Contacts of the helix formed by residues 32 - 45 (chain B) in PDB entry 5ICN
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 PRO 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A TYR* 6.0 0.7 - - - +
19B VAL 3.1 23.3 - - - +
20B GLY* 3.8 5.0 - - - -
22B TYR 3.1 26.5 - - - +
23B TYR* 4.7 5.4 - - + -
24B TYR* 4.0 26.7 - - + +
30B MET* 3.9 9.4 - - + +
31B LYS* 1.3 84.2 - - + +
33B HIS* 1.3 62.4 + - + +
34B ARG* 3.0 6.7 + - - +
35B ILE* 3.1 30.7 + - + +
109B PHE* 4.0 20.6 - - + -
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Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLU* 6.5 0.2 - - - -
328A TYR* 3.3 64.9 - + + +
20B GLY* 3.4 19.8 + - - +
21B ASN* 5.7 0.6 + - - -
31B LYS* 2.8 4.1 + - + +
32B PRO* 1.3 79.5 - - + +
34B ARG* 1.3 62.4 + - - +
35B ILE 3.1 0.4 - - - -
36B ARG* 3.1 21.6 + - + -
37B MET* 3.1 38.8 + - + +
305B ILE* 4.6 3.6 - - + -
333B TYR* 3.5 38.1 - + - -
336B TYR* 3.9 5.2 + + - -
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Residues in contact with ARG 34 (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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30B MET* 3.4 33.2 - - - +
31B LYS 3.2 20.2 + - - +
32B PRO* 3.0 3.4 + - - +
33B HIS* 1.3 77.7 - - - +
35B ILE* 1.3 71.9 + - + +
37B MET* 3.5 15.9 + - - +
38B THR* 2.8 28.6 + - - -
135B TRP 5.4 1.0 + - - -
136B ALA 5.7 3.0 + - - -
139B LEU* 6.1 3.2 - - - +
300B GLY 2.8 30.7 + - - +
301B GLY 3.5 7.5 + - - -
302B GLY* 3.4 26.6 + - - -
305B ILE* 3.6 29.2 - - + +
308B VAL* 3.8 22.2 - - + +
309B ALA* 4.4 2.8 - - - -
312B TRP* 3.4 22.0 - - + -
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Residues in contact with ILE 35 (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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13B TYR* 4.6 3.2 + - - +
15B TYR* 4.0 23.1 - - + -
19B VAL* 4.1 22.0 - - + -
32B PRO* 3.1 23.1 + - + +
34B ARG* 1.3 84.7 - - + +
36B ARG* 1.3 61.7 + - - +
37B MET 3.2 0.2 - - - -
38B THR* 3.3 7.8 + - - -
39B HIS* 2.8 27.7 + - - +
109B PHE* 5.3 4.0 - - + -
135B TRP* 4.2 20.0 - - + +
136B ALA* 3.7 29.8 - - + +
312B TRP* 4.2 20.6 - - + -
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLU* 3.3 31.7 + - - +
329A MET* 3.8 9.9 - - - +
15B TYR* 3.3 27.2 + - - +
17B GLY* 3.2 25.9 + - - -
20B GLY* 4.0 14.3 - - - -
21B ASN* 3.3 24.3 + - - +
32B PRO 4.1 0.6 + - - -
33B HIS* 3.1 26.2 + - + +
35B ILE* 1.3 78.6 - - - +
37B MET* 1.3 57.8 + - - +
39B HIS* 3.5 1.4 - - - +
40B ASN* 3.0 43.5 + - - +
333B TYR* 3.2 25.7 + - + +
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Residues in contact with MET 37 (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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33B HIS* 3.1 28.2 + - + +
34B ARG* 3.5 13.9 - - - +
35B ILE 3.2 0.2 - - - -
36B ARG* 1.3 74.3 - - - +
38B THR* 1.3 59.2 + - - +
40B ASN* 3.5 3.3 + - - +
41B LEU* 3.1 31.5 + - - +
305B ILE* 3.8 30.5 - - - +
306B ARG* 4.1 5.8 - - - -
309B ALA* 3.9 15.9 - - + -
331B ASN* 5.3 1.4 - - - +
333B TYR* 4.3 16.8 - - + -
336B TYR* 3.5 33.2 - - + -
337B PHE* 3.8 30.6 - - + -
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Residues in contact with THR 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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34B ARG 2.8 15.1 + - - -
35B ILE* 3.4 10.7 - - - -
37B MET* 1.3 75.2 - - - +
39B HIS* 1.3 67.7 + - - +
41B LEU* 2.8 13.7 + - - +
