Contacts of the helix formed by residues 9 - 30 (chain B) in PDB entry 1A4I
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 GLY 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU 3.2 5.4 + - - -
8B ASN* 1.3 69.4 - - - +
10B LYS* 1.4 60.1 + - - +
12B ILE* 4.5 0.2 - - - -
13B SER* 2.7 33.8 + - - -
155B LEU* 4.5 4.3 - - - -
273B GLY 2.9 11.0 + - - -
274B GLY 3.2 24.7 - - - -
277B PRO* 3.7 8.0 - - - +
278B MET* 3.9 11.1 - - - +
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 3.1 9.2 + - - +
9B GLY* 1.4 76.7 - - - +
11B GLU* 1.3 60.4 + - + +
13B SER* 3.0 18.5 + - - +
14B ALA* 3.0 17.1 + - + +
17B ARG* 4.8 2.4 + - - +
273B GLY* 3.5 9.0 + - - +
277B PRO* 3.8 14.7 - - + +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 2.9 42.6 + - + +
10B LYS* 1.3 74.4 - - + +
12B ILE* 1.3 68.3 + - + +
14B ALA* 3.3 7.1 + - - +
15B GLN* 3.1 30.3 + - + +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.5 6.1 - - + -
8B ASN* 2.9 31.7 + - + +
11B GLU* 1.3 78.9 - - + +
13B SER* 1.3 62.4 + - - +
15B GLN* 3.2 18.6 + - - +
16B ILE* 3.0 30.8 + - + +
154B GLU* 4.8 0.2 - - + -
155B LEU* 3.6 21.5 - - + -
158B GLU* 4.1 39.7 - - + +
278B MET* 3.7 26.7 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY 2.7 24.4 + - - -
10B LYS* 3.0 12.5 + - - +
12B ILE* 1.3 76.8 - - - +
14B ALA* 1.3 57.8 + - - +
16B ILE* 3.2 6.8 + - - +
17B ARG* 2.9 41.6 + - - +
277B PRO* 3.2 31.3 + - - +
278B MET* 3.8 12.7 - - - -
281B ALA* 4.1 9.4 - - - +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 3.0 20.4 + - + +
11B GLU* 3.7 7.2 - - - +
12B ILE 3.2 0.2 - - - -
13B SER* 1.3 75.7 + - - +
15B GLN* 1.3 58.0 + - + +
17B ARG* 3.4 26.5 + - - +
18B ALA* 2.9 28.6 + - - +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU* 3.1 17.2 + - + +
12B ILE* 3.5 27.6 - - - +
14B ALA* 1.3 76.0 - - + +
16B ILE* 1.3 58.1 + - + +
18B ALA* 3.2 7.2 + - - +
19B ARG* 2.9 63.1 + - - +
158B GLU* 4.8 6.1 - - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.0 19.4 + - + +
13B SER* 3.6 7.4 - - - +
15B GLN* 1.3 76.7 - - + +
17B ARG* 1.3 58.1 - - - +
19B ARG* 3.2 20.9 + - - +
20B LEU* 2.9 37.1 + - + +
154B GLU* 3.6 38.4 - - + +
158B GLU* 6.1 0.2 - - - +
278B MET* 3.7 17.9 - - + -
281B ALA* 4.2 9.0 - - + +
282B MET* 3.8 21.5 - - + -
285B GLN* 4.2 17.7 - - - +
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 4.8 2.2 + - - +
13B SER* 2.9 25.5 + - - +
14B ALA* 3.5 35.2 + - - +
16B ILE* 1.3 72.4 - - - +
18B ALA* 1.3 60.9 + - - +
20B LEU* 3.3 8.1 + - + +
21B LYS* 2.9 28.6 + - - +
59B ALA* 4.7 20.4 - - - +
62B GLU* 6.1 3.2 - - - +
63B ILE* 3.8 20.8 - - + +
277B PRO 5.7 0.6 + - - -
280B VAL* 5.5 1.6 - - - -
281B ALA* 3.8 26.7 - - + +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 2.9 17.3 + - - +
15B GLN* 3.6 8.1 - - - +
17B ARG* 1.3 75.0 - - - +
19B ARG* 1.3 64.5 + - + +
21B LYS* 3.3 10.6 + - - +
22B ASN* 3.1 27.9 + - - +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN* 2.9 51.5 + - - +
16B ILE* 3.5 23.2 - - - +
18B ALA* 1.3 77.6 - - + +
20B LEU* 1.3 56.5 + - - +
22B ASN* 3.2 9.3 + - - +
23B GLN* 2.9 42.9 + - - +
154B GLU* 4.9 4.8 + - - -
158B GLU* 4.8 12.5 + - - -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 2.9 27.4 + - + +
