Contacts of the helix formed by residues 29 - 52 (chain B) in PDB entry 1PM9
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 LYS 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ASN* 3.8 18.6 - - + +
24B GLN* 5.9 1.3 - - - +
25B LEU* 3.0 35.2 + - + +
28B SER* 1.3 95.1 - - - +
30B ASN* 1.3 69.6 + - - +
31B HIS 3.6 0.2 - - - -
32B ALA* 3.8 1.1 - - - +
33B ALA* 2.9 26.0 + - - +
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Residues in contact with ASN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU* 5.2 0.6 + - - -
171A ASN* 4.0 17.1 + - - +
25B LEU 3.1 2.7 + - - +
26B HIS* 2.9 23.6 - - - +
29B LYS* 1.3 79.2 - - - +
31B HIS* 1.3 63.8 + - - +
33B ALA* 2.9 17.9 + - - +
34B TYR* 3.2 39.9 + - - -
74B HIS* 3.2 7.4 + - - -
161B TRP* 5.6 0.4 - - - -
163B HIS* 3.1 38.3 + - + -
200B MN3 3.1 10.4 + - - -
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Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.3 15.9 - - + +
5B PRO* 3.7 8.8 - - + +
26B HIS 3.0 9.0 + - - +
27B HIS 3.3 13.7 - - - +
29B LYS 3.6 0.2 - - - -
30B ASN* 1.3 79.1 + - - +
32B ALA* 1.3 64.4 + - - +
34B TYR* 3.0 20.0 + - - +
35B VAL* 3.1 14.3 + - + +
70B GLY 4.4 0.8 + - - -
71B HIS* 3.2 47.8 - + - -
74B HIS* 3.7 14.1 - - + +
75B SER* 3.4 16.6 + - - -
78B TRP* 2.8 36.9 + + + -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.8 19.7 - - + +
27B HIS 3.3 3.8 + - - -
28B SER 3.2 28.9 - - - +
29B LYS 3.8 1.3 - - - +
30B ASN 3.3 0.2 - - - -
31B HIS* 1.3 77.9 - - - +
33B ALA* 1.3 61.7 + - - +
35B VAL* 2.7 30.5 - - + +
36B ASN* 3.0 10.6 + - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS 2.9 15.8 + - - +
30B ASN* 2.9 11.4 + - - +
32B ALA* 1.3 77.6 - - - +
34B TYR* 1.3 66.2 + - + +
36B ASN* 3.2 6.7 + - - +
37B ASN* 3.0 36.8 + - - +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASN* 3.2 49.1 + - - -
31B HIS* 3.0 14.4 + - - +
33B ALA* 1.3 81.6 - - + +
35B VAL* 1.3 56.5 + - - +
37B ASN 3.3 0.2 + - - -
38B LEU* 2.8 30.0 + - - +
66B PHE* 3.8 25.4 - + - -
67B ASN* 3.4 43.5 - - - +
70B GLY* 3.8 14.4 - - - -
71B HIS* 4.0 8.1 - - - +
74B HIS* 3.5 15.0 - + - -
143B GLN* 2.9 25.9 + - + -
161B TRP* 3.8 16.5 - - - -
163B HIS* 4.3 0.2 - - - -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B HIS* 5.1 2.0 - - + +
3B SER* 4.2 14.1 - - - +
4B LEU* 4.3 17.9 - - + +
31B HIS* 3.1 16.6 + - + +
32B ALA* 2.7 35.2 - - + +
34B TYR* 1.3 74.8 - - - +
36B ASN* 1.3 63.1 + - - +
38B LEU* 3.3 8.9 + - - +
39B ASN* 3.1 34.0 + - - +
71B HIS* 3.2 39.3 - - + +
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Residues in contact with ASN 36 (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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32B ALA 3.0 14.2 + - - +
33B ALA* 3.5 10.4 + - - +
35B VAL* 1.3 79.4 - - + +
37B ASN* 1.3 81.4 + - - +
39B ASN* 3.4 7.1 + - - +
40B VAL* 3.2 33.9 + - - +
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.0 20.9 + - - +
34B TYR* 5.4 0.2 - - - -
36B ASN* 1.3 88.4 + - - +
38B LEU* 1.3 55.1 + - - +
40B VAL* 3.5 8.2 - - - +
41B THR* 2.8 41.3 + - - +
67B ASN* 3.1 40.0 + - - +
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Residues in contact with LEU 38 (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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2B HIS* 3.5 40.4 - - + +
34B TYR 2.8 17.9 + - - +
35B VAL* 3.6 5.2 - - - +
36B ASN 3.3 0.4 - - - -
37B ASN* 1.3 77.3 - - - +
39B ASN* 1.3 57.4 + - - +
41B THR* 3.7 2.6 - - - -
42B GLU* 2.8 44.4 + - + +
64B LEU* 3.7 21.8 - - + -
67B ASN* 3.9 10.0 - - + +
68B GLY* 3.6 23.6 - - - +
71B HIS* 3.7 28.3 - - + +
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS* 3.7 10.6 - - - +
2B HIS* 2.9 54.6 + - - +
35B VAL* 3.1 22.9 + - - +
36B ASN* 3.8 7.2 + - - +
38B LEU* 1.3 79.0 - - - +
40B VAL* 1.3 63.4 + - + +
42B GLU* 3.9 6.1 - - - +
43B GLU* 3.3 22.0 + - - +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASN* 3.2 28.9 + - - +
37B ASN* 3.5 11.7 - - - +
38B LEU 3.2 0.2 - - - -
39B ASN* 1.3 80.0 - - + +
41B THR* 1.3 63.3 - - - +
43B GLU* 3.4 3.7 + - - +
44B LYS* 3.2 49.4 + - + +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 2.8 25.7 + - - +
