Contacts of the helix formed by residues 20 - 38 (chain A) in PDB entry 3PMM
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 5.6 2.7 - - - +
19A ILE* 1.3 74.9 - - - +
21A ARG* 1.3 67.1 + - - +
22A SER* 4.1 11.0 - - - +
23A GLU* 2.9 29.9 + - + +
24A LEU* 3.0 21.1 + - - +
378A TYR* 4.1 1.3 - - - -
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Residues in contact with ARG 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 ARG* 5.7 2.2 - - - +
20A ALA* 1.3 71.6 - - - +
22A SER* 1.3 64.0 + - - +
24A LEU* 3.3 5.8 + - - +
25A GLN* 2.9 46.7 + - - +
375A LEU* 3.7 20.4 - - + -
378A TYR* 3.6 37.8 - - + -
379A PHE* 5.5 11.1 - - - -
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Residues in contact with SER 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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20A ALA* 4.1 10.4 - - - +
21A ARG* 1.3 80.1 - - - +
23A GLU* 1.3 63.3 + - - +
25A GLN* 3.5 11.4 + - - +
26A ALA* 3.1 27.5 + - - +
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Residues in contact with GLU 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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18A PHE 4.9 1.2 - - - +
19A ILE* 3.6 24.2 - - + +
20A ALA* 2.9 34.9 + - + +
22A SER* 1.3 77.6 + - - +
24A LEU* 1.3 61.0 + - - +
26A ALA* 3.3 7.5 + - - +
27A LEU* 2.8 29.3 + - - +
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Residues in contact with LEU 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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19A ILE* 3.9 22.9 - - + -
20A ALA 3.0 16.2 + - - +
21A ARG 3.6 4.0 - - - +
23A GLU* 1.3 75.4 - - - +
25A GLN* 1.3 65.4 + - - +
27A LEU* 3.2 9.6 + - + +
28A ILE* 3.0 28.8 + - + +
327A VAL* 5.1 1.8 - - + -
371A LEU* 4.0 37.7 - - + +
374A TYR* 3.7 26.5 - - + -
375A LEU* 3.5 32.1 - - + +
378A TYR* 3.7 15.7 - - + +
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Residues in contact with GLN 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 ARG* 2.9 49.1 + - - +
22A SER* 3.8 9.8 - - - +
24A LEU* 1.3 75.9 - - - +
26A ALA* 1.3 63.4 + - - +
28A ILE* 3.4 7.2 + - - +
29A ARG* 3.0 31.6 + - + +
77A TYR* 3.4 23.4 + - - +
80A GLN* 5.5 0.8 + - - -
81A THR* 4.5 14.6 - - - +
375A LEU* 3.9 19.6 - - + +
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Residues in contact with ALA 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 SER 3.1 17.6 + - - +
23A GLU* 3.6 8.1 - - - +
24A LEU 3.2 0.2 - - - -
25A GLN* 1.3 75.7 - - - +
27A LEU* 1.3 63.2 + - - +
29A ARG* 3.3 10.3 + - - +
30A ASN* 3.0 24.5 + - - +
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Residues in contact with LEU 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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19A ILE* 4.4 10.8 - - + -
23A GLU 2.8 17.0 + - - +
24A LEU* 3.4 7.9 - - + +
26A ALA* 1.3 76.8 - - - +
28A ILE* 1.3 62.2 + - - +
30A ASN* 3.2 11.5 + - + +
31A VAL* 3.0 29.9 + - + +
327A VAL* 4.1 32.5 - - + -
330A ILE* 3.7 33.7 - - + +
331A SER 5.3 2.2 - - - +
371A LEU* 3.9 24.5 - - + -
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Residues in contact with ILE 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 LEU* 3.0 20.0 + - + +
25A GLN 3.8 4.5 - - - +
26A ALA 3.3 0.2 - - - -
27A LEU* 1.3 74.6 - - - +
29A ARG* 1.3 59.7 + - - +
31A VAL* 3.4 7.3 + - - +
32A THR* 2.9 39.5 + - - +
77A TYR* 3.8 25.4 - - + -
86A MSE 4.4 2.9 - - + -
368A ILE* 4.3 15.6 - - + +
371A LEU* 3.6 28.0 - - + +
372A THR* 3.7 28.3 - - - +
375A LEU* 3.5 32.8 - - + -
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Residues in contact with ARG 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 GLN* 3.0 22.4 + - - +
26A ALA* 3.6 8.3 - - - +
27A LEU 3.3 0.2 - - - -
28A ILE* 1.3 75.9 - - + +
30A ASN* 1.3 57.7 + - - +
32A THR* 3.3 5.2 + - - -
33A GLN* 2.9 25.7 + - - +
77A TYR* 4.4 15.8 + - + +
83A ASP* 2.8 37.8 + - - -
85A GLU* 2.7 27.7 + - - +
86A MSE 4.8 4.8 - - - +
387A FMT 3.1 41.1 + - - +
