105A LYS* 4.8 7.4 - - + +
159A LEU* 2.9 42.6 - - + +
162A ALA* 3.0 32.1 - - + -
163A ALA* 3.7 2.9 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE 3.9 2.2 + - - +
28A ASN* 2.7 33.5 + - - +
29A SER* 4.2 0.7 - - - +
30A LEU* 1.3 77.9 - - - +
32A ASN* 1.3 62.0 + - + +
33A SER* 2.8 10.1 + - - +
105A LYS* 5.3 10.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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