Contacts of the helix formed by residues 21 - 39 (chain A) in PDB entry 1PEA
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 ALA 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A SER 3.5 12.8 - - - +
16A GLU 3.3 25.8 - - - +
17A THR* 3.4 24.1 + - - -
18A GLY 3.3 9.5 + - - +
19A VAL 3.6 0.8 + - - -
20A THR* 1.3 77.4 - - - +
22A ASP* 1.3 59.8 + - - +
25A ARG* 2.9 39.8 + - - +
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Residues in contact with ASP 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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19A VAL 5.5 0.2 + - - -
20A THR 3.2 1.0 - - - -
21A ALA* 1.3 78.7 - - - +
23A ILE* 1.3 65.1 + - - +
25A ARG* 3.0 31.9 + - - +
26A SER* 3.3 17.3 + - - -
237A ALA* 4.2 20.1 - - + +
238A GLU* 5.8 2.0 - - + +
241A LYS* 3.5 37.4 + - - +
279A ASN 5.3 3.8 - - - +
281A THR* 5.3 1.9 + - - -
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Residues in contact with ILE 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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20A THR* 3.2 29.5 - - + +
22A ASP* 1.3 77.0 - - - +
24A GLU* 1.3 68.9 + - + +
26A SER* 2.9 26.6 + - - -
27A GLN* 3.0 8.1 + - - +
83A TYR* 3.4 42.2 - - + +
207A GLY* 5.5 0.7 - - - -
233A THR 5.5 0.2 - - - +
235A SER* 3.6 18.8 - - - +
237A ALA* 4.4 3.8 - - + +
238A GLU* 3.7 17.0 + - - +
283A THR* 3.8 18.4 - - + +
285A TRP* 3.5 28.3 - - + -
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Residues in contact with GLU 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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14A PHE* 3.4 20.2 - - + +
15A SER* 2.8 35.7 + - - +
20A THR* 2.9 36.5 + - - +
23A ILE* 1.3 77.8 - - + +
25A ARG* 1.3 56.7 + - - +
27A GLN* 3.2 22.4 + - - +
28A ARG 2.8 23.6 + - - -
63A TYR* 2.5 32.4 + - - -
83A TYR* 3.5 25.9 + - + +
84A MET* 4.6 4.5 + - - +
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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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15A SER 3.9 3.8 + - - +
16A GLU* 3.2 51.6 + - - +
21A ALA* 2.9 24.5 + - - +
22A ASP* 3.0 36.5 + - - +
23A ILE 3.2 0.2 - - - -
24A GLU* 1.3 72.1 - - - +
26A SER* 1.3 66.3 + - - +
28A ARG* 3.3 7.5 + - - +
29A TYR* 3.0 39.8 + - + -
279A ASN* 3.1 60.8 + - - +
280A ALA* 4.0 9.2 - - + +
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Residues in contact with SER 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 ASP 3.3 9.4 + - - -
23A ILE* 2.9 16.3 + - - -
25A ARG* 1.3 81.1 - - - +
27A GLN* 1.3 57.4 + - - +
29A TYR* 3.7 0.7 + - - -
30A GLY 3.4 9.2 + - - -
276A PHE* 4.1 2.4 - - - -
280A ALA* 4.8 3.5 - - - +
281A THR* 2.8 35.1 + - - +
283A THR* 3.0 30.3 + - - +
286A ALA* 2.9 23.2 - - - +
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Residues in contact with GLN 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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14A PHE* 3.6 19.5 - - + -
23A ILE 3.0 11.4 + - - +
24A GLU* 3.4 33.6 + - - +
25A ARG 3.1 0.2 - - - -
26A SER* 1.3 77.2 - - - +
28A ARG* 1.3 67.1 + - - +
30A GLY 3.4 0.5 + - - -
31A ALA* 3.1 17.7 + - - +
82A CYS 3.9 1.0 + - - -
83A TYR* 3.4 19.2 - - - +
105A PRO* 3.2 28.1 + - - +
106A THR* 3.2 24.5 + - - -
285A TRP* 3.7 24.5 - - + +
286A ALA* 3.9 6.5 - - - +
289A ALA* 3.3 12.7 - - + +
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Residues in contact with ARG 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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12A LEU* 3.9 17.5 - - + -
14A PHE* 3.5 35.4 + - + +
15A SER 5.7 0.4 + - - -
16A GLU* 3.1 29.9 + - - +
24A GLU 2.8 17.1 + - - +
25A ARG* 3.3 8.5 + - - +
27A GLN* 1.3 76.1 - - - +
29A TYR* 1.3 84.4 + - - +
31A ALA* 3.0 6.3 + - - +
32A LEU* 2.9 44.6 + - + +
53A SER* 4.1 28.1 + - - -
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Residues in contact with TYR 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* 3.0 31.3 + - + +
28A ARG* 1.3 102.8 + - - +
30A GLY* 1.3 64.7 + - - +
32A LEU* 3.2 25.9 + - + +
33A LEU* 2.9 25.6 + - - +
275A PHE* 3.9 27.4 - + - -
276A PHE* 3.5 27.6 - + + -
277A PRO* 3.6 40.0 - - + +
280A ALA* 3.8 7.2 - - + -
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Residues in contact with GLY 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 SER 3.4 10.8 + - - -
27A GLN 3.4 1.3 + - - -
28A ARG 3.4 1.0 - - - -
29A TYR* 1.3 76.6 - - - +