17B ARG* 3.3 7.4 + - - +
19B ARG* 1.3 71.7 - - + +
21B LYS* 1.3 61.7 + - - +
23B GLN* 3.2 26.7 + - - +
24B VAL* 2.8 32.2 + - - +
63B ILE* 3.9 16.8 - - + -
281B ALA* 3.9 7.0 - - - +
284B MET* 3.7 18.2 - - + +
285B GLN* 3.5 50.5 - - + +
288B VAL* 4.1 15.9 - - + -
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG 2.9 13.7 + - - +
18B ALA* 3.4 13.2 - - - +
19B ARG 3.3 0.2 - - - -
20B LEU* 1.3 76.9 - - - +
22B ASN* 1.3 71.9 + - - +
24B VAL* 3.2 2.1 + - - +
25B THR* 2.9 35.7 + - - +
62B GLU* 2.7 49.7 + - + +
63B ILE* 3.5 22.3 - - + +
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 3.1 16.4 + - - +
19B ARG* 3.2 9.4 + - - +
21B LYS* 1.3 91.3 - - - +
23B GLN* 1.3 62.9 + - + +
25B THR* 3.4 8.0 + - - -
26B GLN* 3.0 30.1 + - + +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 2.9 31.5 + - - +
20B LEU* 3.2 23.0 + - - +
22B ASN* 1.3 76.1 - - + +
24B VAL* 1.3 62.3 + - + +
26B GLN* 3.2 6.7 + - - +
27B LEU* 2.9 33.5 + - - +
285B GLN* 5.6 2.8 - - - +
288B VAL* 3.9 10.0 - - + +
292B LYS* 3.0 34.4 + - - +
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU 2.8 17.8 + - - +
23B GLN* 1.3 75.3 - - - +
25B THR* 1.3 66.4 + - - +
27B LEU* 3.2 8.0 + - + +
28B LYS* 3.1 35.0 + - - +
36B PRO* 4.0 16.8 - - + -
63B ILE* 3.5 27.4 - - + +
64B GLY* 3.6 26.0 - - - +
65B ILE* 4.4 4.3 - - + -
288B VAL* 3.7 31.6 - - + -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS* 2.9 28.9 + - - +
22B ASN* 3.6 10.2 + - - +
24B VAL* 1.3 77.7 - - - +
26B GLN* 1.4 71.2 + - - +
28B LYS* 3.3 8.5 + - - +
29B GLU* 3.1 43.9 + - - +
63B ILE 5.0 0.9 + - - -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASN* 3.0 22.1 + - + +
23B GLN* 3.6 6.3 - - - +
25B THR* 1.4 80.0 - - - +
27B LEU* 1.3 60.8 + - - +
29B GLU* 3.2 21.5 + - - +
30B GLN* 2.8 46.8 + - + +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN 2.9 19.1 + - - +
24B VAL* 3.2 12.1 + - + +
26B GLN* 1.3 75.6 - - - +
28B LYS* 1.3 58.8 + - + +
30B GLN* 3.3 6.5 + - + +
31B VAL* 2.9 35.5 + - + +
34B PHE* 4.6 23.1 - - + +
36B PRO* 4.8 8.3 - - + -
288B VAL* 4.6 8.5 - - + +
291B ALA* 5.4 0.9 - - + -
292B LYS* 3.7 43.1 - - + +
295B LEU* 3.6 26.5 - - + -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.1 24.2 + - - +
25B THR* 3.6 7.5 - - - +
27B LEU* 1.3 81.0 - - + +
29B GLU* 1.3 62.1 + - + +
31B VAL 3.4 14.7 - - - +
32B PRO* 3.4 11.8 - - - +
33B GLY 4.4 1.8 + - - +
34B PHE* 3.5 24.7 - - - +
35B THR* 4.8 7.4 - - - +
36B PRO* 4.0 16.6 - - + -
64B GLY* 2.8 39.0 + - - -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 3.1 33.5 + - - +
26B GLN* 3.8 23.5 + - - +
28B LYS* 1.3 78.0 - - + +
30B GLN* 1.3 65.4 + - - +
31B VAL 3.3 0.6 + - - -
32B PRO* 3.7 13.3 - - - +
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Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN* 2.8 30.8 + - + +
27B LEU* 3.9 7.4 - - + +
29B GLU* 1.3 79.1 - - - +
31B VAL* 1.3 68.4 + - + +
32B PRO* 3.6 6.3 - - - +
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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
------------------------------------------------------------
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