Contacts of the helix formed by residues 37 - 53 (chain B) in PDB entry 2Z1Z
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 TYR 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 5.8 0.2 - - - -
302A ARG* 3.5 22.4 - - - +
305A CYS* 3.8 30.5 - - + -
306A THR* 4.2 10.5 - - - -
34B GLN 4.1 0.2 + - - -
35B ALA 3.4 0.8 - - - -
36B GLY 1.3 86.9 + - - +
38B LEU* 1.4 69.2 - - - +
39B PHE* 3.3 29.0 + + + -
40B PRO* 3.5 29.0 - - + +
41B GLU* 3.3 17.2 + - - +
129B LYS* 4.1 22.3 + - - +
152B TYR* 5.1 5.0 - - - -
153B PRO* 3.6 20.8 - - + +
154B ALA* 4.3 12.6 + - - +
157B ASP* 2.9 29.4 - - - -
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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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35B ALA 5.2 2.2 + - - -
37B TYR* 1.4 79.6 - - - +
39B PHE* 1.3 88.9 + - + +
41B GLU* 3.0 11.4 - - - +
42B ILE* 2.9 54.5 + - + +
153B PRO* 4.6 8.5 - - + -
375B TRP* 3.9 17.7 - - + -
390B THR* 4.0 10.5 - - + -
391B PRO* 4.1 5.8 - - + -
394B GLY* 3.8 43.5 - - - +
395B PHE* 4.4 6.7 - - + -
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 4.0 26.7 - + + -
38B LEU* 1.3 92.0 - - + +
40B PRO* 1.4 65.3 - - + +
42B ILE* 3.4 17.2 + - + +
43B ALA* 2.8 32.8 + - - +
63B ILE* 4.0 51.8 - - + -
64B GLY 5.4 0.9 - - - -
152B TYR* 5.2 10.3 - + - -
153B PRO* 4.9 12.1 - - + -
209B ASN* 6.3 0.2 - - - -
390B THR* 3.9 21.1 - - + -
395B PHE* 4.3 16.2 - + - -
404B ARG* 4.6 7.0 - - - -
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Residues in contact with PRO 40 (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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305A CYS* 5.2 13.5 - - + -
36B GLY 5.1 4.3 - - - +
37B TYR* 3.5 31.9 - - + +
39B PHE* 1.4 92.8 - - + +
41B GLU* 1.3 55.3 + - - +
43B ALA* 3.6 8.5 - - + +
44B ARG* 2.8 39.1 + - - +
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Residues in contact with GLU 41 (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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35B ALA* 4.3 19.1 - - + +
36B GLY 5.3 0.2 - - - +
37B TYR 3.3 9.0 + - - +
38B LEU* 3.0 18.9 + - - +
40B PRO* 1.3 76.6 - - - +
42B ILE* 1.3 62.7 + - - +
44B ARG* 2.8 36.4 + - - +
45B ARG* 3.2 38.0 + - - +
375B TRP* 3.3 22.0 - - + -
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Residues in contact with ILE 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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38B LEU* 2.9 48.4 + - + +
39B PHE* 3.7 24.0 - - + +
41B GLU* 1.3 75.2 - - - +
43B ALA* 1.3 66.4 + - - +
45B ARG* 3.2 7.1 + - - +
46B ARG* 2.9 23.5 + - + +
62B GLY* 5.9 0.2 - - - -
63B ILE 5.6 2.2 - - - +
375B TRP* 4.2 9.4 - - + -
378B PHE* 3.5 30.5 - - + -
388B VAL* 3.6 20.9 - - + -
389B THR 4.0 2.7 - - - +
390B THR* 3.8 16.8 - - + +
391B PRO* 4.2 4.5 - - + -
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Residues in contact with ALA 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 PHE 2.8 21.8 + - - +
40B PRO* 3.4 11.2 + - + +
42B ILE* 1.3 72.7 - - - +
44B ARG* 1.4 60.8 + - - +
46B ARG* 3.4 13.6 + - + +
47B SER* 3.0 26.4 + - - -
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Residues in contact with ARG 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 PRO* 2.8 17.2 + - - +
41B GLU* 2.8 60.4 + - - +
42B ILE 3.2 0.2 - - - -
43B ALA* 1.4 71.8 - - - +
45B ARG* 1.3 61.8 + - + +
47B SER* 2.9 10.9 + - - -
48B ALA* 2.7 39.9 + - + +