38B LEU* 3.9 4.3 - - - -
40B VAL* 1.3 74.1 - - - +
42B GLU* 1.3 62.1 + - - +
44B LYS* 3.3 16.3 + - - +
45B TYR* 2.9 23.2 + - + +
60B LEU* 3.9 21.0 - - + +
63B ALA* 3.8 20.0 + - + +
64B LEU* 3.7 41.1 - - + +
67B ASN* 4.6 1.6 + - - -
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Residues in contact with GLU 42 (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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1B LYS* 5.8 1.2 - - - -
2B HIS* 2.8 37.2 + - + -
38B LEU* 2.8 38.3 + - + +
39B ASN* 3.9 6.3 - - - +
40B VAL 3.3 0.2 - - - -
41B THR* 1.3 72.8 - - - +
43B GLU* 1.3 63.7 + - - +
45B TYR* 3.1 8.7 + - - +
46B GLN* 2.9 21.2 + - - +
64B LEU* 4.2 10.5 - - + +
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Residues in contact with GLU 43 (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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39B ASN 3.3 15.0 + - - +
40B VAL* 3.8 4.5 - - - +
41B THR 3.3 0.2 - - - -
42B GLU* 1.3 78.6 - - - +
44B LYS* 1.3 65.4 + - + +
46B GLN* 2.9 20.3 + - + +
47B GLU* 3.0 28.3 + - + +
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Residues in contact with LYS 44 (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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40B VAL* 3.2 36.1 + - + +
41B THR* 3.3 17.7 + - - +
43B GLU* 1.3 78.0 - - + +
45B TYR* 1.3 62.7 + - - +
47B GLU* 3.2 20.6 + - - +
48B ALA* 3.0 23.9 + - - +
60B LEU* 3.8 30.3 - - + +
63B ALA* 5.9 2.0 - - - +
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Residues in contact with TYR 45 (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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41B THR* 2.9 14.7 + - + +
42B GLU* 3.4 11.9 - - - +
43B GLU 3.1 0.2 - - - -
44B LYS* 1.3 77.8 - - - +
46B GLN* 1.3 58.1 + - - +
48B ALA* 3.3 1.6 + - - +
49B LEU* 2.8 47.5 + - + +
57B GLN* 2.7 62.0 + - + +
60B LEU* 3.8 21.7 - - + +
61B GLN* 5.3 10.6 + - + -
64B LEU* 5.3 14.6 - - + -
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Residues in contact with GLN 46 (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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42B GLU 2.9 12.6 + - - +
43B GLU* 2.9 14.1 + - + +
45B TYR* 1.3 79.5 - - - +
47B GLU* 1.3 60.5 - - + +
49B LEU* 3.6 23.4 - - - +
50B ALA* 3.2 23.3 + - + +
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Residues in contact with GLU 47 (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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43B GLU* 3.0 29.5 + - + +
44B LYS* 3.6 25.9 + - - +
45B TYR 3.2 0.2 - - - -
46B GLN* 1.3 75.7 - - + +
48B ALA* 1.3 64.9 + - - +
50B ALA* 3.5 4.0 + - - +
51B LYS* 3.2 48.2 + - + +
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Residues in contact with ALA 48 (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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44B LYS 3.0 16.4 + - - +
45B TYR* 3.8 5.6 - - - +
47B GLU* 1.3 77.1 - - - +
49B LEU* 1.3 62.9 + - - +
51B LYS* 3.1 3.8 + - - -
52B GLY 3.0 4.3 + - - -
53B ASP* 2.9 39.8 + - - +
56B ALA* 3.6 32.1 - - + -
57B GLN* 4.0 9.6 + - + +
60B LEU* 4.6 2.2 - - + -
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Residues in contact with LEU 49 (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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45B TYR* 2.8 33.4 + - + +
46B GLN* 3.6 22.4 - - - +
48B ALA* 1.3 76.7 - - - +
50B ALA* 1.3 60.8 + - - +
52B GLY* 3.2 13.3 + - - -
57B GLN* 3.6 29.2 + - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 3.2 19.0 + - + +
47B GLU* 3.9 5.2 - - - +
49B LEU* 1.3 79.8 - - - +
51B LYS* 1.3 62.4 + - + +
52B GLY 3.4 0.4 + - - -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 3.2 35.2 + - + +
48B ALA* 3.1 7.6 + - - +
50B ALA* 1.3 80.1 - - + +
52B GLY* 1.3 62.8 + - - +
53B ASP* 3.4 9.5 + - + +
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA 3.0 4.5 + - - -
49B LEU 3.2 11.1 + - - -
50B ALA 3.4 1.0 - - - -
51B LYS* 1.3 79.3 - - - +
53B ASP* 1.3 58.9 + - - +
54B VAL* 3.1 16.7 + - - +
57B GLN* 4.4 5.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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