Contacts of the helix formed by residues 34 - 49 (chain A) in PDB entry 1PS9
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 ASP 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 5.0 2.2 - - - +
33A PRO* 1.3 84.2 - - + +
35A GLY* 1.3 63.8 + - - +
36A ALA* 3.3 2.7 - - - +
37A GLU* 3.3 15.6 + - + +
38A ARG* 3.1 35.8 + - + +
364A LYS* 6.3 0.4 - - - +
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Residues in contact with GLY 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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29A LEU* 3.3 35.2 - - - -
32A TYR* 3.1 13.4 + - - +
33A PRO 3.3 0.8 + - - -
34A ASP* 1.3 73.6 - - - +
36A ALA* 1.3 59.2 + - - +
38A ARG* 2.9 4.3 + - - -
39A LEU* 2.6 40.6 + - - +
82A HIS* 4.4 2.4 - - - -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 5.3 0.2 + - - -
34A ASP* 3.3 1.1 - - - -
35A GLY* 1.3 74.6 - - - +
37A GLU* 1.3 57.5 + - - +
40A ALA* 3.0 29.8 + - - +
82A HIS* 3.2 56.8 - - + +
85A THR* 4.1 9.9 - - + +
86A ILE* 3.6 12.5 - - - +
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Residues in contact with GLU 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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34A ASP* 3.3 22.0 + - + +
35A GLY 3.1 0.6 - - - -
36A ALA* 1.3 79.0 - - - +
38A ARG* 1.3 66.1 + - + +
40A ALA* 3.6 7.2 - - - +
41A ALA* 3.3 21.7 + - - +
85A THR* 3.9 19.8 - - - +
363A THR* 4.3 6.0 - - + +
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Residues in contact with ARG 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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29A LEU* 3.3 35.9 - - + +
32A TYR* 3.6 24.9 - - - -
34A ASP* 3.1 26.4 + - + +
35A GLY* 2.9 4.3 + - - +
37A GLU* 1.3 75.5 - - + +
39A LEU* 1.3 60.7 + - - +
41A ALA* 3.3 3.8 + - - +
42A PHE* 2.9 28.8 + - - +
350A VAL* 4.4 2.8 - - - +
360A CYS 2.9 26.3 + - - +
361A HIS* 3.4 28.1 + - - +
362A GLU* 4.6 3.5 - - - +
363A THR* 3.5 24.8 + - - +
364A LYS* 3.5 38.2 - - + +
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Residues in contact with LEU 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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27A THR* 3.6 31.4 - - + +
29A LEU* 3.9 13.5 - - + -
30A GLU* 3.4 33.7 - - + +
35A GLY 2.6 24.5 + - - +
38A ARG* 1.3 70.4 - - - +
40A ALA* 1.3 59.0 + - - +
42A PHE* 3.4 9.1 - - + +
43A TYR* 2.8 58.3 + - + +
82A HIS* 4.8 4.5 - - - +
86A ILE* 3.8 28.0 - - + -
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Residues in contact with ALA 40 (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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36A ALA 3.0 20.7 + - - +
37A GLU* 3.6 12.1 - - - +
39A LEU* 1.3 77.4 - - - +
41A ALA* 1.3 56.9 + - - +
43A TYR* 4.2 1.1 - - - +
44A ALA* 2.9 30.0 + - - +
85A THR* 3.7 29.4 - - + +
86A ILE* 4.1 11.6 - - - +
89A ALA* 3.5 15.4 - - + +
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Residues in contact with ALA 41 (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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37A GLU 3.3 7.1 + - - +
38A ARG 3.9 1.1 - - - +
39A LEU 3.3 0.4 - - - -
40A ALA* 1.3 78.6 - - - +
42A PHE* 1.3 66.8 + - - +
44A ALA* 4.0 5.7 - - - +
45A GLU* 3.3 21.5 + - - +
362A GLU* 4.3 9.6 - - + +
363A THR* 3.4 33.2 - - + -
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Residues in contact with PHE 42 (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 MET* 3.7 14.4 - - + -
25A MET* 4.8 2.0 - - + -
27A THR* 4.2 13.9 - - + -
29A LEU* 5.3 1.1 - - + -
38A ARG 2.9 18.2 + - - +
39A LEU* 3.4 15.9 - - + +
41A ALA* 1.3 78.8 - - - +
43A TYR* 1.3 96.8 + + - +