31A ALA* 1.3 60.5 + - - +
33A LEU* 3.6 4.6 + - - +
34A ALA 3.2 16.3 + - - -
268A PHE* 5.5 1.6 - - - -
276A PHE* 3.5 13.1 - - - -
286A ALA 3.6 19.7 - - - -
290A TYR* 3.4 26.0 - - - +
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Residues in contact with ALA 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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12A LEU* 4.1 24.0 - - + -
14A PHE* 4.4 4.7 - - + -
27A GLN 3.1 12.2 + - - +
28A ARG* 3.0 12.0 + - - +
30A GLY* 1.3 75.6 - - - +
32A LEU* 1.3 64.7 + - - +
34A ALA* 3.1 13.7 + - - +
35A VAL* 3.2 17.3 + - - +
80A VAL* 4.5 1.8 - - + -
289A ALA* 4.0 8.2 - - + +
293A THR* 3.9 22.0 - - + +
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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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12A LEU* 3.7 17.7 - - + -
28A ARG* 2.9 38.7 + - + +
29A TYR* 3.2 36.1 + - + +
31A ALA* 1.3 74.3 - - - +
33A LEU* 1.3 51.8 + - - +
35A VAL* 3.2 8.8 + - + +
36A GLU* 2.8 33.3 + - - +
51A THR* 3.7 24.7 - - + +
53A SER* 5.2 1.8 - - - +
275A PHE* 3.9 16.6 - - + -
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Residues in contact with LEU 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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29A TYR 2.9 16.7 + - - +
30A GLY* 3.7 4.7 - - - +
32A LEU* 1.3 75.1 - - - +
34A ALA* 1.3 64.2 + - - +
36A GLU* 3.9 10.8 - - + -
37A GLN* 3.1 40.0 + - + +
268A PHE* 4.7 6.3 - - + +
271A ALA* 4.9 9.6 - - + +
272A CYS* 4.0 31.6 - - - +
275A PHE* 3.5 32.6 - - + -
276A PHE* 4.6 1.3 - - + -
290A TYR* 3.8 22.7 - - + -
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Residues in contact with ALA 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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30A GLY 3.2 8.6 + - - +
31A ALA 3.1 5.4 + - - +
33A LEU* 1.3 79.1 - - - +
35A VAL* 1.3 57.1 + - - +
37A GLN* 3.7 2.7 + - - +
38A LEU* 2.9 34.6 + - - +
290A TYR* 3.4 28.7 - - + +
293A THR* 3.4 31.6 - - + -
294A LEU* 4.0 10.2 - - + +
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Residues in contact with VAL 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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10A ILE* 4.2 11.4 - - + -
12A LEU* 6.3 1.1 - - + -
31A ALA 3.2 12.4 + - - +
32A LEU* 3.6 9.2 - - + +
34A ALA* 1.3 75.6 - - - +
36A GLU* 1.3 68.5 + - - +
38A LEU* 3.9 8.0 - - + +
39A ASN* 2.9 23.0 + - - +
49A ILE* 3.6 33.4 - - + +
51A THR* 3.9 28.5 - - + +
293A THR* 3.7 19.3 - - + -
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Residues in contact with GLU 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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32A LEU 2.8 13.3 + - - +
33A LEU* 3.3 20.4 - - + +
35A VAL* 1.3 82.0 - - - +
37A GLN* 1.3 61.1 + - + +
39A ASN* 2.8 5.2 + - - +
40A ARG* 2.8 62.6 + - + +
275A PHE* 4.0 26.1 - - + -
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Residues in contact with GLN 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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33A LEU* 3.1 31.9 + - + +
34A ALA 4.0 1.8 - - - +
36A GLU* 1.3 77.5 - - + +
38A LEU* 1.3 62.1 + - - +
40A ARG* 3.3 14.9 - - - +
41A GLU* 3.1 30.2 + - + +
271A ALA* 5.0 7.8 - - - +
290A TYR* 2.9 39.1 + - - -
294A LEU* 4.2 13.2 - - + +
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Residues in contact with LEU 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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10A ILE* 6.0 0.9 - - + -
34A ALA 2.9 33.0 + - - +
35A VAL* 3.9 4.3 - - + +
36A GLU 3.3 0.2 - - - -
37A GLN* 1.3 77.4 - - - +
39A ASN* 1.3 59.2 + - - +
41A GLU* 3.6 10.7 - - - +
43A GLY* 2.8 32.9 + - - +
44A VAL* 5.2 0.7 - - + -
49A ILE* 3.7 27.8 - - + -
293A THR* 3.5 27.6 - - + +
294A LEU* 3.9 17.9 - - + +
297A GLY* 4.1 9.9 - - - -
298A ARG* 3.4 39.5 - - - +
301A GLN* 4.5 6.1 - - - +
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Residues in contact with ASN 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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35A VAL* 2.9 23.6 + - - +
36A GLU* 2.8 6.1 + - - +
38A LEU* 1.3 74.3 - - - +
40A ARG* 1.3 55.3 + - + +
41A GLU 2.7 16.7 + - - -
42A GLY* 2.8 4.7 + - - -
43A GLY* 2.8 19.5 + - - -
48A PRO* 3.6 15.9 - - - +
49A ILE* 2.7 55.8 + - - +
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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