Contacts of the helix formed by residues 37 - 53 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY* 1.3 70.9 - - - -
38A LEU* 1.3 74.0 + - - +
39A PHE* 3.1 24.4 + + + -
40A PRO* 3.3 33.3 - - + +
41A GLU* 3.4 10.6 + - - +
129A LYS* 3.7 14.0 - - - -
152A TYR* 3.9 14.9 + - - -
153A PRO* 3.9 32.5 - - + +
154A ALA* 3.3 30.3 + - + +
157A ASP* 3.5 15.3 - - - -
433A MLT 4.4 1.3 - - - -
97B GLU* 5.2 0.2 - - - -
302B ARG* 3.1 14.4 - - - +
305B CYS* 3.2 27.8 - - + -
306B THR* 3.8 27.6 - - + -
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Residues in contact with LEU 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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36A GLY 3.5 4.2 + - - -
37A TYR* 1.3 78.7 - - - +
39A PHE* 1.3 86.9 + - + +
41A GLU* 3.4 6.6 - - - +
42A ILE* 2.9 44.1 + - + +
153A PRO* 4.1 20.1 - - + +
157A ASP* 5.0 0.6 + - - -
375A TRP* 3.9 22.9 - - + -
390A THR* 3.7 14.6 - - + -
391A PRO* 4.6 3.4 - - + -
394A GLY* 3.2 42.8 - - - +
395A PHE* 4.2 5.2 - - + -
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Residues in contact with PHE 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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37A TYR* 3.1 19.2 + + + -
38A LEU* 1.3 95.9 - - + +
40A PRO* 1.3 75.6 - - + +
42A ILE* 3.0 13.6 + - + +
43A ALA* 2.9 23.0 + - - +
62A GLY 4.9 0.7 - - - -
63A ILE* 4.4 30.5 - - + +
152A TYR* 4.4 4.3 - + - -
153A PRO* 4.0 18.8 - - + -
390A THR* 4.1 13.7 - - + -
395A PHE* 4.0 11.7 - + - -
404A ARG* 4.2 4.5 - - - -
433A MLT 3.5 55.2 - - - +
97B GLU* 6.0 0.2 - - - +
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Residues in contact with PRO 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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37A TYR* 3.3 27.1 - - + +
39A PHE* 1.3 90.2 - - + +
41A GLU* 1.3 49.7 + - - +
43A ALA* 3.1 8.5 + - + +
44A ARG* 2.7 35.6 + - - +
97B GLU* 4.3 9.9 - - - +
301B ASN* 6.2 0.7 - - - +
305B CYS* 3.6 35.9 - - + -
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Residues in contact with GLU 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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36A GLY* 4.8 9.9 - - - +
37A TYR 3.4 11.5 + - - +
38A LEU* 3.4 10.8 - - - +
40A PRO* 1.3 73.1 - - - +
42A ILE* 1.3 60.1 + - - +
44A ARG* 3.3 37.5 + - - +
45A ARG* 2.9 45.7 + - - +
375A TRP* 4.1 20.6 - - + -
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Residues in contact with ILE 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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38A LEU* 2.9 35.2 + - + +
39A PHE* 3.0 12.7 + - + +
41A GLU* 1.3 70.3 - - - +
43A ALA* 1.3 65.3 + - - +
45A ARG* 3.0 18.1 + - - +
46A ARG* 3.0 12.0 + - - +
62A GLY* 5.1 5.4 - - - -
63A ILE* 5.6 7.0 - - + +
375A TRP* 3.4 34.3 - - + -
378A PHE* 4.1 9.2 - - + -
388A VAL* 3.4 31.6 - - + -
389A THR 4.1 3.4 - - - +
390A THR* 4.6 7.4 - - + +
391A PRO* 3.7 21.5 - - + -
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Residues in contact with ALA 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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39A PHE 2.9 12.2 + - - +
40A PRO* 3.4 12.1 - - + +
42A ILE* 1.3 75.8 - - - +
44A ARG* 1.3 60.1 + - - +
46A ARG* 3.4 13.1 + - + +
47A SER* 3.0 31.1 + - - -
63A ILE* 6.2 4.7 - - + -
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Residues in contact with ARG 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 PRO 2.7 17.7 + - - +
41A GLU* 3.3 43.8 + - - +
42A ILE 3.2 0.2 - - - -
43A ALA* 1.3 72.7 - - - +
45A ARG* 1.3 86.6 + - - +
46A ARG 3.0 1.6 + - - -
