Contacts of the helix formed by residues 34 - 48 (chain A) in PDB entry 3DAN
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 3.3 0.2 + - - -
33A THR* 1.3 72.6 - - - +
35A GLY* 1.3 66.7 + - - +
37A ASP* 3.8 9.2 + - - +
38A GLU* 3.4 20.4 + - - +
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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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28A GLU 4.8 2.8 - - - +
29A TYR 3.8 12.6 - - - -
30A PHE 5.7 2.9 - - - -
32A GLY 3.1 16.0 + - - +
33A THR 3.3 0.9 - - - +
34A GLY* 1.3 79.1 - - - +
36A ARG* 1.3 62.2 + - - -
38A GLU* 3.1 11.3 + - - +
39A TYR* 3.1 10.0 + - - +
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Residues in contact with ARG 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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29A TYR* 3.5 61.4 + - + +
30A PHE* 4.2 4.9 - - - -
35A GLY* 1.3 70.0 - - - -
37A ASP* 1.3 71.5 + - - +
39A TYR* 3.0 18.7 + - - +
40A PHE* 3.1 22.3 - - + -
209A THR 4.8 6.7 + - - -
210A LEU* 5.6 0.4 - - - +
211A ASP* 3.8 31.1 + - - +
375A TYR* 3.7 27.8 - - + +
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Residues in contact with ASP 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 GLY 3.8 7.8 + - - +
35A GLY 3.2 1.0 - - - -
36A ARG* 1.3 80.3 - - - +
38A GLU* 1.3 57.5 + - - +
40A PHE* 3.3 2.0 + - - -
41A ARG* 2.8 29.0 + - - +
375A TYR* 2.6 35.0 + - - -
377A PRO* 5.4 0.9 - - - +
378A PHE* 3.4 22.2 - - + -
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Residues in contact with GLU 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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28A GLU* 6.2 0.2 - - - +
33A THR* 3.3 28.7 - - - +
34A GLY* 3.4 12.7 + - - -
35A GLY 3.1 6.8 + - - +
37A ASP* 1.3 76.8 - - - +
39A TYR* 1.3 66.7 + - - +
41A ARG* 2.9 47.0 + - - -
42A SER* 2.8 42.4 + - - -
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP* 3.4 36.2 - - - +
28A GLU* 3.7 18.2 - - - +
29A TYR* 3.8 36.3 - + + -
35A GLY 3.1 6.9 + - - +
36A ARG* 3.0 21.0 + - - +
38A GLU* 1.3 76.0 - - - +
40A PHE* 1.3 80.9 + + - +
42A SER* 3.2 8.9 + - - -
43A ARG* 2.9 68.2 + - - +
54A ALA* 4.8 3.4 - - + -
55A ASN 2.6 30.3 + - - -
56A MET* 4.4 4.3 - - - -
57A PRO* 5.8 0.7 - - + -
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Residues in contact with PHE 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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29A TYR* 4.2 17.0 - + - -
36A ARG* 3.1 23.8 + - + -
37A ASP* 3.8 3.6 - - - +
38A GLU 3.1 0.2 - - - -
39A TYR* 1.3 92.0 - + - +
41A ARG* 1.3 65.2 + - - +
43A ARG* 3.2 4.5 + - - +
44A MET* 3.0 21.0 + - - +
52A PHE* 3.8 11.9 - + - -
56A MET* 4.0 19.1 - - + -
70A VAL* 4.1 20.2 - - + -
72A LEU* 4.0 10.0 - - + +
373A PHE* 3.4 35.9 - + - -
375A TYR* 3.6 40.8 - + - -
378A PHE* 3.9 15.5 - - + -
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Residues in contact with ARG 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 ASP 2.8 21.8 + - - +
38A GLU* 2.9 42.6 + - - +
40A PHE* 1.3 73.1 - - - +
42A SER* 1.3 69.4 + - - +
44A MET* 3.2 11.2 + - + +
45A GLN* 2.7 57.3 + - - +
378A PHE* 3.9 16.7 - - + -
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.9 6.4 + - - -
38A GLU* 2.8 37.3 + - - -
39A TYR 3.2 7.6 + - - -
41A ARG* 1.3 88.8 - - - +
43A ARG* 1.3 69.4 + - - +
45A GLN* 3.5 3.4 + - - +
46A LYS* 2.9 29.0 + - - +
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Residues in contact with ARG 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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25A ASP* 3.7 14.1 + - - -
28A GLU* 3.0 38.8 + - - -
39A TYR* 2.9 58.5 + - - +
40A PHE 3.2 2.6 + - - +
41A ARG 3.2 0.6 - - - -
42A SER* 1.3 82.1 + - - +
44A MET* 1.3 66.1 + - - +
46A LYS* 4.2 9.4 - - + -
47A TYR* 2.9 40.7 + - + +
52A PHE* 3.5 39.9 - - + -
53A ARG 5.1 1.3 + - - -
54A ALA* 4.2 13.7 - - - +
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Residues in contact with MET 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 PHE 3.0 12.3 + - - +
41A ARG* 3.2 15.0 + - - +
43A ARG* 1.3 75.7 - - - +
45A GLN* 1.3 57.9 + - - +
48A GLN* 2.8 30.1 + - - -
49A SER 3.2 28.8 + - - +
50A THR* 3.4 25.8 - - + -
52A PHE* 3.8 2.4 - - - -
72A LEU* 3.2 40.2 - - + +
378A PHE* 4.1 15.0 - - + -
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Residues in contact with GLN 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 ARG* 2.7 56.9 + - - +
42A SER* 3.7 5.4 - - - +
44A MET* 1.3 76.0 - - - +
46A LYS* 1.3 67.9 + - - +
48A GLN* 2.7 35.2 + - - +
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Residues in contact with LYS 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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42A SER 2.9 18.8 + - - +
43A ARG* 3.3 9.2 + - + +
45A GLN* 1.3 78.8 - - - +
47A TYR* 1.3 102.3 + - + +
48A GLN* 4.8 2.6 - - - +
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Residues in contact with TYR 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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12A PRO* 3.8 31.2 - - + +
13A GLY* 3.6 31.0 - - - -
14A SER* 4.2 4.7 + - - -
43A ARG* 2.9 37.2 + - + +
46A LYS* 1.3 121.4 + - + +
48A GLN* 1.3 72.5 + - - +
49A SER* 3.1 10.2 + - - +
52A PHE* 3.8 22.2 - + + -
53A ARG 4.7 4.2 + - - -
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Residues in contact with GLN 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 MET 2.8 10.7 + - - -
45A GLN* 2.7 38.5 + - - +
46A LYS 4.8 2.7 - - - +
47A TYR* 1.3 80.2 - - - +
49A SER* 1.3 58.0 + - - +
361A ASP* 4.9 9.2 - - - +
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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