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Residues in contact with ARG 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 GLU* 3.2 32.2 + - - +
42B ILE 3.2 8.1 + - - +
44B ARG* 1.3 87.4 - - + +
46B ARG* 1.3 51.9 + - - +
48B ALA* 3.6 9.2 - - + +
49B HIS* 2.8 34.7 + - - +
375B TRP* 3.8 28.7 + - - +
378B PHE* 3.6 26.6 - - + -
379B ALA* 3.7 26.3 - - - +
382B LEU* 3.8 9.3 - - + +
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Residues in contact with ARG 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 ILE* 2.9 16.4 + - + +
43B ALA* 3.5 11.7 - - - +
45B ARG* 1.3 73.7 - - - +
47B SER* 1.3 64.8 + - - +
49B HIS* 3.4 9.1 - - - +
50B LEU* 3.0 62.1 + - - +
58B VAL* 3.7 35.5 + - - +
60B SER* 5.5 4.4 - - - -
378B PHE* 6.2 0.2 - - + -
382B LEU* 4.4 7.9 - - + +
388B VAL* 4.2 20.4 - - + +
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Residues in contact with SER 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 ALA 3.0 11.7 + - - -
44B ARG* 2.9 13.6 + - - -
46B ARG* 1.3 74.3 + - - +
48B ALA* 1.3 66.4 + - - +
50B LEU* 3.0 9.9 + - - +
51B LEU* 2.9 37.2 + - - +
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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 ARG* 2.7 24.9 + - + +
45B ARG* 3.6 12.1 - - + +
47B SER* 1.3 73.1 - - - +
49B HIS* 1.3 62.0 + - - +
51B LEU* 3.2 13.9 + - - +
52B LYS* 3.2 18.5 + - - +
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Residues in contact with HIS 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 ARG 2.8 23.0 + - - +
46B ARG* 3.4 8.1 - - - +
48B ALA* 1.3 72.5 - - - +
50B LEU* 1.3 51.2 + - - +
52B LYS* 3.3 10.7 - - - +
53B TYR* 2.7 54.9 + + + +
56B ALA* 5.0 0.2 - - + -
58B VAL* 3.9 18.2 - - + -
382B LEU* 3.3 45.0 + - + +
383B GLU* 3.7 11.4 + - - -
386B HIS* 2.5 40.5 - + - -
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Residues in contact with LEU 50 (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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46B ARG* 3.0 51.3 + - - +
47B SER* 3.0 8.7 + - - +
49B HIS* 1.3 71.7 - - - +
51B LEU* 1.3 68.3 + - + +
52B LYS 3.2 1.1 - - - -
53B TYR 3.3 33.1 - - - +
54B PRO* 3.3 15.3 - - - +
56B ALA* 4.1 11.0 - - + +
58B VAL* 3.8 27.8 - - + -
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Residues in contact with LEU 51 (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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47B SER* 2.9 29.7 + - - +
48B ALA* 3.2 14.8 + - - +
50B LEU* 1.3 76.3 - - + +
52B LYS* 1.4 59.5 + - - +
54B PRO* 4.1 9.9 - - - +
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Residues in contact with LYS 52 (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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48B ALA 3.2 11.9 + - - +
49B HIS* 3.3 13.0 - - - +
50B LEU 3.2 0.2 - - - -
51B LEU* 1.4 76.9 - - - +
53B TYR* 1.3 90.9 + - + +
54B PRO* 3.3 8.6 - - - +
383B GLU* 2.9 26.5 + - - -
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Residues in contact with TYR 53 (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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49B HIS* 2.7 47.0 + + - +
50B LEU* 3.3 17.6 - - - +
52B LYS* 1.3 104.0 - - + +
54B PRO* 1.4 63.9 - - + +
55B ASP 3.4 2.0 - - - +
56B ALA* 3.1 35.1 + - + +
383B GLU* 2.7 30.2 + - - -
386B HIS* 3.6 16.8 - + + -
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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