47A SER* 3.1 17.9 + - - -
48A ALA* 3.1 25.1 + - - +
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Residues in contact with ARG 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 GLU* 2.9 30.0 + - - +
42A ILE 3.0 8.0 + - - +
44A ARG* 1.3 97.4 - - - +
46A ARG* 1.3 55.9 + - - +
48A ALA* 3.5 5.4 - - - +
49A HIS* 3.3 21.8 + - - +
375A TRP* 3.6 38.5 + - - +
378A PHE* 3.8 26.3 - - + -
379A ALA* 4.2 23.6 - - - +
382A LEU* 3.8 10.5 - - + +
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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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42A ILE 3.0 10.1 + - - +
43A ALA* 3.5 17.0 - - - +
44A ARG 3.0 0.8 - - - -
45A ARG* 1.3 76.8 - - - +
47A SER* 1.3 67.4 + - - +
48A ALA 3.1 1.3 - - - -
49A HIS* 3.3 9.7 + - - +
50A LEU* 3.2 43.1 + - - +
58A VAL* 3.8 30.0 + - - +
60A SER* 3.9 20.0 + - - -
378A PHE* 5.9 0.2 - - + -
382A LEU* 4.3 10.5 - - + -
388A VAL* 3.9 21.3 - - + +
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Residues in contact with SER 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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43A ALA 3.0 14.3 + - - -
44A ARG* 3.5 12.3 - - - -
46A ARG* 1.3 78.3 + - - +
48A ALA* 1.3 57.6 + - - +
50A LEU* 3.6 7.5 + - - +
51A LEU* 3.0 38.9 + - - +
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Residues in contact with ALA 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 ARG* 3.1 21.3 + - - +
45A ARG* 3.5 14.8 - - - +
46A ARG 3.1 0.2 - - - -
47A SER* 1.3 75.5 - - - +
49A HIS* 1.3 65.5 + - - +
50A LEU 3.2 0.2 - - - -
51A LEU* 3.1 12.8 + - - +
52A LYS* 3.0 22.2 + - - +
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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 ARG 3.3 12.7 + - - +
46A ARG 3.3 7.8 + - - +
48A ALA* 1.3 81.1 - - - +
50A LEU* 1.3 56.2 + - + +
52A LYS* 3.5 7.1 + - - +
53A TYR* 2.8 46.0 + + - +
56A ALA* 4.1 3.3 - - + +
58A VAL* 4.0 19.3 - - + -
382A LEU* 3.3 46.2 + - + +
383A GLU* 3.7 18.5 + - - -
386A HIS* 2.7 38.7 - + - +
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Residues in contact with LEU 50 (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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46A ARG* 3.2 43.7 + - - +
47A SER* 3.8 6.7 - - - +
48A ALA 3.2 0.6 - - - -
49A HIS* 1.3 73.3 - - - +
51A LEU* 1.3 60.8 + - - +
53A TYR 3.8 16.6 - - - +
54A PRO* 3.2 34.7 - - - +
56A ALA* 3.8 14.8 - - + +
58A VAL* 3.5 34.8 - - + -
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Residues in contact with LEU 51 (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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47A SER* 3.0 34.5 + - - +
48A ALA* 3.3 11.9 - - - +
50A LEU* 1.3 78.1 - - - +
52A LYS* 1.3 64.9 + - - +
53A TYR 3.3 0.3 + - - -
54A PRO* 3.7 12.0 - - - +
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Residues in contact with LYS 52 (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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48A ALA 3.0 11.7 + - - +
49A HIS* 3.8 11.4 - - - +
51A LEU* 1.3 76.0 - - - +
53A TYR* 1.3 96.1 + - + +
54A PRO* 3.7 5.8 - - - +
383A GLU* 3.0 29.3 + - - +
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Residues in contact with TYR 53 (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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49A HIS* 2.8 38.8 + + - +
50A LEU* 3.6 11.1 - - - +
52A LYS* 1.3 110.4 - - + +
54A PRO* 1.4 68.0 - - - +
55A ASP 2.9 4.5 + - - -
56A ALA* 3.1 25.5 + - + +
383A GLU* 2.4 45.9 + - - -
386A HIS* 4.3 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