42B LEU* 2.8 23.0 + - + +
135B TRP* 4.0 27.8 - - + +
308B VAL 4.3 0.2 + - - -
309B ALA* 3.6 16.2 - - - +
312B TRP* 4.0 12.7 - - + -
313B THR* 3.6 33.9 - - - +
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Residues in contact with HIS 39 (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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252A PHE* 3.2 39.6 - + - -
13B TYR* 3.3 38.7 + + - +
15B TYR* 3.1 49.4 - + + -
35B ILE 2.8 20.2 + - - +
36B ARG 3.5 5.8 - - - +
38B THR* 1.3 74.1 - - - +
40B ASN* 1.3 66.2 + - - +
42B LEU* 3.2 7.0 + - - +
43B LEU* 3.1 19.8 + - - +
48B TYR* 4.0 22.2 - + - -
53B ILE* 4.9 3.4 - - + -
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASP* 2.8 35.4 + - - +
252A PHE* 3.3 26.7 - - - -
36B ARG* 3.0 27.5 + - - +
37B MET 3.8 4.9 - - - +
39B HIS* 1.3 78.6 - - - +
41B LEU* 1.3 65.8 + - - +
43B LEU* 3.4 2.5 + - - +
44B ASN* 3.1 29.1 + - - -
331B ASN* 4.8 5.6 - - + +
332B ASP* 4.0 3.8 + - - +
333B TYR* 3.6 28.7 + - + -
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Residues in contact with LEU 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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37B MET 3.1 16.2 + - - +
38B THR 2.8 10.7 + - - +
40B ASN* 1.3 68.9 - - - +
42B LEU* 1.3 57.4 + - - +
44B ASN* 2.9 4.9 + - - -
45B TYR* 2.6 40.6 + - + +
309B ALA* 4.2 14.4 - - + +
310B ARG* 4.5 2.2 - - - +
313B THR* 3.5 27.6 - - + +
328B LEU* 4.2 27.8 - - + -
329B PRO* 4.2 12.1 - - + +
331B ASN* 3.2 31.9 - - - +
337B PHE* 3.9 26.2 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 3.4 47.1 - - + +
38B THR* 2.8 25.6 + - + +
39B HIS* 3.3 7.4 - - - +
41B LEU* 1.3 76.6 - - - +
43B LEU* 1.3 59.5 + - - +
46B GLY 3.3 2.3 + - - -
47B LEU* 2.9 53.1 + - + +
48B TYR* 3.1 15.6 + - + +
51B MET* 4.7 3.1 - - + -
313B THR* 3.9 14.1 - - - +
316B THR* 3.6 36.6 - - + +
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Residues in contact with LEU 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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214A LEU* 5.7 4.7 - - + -
248A ASP* 4.1 16.2 - - - +
251A LEU* 3.9 30.1 - - + -
252A PHE* 3.6 49.6 - - + -
255A MET* 4.1 26.0 - - + -
39B HIS 3.1 6.2 + - - +
40B ASN 3.6 7.6 - - - +
41B LEU 3.1 0.4 - - - -
42B LEU* 1.3 75.2 - - - +
44B ASN* 1.3 60.2 + - - +
46B GLY* 3.2 16.6 + - - -
48B TYR* 3.6 23.3 - - + +
49B ARG* 5.4 3.3 + - - -
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Residues in contact with ASN 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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248A ASP* 3.0 27.2 + - - +
251A LEU* 3.9 15.2 - - - +
40B ASN 3.1 19.9 + - - +
41B LEU 2.9 2.3 + - - +
43B LEU* 1.3 75.6 - - - +
45B TYR* 1.3 59.0 + - - +
46B GLY 3.1 5.9 + - - -
329B PRO* 3.4 25.8 - - + +
330B TYR 3.1 29.1 + - - +
331B ASN* 3.2 10.6 - - + +
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Residues in contact with TYR 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 LEU* 2.6 19.1 + - + +
42B LEU 4.2 0.2 - - - +
44B ASN* 1.3 72.3 - - - +
46B GLY* 1.3 61.5 + - - +
47B LEU* 3.5 23.2 + - + +
50B LYS* 5.8 0.9 + - - -
313B THR* 3.8 26.2 - - + -
324B ILE* 3.5 36.7 - - + +
325B PRO* 2.5 41.5 + - + -
327B GLU 3.0 20.8 + - - -
328B LEU* 3.6 13.1 - - + -
329B PRO* 3.3 30.7 - - + -
343B LEU* 3.6 16.0 - - + +
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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