Contacts of the helix formed by residues 32 - 52 (chain N) in PDB entry 1CZA
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 SER 32 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30N ARG 3.7 3.6 + - - -
31N LEU* 1.3 75.7 - - - +
33N ASP* 1.3 66.2 + - - +
34N GLU* 3.5 9.3 + - - +
35N THR* 3.1 27.7 + - - -
36N LEU* 3.0 21.4 + - - +
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Residues in contact with ASP 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N LEU 5.0 0.9 - - - +
32N SER* 1.3 73.3 - - - +
34N GLU* 1.3 59.9 + - - +
36N LEU* 3.1 14.3 + - - +
37N ILE* 2.8 42.0 + - + +
433N ARG* 2.6 52.2 + - - +
434N LEU* 4.2 14.6 - - + +
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Residues in contact with GLU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N SER* 3.2 9.4 + - - +
33N ASP* 1.3 78.0 - - - +
35N THR* 1.3 63.1 + - - +
37N ILE* 3.5 10.1 + - - +
38N ASP* 3.0 21.4 + - + +
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Residues in contact with THR 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N LEU* 4.1 16.1 - - + +
32N SER* 3.1 25.8 + - - -
34N GLU* 1.3 81.0 - - - +
36N LEU* 1.3 56.9 + - - +
38N ASP* 3.0 11.5 + - + +
39N ILE* 2.8 35.4 + - + +
42N ARG* 6.1 0.7 - - - +
273N ILE* 3.7 29.2 - - + -
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Residues in contact with LEU 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N LEU* 3.8 30.3 - - + +
32N SER 3.0 19.0 + - - +
33N ASP* 3.1 20.4 + - - +
35N THR* 1.3 76.3 - - - +
37N ILE* 1.3 56.0 + - - +
39N ILE* 3.2 10.8 + - + +
40N MET* 2.8 30.1 + - - +
384N ASN* 3.6 51.8 - - + +
385N LEU* 4.3 0.9 - - + +
388N ALA* 3.7 7.9 - - + +
430N THR* 3.9 19.1 - - + -
434N LEU* 4.1 15.5 - - + -
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Residues in contact with ILE 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N ASP* 2.8 30.9 + - + +
34N GLU* 3.8 7.4 - - - +
36N LEU* 1.3 68.6 - - - +
38N ASP* 1.4 61.5 + - - +
40N MET* 3.3 13.7 + - + +
41N THR* 2.7 40.3 + - - +
434N LEU* 4.2 22.4 - - + +
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Residues in contact with ASP 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N GLU* 3.0 16.3 + - + +
35N THR* 3.0 13.6 + - + +
37N ILE* 1.4 76.4 - - - +
39N ILE* 1.3 62.6 - - - +
41N THR* 3.1 9.0 + - - -
42N ARG* 2.9 63.8 + - - +
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Residues in contact with ILE 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N LEU* 4.1 6.1 - - + -
35N THR* 2.8 37.3 + - + +
36N LEU* 3.2 9.6 + - + +
38N ASP* 1.3 75.4 - - + +
40N MET* 1.4 62.9 + - - +
42N ARG* 3.2 15.3 + - - +
43N PHE* 2.9 22.9 + - - +
264N PHE* 3.7 24.4 - - + -
270N LEU* 4.6 9.0 - - + -
273N ILE* 4.1 22.0 - - + -
293N PHE* 5.0 1.1 - - + -
385N LEU* 3.8 29.8 - - + -
388N ALA* 4.2 13.9 - - + -
389N THR* 4.8 4.0 - - + -
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Residues in contact with MET 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N LEU 2.8 17.9 + - - +
37N ILE* 3.5 13.7 - - + +
39N ILE* 1.4 73.4 - - - +
41N THR* 1.4 59.0 + - - +
43N PHE* 3.3 2.2 + - - -
44N ARG* 3.0 24.6 + - + +
388N ALA* 3.2 30.3 - - - +
391N GLY* 3.6 15.5 - - - -
392N ALA* 3.4 19.7 - - - +
395N ASN* 3.7 24.5 - - - +
434N LEU* 3.5 47.8 - - + +
435N VAL* 4.4 2.2 - - + -
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Residues in contact with THR 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N ILE* 2.7 27.3 + - - +
38N ASP* 3.1 9.7 + - - -
40N MET* 1.4 73.8 - - - +
42N ARG* 1.3 65.3 + - - +
44N ARG* 3.2 16.3 + - + +
45N LYS* 3.1 21.1 + - - +
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Residues in contact with ARG 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N THR* 6.1 0.6 - - - +
38N ASP* 2.9 53.7 + - - +
39N ILE* 3.4 14.5 - - - +
41N THR* 1.3 77.4 - - - +
43N PHE* 1.3 60.9 + - - +
45N LYS* 3.2 16.6 + - - +
46N GLU* 3.0 25.3 + - + +
264N PHE* 4.0 13.0 - - + -
269N SER* 2.9 28.4 + - - +
270N LEU* 3.8 18.3 - - - +
272N ASP* 2.7 43.2 + - - -
273N ILE* 4.3 7.0 - - - +