45A GLU 3.6 2.8 + - - -
46A ARG* 2.9 71.9 + - - +
314A LEU* 3.5 26.0 - - + -
360A CYS* 3.8 24.2 - - - -
362A GLU* 3.7 25.3 - - - +
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Residues in contact with TYR 43 (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 MET* 4.0 11.4 - - + -
25A MET* 4.3 7.8 + - - +
27A THR* 4.7 0.5 - - - +
30A GLU* 5.3 0.7 + - - -
39A LEU* 2.8 49.6 + - + +
40A ALA* 4.2 1.3 - - - +
42A PHE* 1.3 97.7 - + - +
44A ALA* 1.3 66.2 + - - +
45A GLU 3.1 2.5 - - - -
46A ARG* 2.9 16.2 + - - +
47A ALA* 3.0 13.0 + - - +
54A ILE* 3.8 30.3 - - + +
55A VAL 4.5 1.2 + - - -
56A SER* 3.4 29.0 - - - -
57A GLY 3.5 8.1 + - - -
86A ILE* 3.9 12.8 - - + -
90A VAL* 3.7 19.3 - - + -
97A ILE* 3.8 21.3 - - + -
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Residues in contact with ALA 44 (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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40A ALA 2.9 22.1 + - - +
41A ALA* 4.0 6.3 - - - +
42A PHE 3.5 0.2 - - - -
43A TYR* 1.3 75.7 - - - +
45A GLU* 1.3 58.0 + - - +
47A ALA* 4.4 3.8 - - - -
48A ARG* 2.7 31.8 + - - +
89A ALA* 3.7 26.0 - - + +
90A VAL* 4.4 2.8 - - - +
93A GLU* 3.6 17.7 - - + +
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Residues in contact with GLU 45 (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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41A ALA 3.3 13.6 + - - +
42A PHE 3.9 5.2 - - - +
43A TYR 3.1 1.0 - - - -
44A ALA* 1.3 79.7 - - - +
46A ARG* 1.3 71.0 + - - +
48A ARG* 3.4 13.8 + - - +
49A HIS* 3.1 44.3 + - + +
317A ALA* 3.9 19.2 - - + +
318A GLU* 4.5 12.6 - - - +
358A ARG* 5.0 9.5 + - - -
362A GLU* 4.3 18.0 - - - +
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Residues in contact with ARG 46 (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 MET* 3.6 27.4 - - - -
42A PHE* 2.9 59.9 + - - +
43A TYR* 2.9 8.2 + - - +
45A GLU* 1.3 79.2 + - - +
47A ALA* 1.3 65.4 + - - +
49A HIS* 3.2 10.7 + - - +
50A GLY 3.5 0.7 + - - -
51A VAL* 3.3 32.8 + - + +
54A ILE* 4.3 2.7 - - + -
313A PHE* 2.7 41.6 + - + -
314A LEU* 3.8 14.3 + - - +
317A ALA* 3.2 31.5 - - + +
356A ASN* 4.5 6.3 - - - +
359A ALA* 4.6 2.6 - - - +
362A GLU* 3.3 16.6 + - - -
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Residues in contact with ALA 47 (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* 4.7 6.8 + - - -
43A TYR 3.0 11.7 + - - +
44A ALA* 3.7 7.9 - - - +
46A ARG* 1.3 74.0 - - - +
48A ARG* 1.3 65.6 + - - +
49A HIS 3.0 0.9 + - - -
50A GLY* 3.4 11.3 + - - -
51A VAL 4.4 11.2 + - - +
54A ILE* 4.3 7.3 - - + +
90A VAL* 3.9 36.3 - - + +
93A GLU* 3.8 14.3 - - + +
95A GLY* 4.1 10.0 + - - -
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Residues in contact with ARG 48 (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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44A ALA 2.7 18.3 + - - +
45A GLU* 3.6 16.7 + - - +
47A ALA* 1.3 76.6 - - - +
49A HIS* 1.3 92.3 + - - +
50A GLY 3.5 1.3 + - - -
93A GLU* 3.3 37.6 - - - +
318A GLU* 5.8 0.6 + - - -
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Residues in contact with HIS 49 (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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45A GLU* 3.1 33.8 + - + +
46A ARG 3.2 7.8 + - - +
47A ALA 3.0 1.4 - - - -
48A ARG* 1.3 118.4 + - + +
50A GLY* 1.3 55.5 + - - +
51A VAL* 3.9 1.0 + - - +
313A PHE* 5.9 0.3 - - - -
317A ALA 3.5 19.4 - - - +
318A GLU* 3.4 36.3 + - + +
320A LEU* 3.4 9.2 + - - +
321A SER* 2.7 51.8 + - - +
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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