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Residues in contact with ASN 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 ALA 3.0 16.8 + - - +
27A LEU* 3.2 11.6 + - + +
29A ARG* 1.3 74.5 - - - +
31A VAL* 1.3 59.1 + - - +
33A GLN* 3.3 21.5 + - - +
34A ASN* 3.0 25.8 + - - +
331A SER 4.5 1.0 + - - -
332A PRO* 3.0 28.4 + - - +
333A GLN 3.7 4.2 - - - +
334A GLY* 3.4 18.9 - - - +
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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
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27A LEU* 3.0 22.8 + - + +
28A ILE* 3.7 6.3 - - - +
30A ASN* 1.3 72.3 - - - +
32A THR* 1.3 61.0 + - - +
34A ASN* 3.2 3.5 + - - +
35A LEU* 2.9 26.5 + - - +
330A ILE* 3.9 35.0 - - + -
334A GLY* 3.6 19.5 - - - +
336A LEU* 6.0 0.4 - - + +
364A GLN* 3.3 40.0 - - + +
367A ALA* 4.3 8.1 - - + -
368A ILE* 3.7 9.6 - - + +
371A LEU* 5.1 2.2 - - + -
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Residues in contact with THR 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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28A ILE* 2.9 23.9 + - - +
29A ARG 3.5 6.3 - - - -
31A VAL* 1.3 78.0 - - - +
33A GLN* 1.3 62.3 + - - +
35A LEU* 3.2 3.5 + - + +
36A VAL* 3.0 23.7 + - + +
74A ILE* 4.0 24.0 - - + -
86A MSE 3.4 37.1 - - + +
89A ILE* 4.0 14.1 - - + -
368A ILE* 3.5 19.8 - - - +
387A FMT 4.2 4.3 - - - +
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Residues in contact with GLN 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 ARG 2.9 14.3 + - - +
30A ASN* 3.5 24.9 - - - +
31A VAL 3.2 0.4 - - - -
32A THR* 1.3 75.8 - - - +
34A ASN* 1.3 63.0 + - - +
36A VAL* 3.5 7.4 - - - +
37A ASN* 2.7 41.8 + - - +
387A FMT 4.1 9.6 + - - +
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Residues in contact with ASN 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 ASN 3.0 7.5 + - - +
31A VAL 3.4 8.3 - - - +
33A GLN* 1.3 77.4 - - - +
35A LEU* 1.3 64.0 + - - +
37A ASN* 3.0 14.7 + - - +
38A ILE* 3.1 19.2 + - - +
333A GLN* 3.0 29.9 + - - +
334A GLY 3.5 23.0 - - - +
335A GLU* 3.9 11.1 - - - +
359A SER* 5.1 0.3 + - - -
364A GLN* 2.9 22.7 - - + +
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Residues in contact with LEU 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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31A VAL 2.9 13.6 + - - +
32A THR* 3.5 8.3 - - - +
34A ASN* 1.3 78.7 + - - +
36A VAL* 1.3 62.5 + - + +
37A ASN 3.2 0.9 + - - -
38A ILE* 3.3 21.8 + - - +
60A TRP* 4.1 16.2 - - + +
70A GLY* 3.9 22.7 - - - -
74A ILE* 4.3 12.1 - - + -
361A PRO* 3.5 29.8 - - + +
364A GLN* 4.1 10.1 - - + +
365A ALA* 4.4 4.9 - - + +
368A ILE* 3.8 22.4 - - + -
380A IMD 3.6 33.3 + - + -
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Residues in contact with VAL 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 THR* 3.0 25.2 + - + +
33A GLN* 3.5 13.7 - - - +
35A LEU* 1.3 76.7 - - + +
37A ASN* 1.3 68.0 + - - +
38A ILE 3.5 0.4 - - - +
60A TRP* 3.3 65.2 - - + +
74A ILE* 4.5 2.5 - - + -
89A ILE* 4.0 23.1 - - + -
387A FMT 6.4 0.4 - - - -
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Residues in contact with ASN 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 GLN* 2.7 38.2 + - - +
34A ASN* 3.0 7.1 + - - +
36A VAL* 1.3 91.7 - - - +
38A ILE* 1.3 63.9 + - - +
39A LYS* 3.0 34.9 + - - +
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Residues in contact with ILE 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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34A ASN* 3.1 17.6 + - - +
35A LEU* 3.3 22.5 + - + +
36A VAL 4.6 0.7 - - - +
37A ASN* 1.3 79.2 - - - +
39A LYS* 1.3 65.5 + - - +
58A LYS* 3.2 34.3 - - + +
59A GLY* 3.4 15.6 - - - -
60A TRP* 3.5 7.6 + - - +
359A SER* 5.4 2.0 - - - +
360A MSE 4.5 0.9 - - - -
361A PRO* 3.6 43.5 - - + -
364A GLN* 3.8 16.8 - - - +
380A IMD 4.4 0.7 - - - +
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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