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Residues in contact with PHE 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N ILE 2.9 15.4 + - - +
40N MET 3.8 4.0 - - - +
41N THR 3.2 0.4 - - - -
42N ARG* 1.3 75.6 - - - +
44N ARG* 1.3 63.1 + - - +
46N GLU* 3.1 3.0 + - + +
47N MET* 2.9 50.2 + - + +
61N VAL* 3.7 27.4 - - + -
259N THR* 4.3 6.3 - - - -
261N TRP* 3.6 43.5 - + + -
264N PHE* 3.6 37.0 - + + -
389N THR* 3.6 33.2 - - + -
392N ALA* 3.7 8.7 - - + -
393N ILE* 4.1 3.8 - - + -
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Residues in contact with ARG 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N MET* 3.0 13.8 + - + +
41N THR* 3.4 19.5 - - - +
43N PHE* 1.3 74.8 - - - +
45N LYS* 1.4 68.2 + - - +
47N MET* 3.4 10.6 + - - +
48N LYS* 3.2 36.2 + - - +
392N ALA* 4.0 15.6 - - + +
395N ASN* 6.0 6.7 - - + -
396N ARG* 5.3 7.1 + - + +
399N ASP* 5.0 11.7 + - - -
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Residues in contact with LYS 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N THR 3.1 11.5 + - - +
42N ARG* 3.2 16.6 + - - +
44N ARG* 1.4 86.0 - - - +
46N GLU* 1.4 69.4 + - - +
48N LYS* 3.2 8.6 + - + +
49N ASN* 3.1 38.6 + - - +
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Residues in contact with GLU 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N ARG* 3.0 19.0 + - - +
43N PHE* 3.1 8.5 + - + +
45N LYS* 1.4 80.0 - - - +
47N MET* 1.4 62.5 + - - +
49N ASN* 3.2 23.1 + - - +
50N GLY* 2.8 26.5 + - - -
59N ALA* 5.0 1.4 - - - +
60N THR* 3.8 21.0 + - - -
61N VAL* 3.6 27.9 + - + +
264N PHE* 4.0 21.5 - - + -
267N ASP* 3.8 17.2 - - - +
269N SER* 4.1 12.3 + - - -
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Residues in contact with MET 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N PHE* 2.9 49.6 + - + +
44N ARG* 3.6 9.2 - - - +
46N GLU* 1.4 76.2 - - - +
48N LYS* 1.3 64.6 + - - +
50N GLY 3.3 0.3 + - - -
51N LEU* 3.1 28.9 + - - +
61N VAL* 4.9 0.4 - - - -
63N MET* 3.6 22.1 - - + +
238N TYR* 3.5 41.5 - - + +
259N THR* 4.7 0.9 - - + -
392N ALA* 4.4 7.4 - - - +
393N ILE* 4.0 24.7 - - + -
396N ARG* 3.6 24.9 - - + -
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Residues in contact with LYS 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N ARG* 3.2 24.8 + - - +
45N LYS* 3.2 10.7 + - + +
47N MET* 1.3 79.3 - - - +
49N ASN* 1.3 63.4 + - - +
51N LEU* 3.3 5.2 + - + +
52N SER* 3.1 26.7 + - - -
55N PHE* 5.9 0.2 - - - -
396N ARG* 4.3 19.4 - - - +
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Residues in contact with ASN 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N LYS* 3.1 35.0 + - - +
46N GLU* 3.2 26.1 + - - +
48N LYS* 1.3 77.1 - - - +
50N GLY* 1.3 62.7 + - - +
52N SER* 3.3 8.0 + - - -
55N PHE* 3.5 36.0 - - + -
56N ASN 3.3 22.5 + - - -
59N ALA* 3.8 12.3 - - + +
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Residues in contact with GLY 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N GLU 2.8 15.4 + - - -
48N LYS 3.3 0.2 - - - -
49N ASN* 1.3 74.0 - - - +
51N LEU* 1.3 60.7 + - - +
56N ASN* 2.9 27.0 + - - +
59N ALA* 3.6 9.8 - - - +
61N VAL 3.2 24.2 - - - -
62N LYS 3.9 2.6 - - - +
63N MET* 3.7 13.1 - - - +
247N LEU* 4.8 1.9 - - - +
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Residues in contact with LEU 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N MET 3.1 17.2 + - - +
48N LYS* 3.3 4.9 + - + +
49N ASN 3.3 0.2 - - - -
50N GLY* 1.3 76.4 - - - +
52N SER* 1.3 63.5 + - - +
56N ASN* 5.1 0.2 - - - -
63N MET* 3.7 29.8 - - + +
240N GLU* 3.7 10.1 - - - +
244N HIS 3.4 19.5 - - - +
245N ILE* 4.0 24.0 - - + +
246N ASP* 3.3 25.7 + - - +
247N LEU* 4.4 4.5 + - - +
257N ILE* 4.2 13.9 - - + -
396N ARG* 3.5 37.5 - - - +
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Residues in contact with SER 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N LYS* 3.1 18.5 + - - -
49N ASN* 3.5 11.2 - - - -
50N GLY 3.3 0.6 - - - -
51N LEU* 1.3 78.2 - - - +
53N ARG* 1.3 58.5 + - - +
54N ASP* 3.0 21.0 + - - +
55N PHE* 3.1 18.3 + - - -
56N ASN* 2.8 35.0 + - - +
246N ASP* 3.5 8.4 + - - -
247N LEU* 5.1 0.2 - - - -
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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