Contacts of the helix formed by residues 28 - 40 (chain B) in PDB entry 1ESQ
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 VAL 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B THR* 3.5 17.0 - - + +
25B ASN* 3.0 34.2 + - - +
27B VAL* 1.3 85.3 - - + +
29B THR* 1.3 55.6 + - - +
30B ASN 3.4 2.7 - - - -
31B PHE* 3.3 5.8 + - + -
32B THR* 2.6 49.3 + - - +
194B THR 4.5 1.1 - - - +
195B GLY* 3.3 35.2 - - - +
198B SER* 3.6 15.7 - - - +
325B TZP 4.1 9.0 - - + -
30C ASN* 4.5 5.4 - - - +
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Residues in contact with THR 29 (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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26A ASN* 2.4 39.4 + - - +
27A VAL* 3.9 12.9 - - - +
24B THR* 4.2 10.1 - - + +
25B ASN 3.2 20.1 + - - +
26B ASN* 3.8 9.1 + - - -
27B VAL 3.8 0.6 - - - -
28B VAL* 1.3 77.5 - - - +
30B ASN* 1.3 67.3 + - - +
32B THR* 4.5 1.1 - - - -
33B ALA* 3.1 22.7 + - - +
45B MET* 3.6 13.8 - - + +
47B TYR* 3.5 24.0 - - - +
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Residues in contact with ASN 30 (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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27A VAL* 2.9 30.1 + - - +
28A VAL* 4.4 1.1 - - - -
30A ASN* 5.6 9.7 + - + +
31A PHE* 4.1 25.0 - - - +
194A THR* 3.2 16.8 - - - +
245A GLN* 4.8 9.1 + - - +
28B VAL 3.4 0.2 - - - -
29B THR* 1.3 79.1 + - - +
31B PHE* 1.3 67.8 + - - +
34B ASN* 3.2 36.3 + - - +
30C ASN* 5.8 10.0 - - + +
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Residues in contact with PHE 31 (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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28B VAL* 3.3 9.2 + - - +
30B ASN* 1.3 81.2 - - - +
32B THR* 1.3 59.2 + - - +
34B ASN* 3.5 2.7 + - - +
35B GLY* 2.8 27.5 + - - -
193B VAL* 4.0 16.2 - - + -
194B THR 3.9 16.2 - - - -
195B GLY* 4.0 21.5 - - - -
196B ALA* 4.4 3.8 - - - -
199B LEU* 3.5 32.9 - - + +
225B TYR* 4.7 0.4 - - - -
245B GLN* 3.7 35.4 - - + -
248B LEU* 4.0 14.6 - - + -
249B LEU* 4.1 23.8 - - + -
30C ASN* 3.8 22.4 - - - +
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Residues in contact with THR 32 (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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22B SER* 4.5 3.1 - - - +
24B THR* 4.9 3.3 - - + +
28B VAL* 2.6 44.0 + - - +
29B THR* 3.7 3.6 - - - -
31B PHE* 1.3 71.9 - - - +
33B ALA* 1.3 65.6 + - - +
35B GLY* 3.8 0.3 - - - -
36B LEU* 2.9 29.4 + - + +
45B MET* 3.9 17.0 - - + -
198B SER* 4.5 1.3 - - - +
199B LEU* 4.0 21.5 + - - +
202B SER* 3.3 34.1 - - - +
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Residues in contact with ALA 33 (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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27A VAL* 3.8 11.7 - - + -
194A THR* 3.6 26.5 - - + +
320A TZP 3.9 15.0 - - + -
29B THR 3.1 16.5 + - - +
32B THR* 1.3 76.4 - - - +
34B ASN* 1.3 57.7 + - - +
36B LEU 3.4 0.3 + - - -
37B LEU* 3.0 36.1 + - - +
43B PRO* 3.5 15.3 - - + +
45B MET* 3.9 5.1 - - + +
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Residues in contact with ASN 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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31A PHE* 5.9 0.5 - - - -
192A LYS 3.9 5.5 + - - +
193A VAL* 3.5 16.0 - - - +
194A THR* 2.9 40.1 - - - +
241A PRO* 5.5 1.0 - - - +
245A GLN* 3.3 25.4 + - - -
30B ASN* 3.2 30.0 + - - +
31B PHE* 3.8 4.0 - - - +
33B ALA* 1.3 73.9 - - - +
35B GLY* 1.3 65.9 + - - +
37B LEU* 3.4 3.3 + - - +
38B ALA* 3.0 24.9 + - - +
249B LEU* 3.8 17.5 - - + +
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Residues in contact with GLY 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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31B PHE 2.8 17.3 + - - -
34B ASN* 1.3 78.2 - - - +
36B LEU* 1.3 61.0 + - - +
38B ALA* 3.3 3.2 + - - +
39B LEU* 3.1 21.5 + - - +
199B LEU* 3.7 21.8 - - - -
203B VAL* 5.9 0.2 - - - -
249B LEU* 3.5 17.6 - - - +
252B LEU* 3.9 9.1 - - - +
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Residues in contact with LEU 36 (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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20B VAL* 4.0 22.9 - - + +
22B SER* 4.7 2.0 - - - +
32B THR* 2.9 23.9 + - + +
33B ALA 3.8 3.1 - - - +
35B GLY* 1.3 76.2 - - - +
37B LEU* 1.3 60.6 + - - +
39B LEU* 3.2 9.8 + - + +
40B GLY 3.0 5.7 + - - -
41B ALA* 2.9 45.4 + - + -
43B PRO* 3.5 30.3 - - + -
45B MET* 5.5 0.4 - - + -
199B LEU* 3.9 1.7 - - + +
202B SER* 3.9 41.7 - - - +
203B VAL* 4.3 7.4 - - + +
206B ALA* 4.3 8.1 - - + -
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Residues in contact with LEU 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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191A THR 4.0 16.4 - - - +
192A LYS* 2.8 55.8 + - + +
193A VAL 3.9 1.6 - - - +
194A THR* 3.4 37.7 - - - +
33B ALA 3.0 23.7 + - - +
34B ASN* 3.7 3.6 - - - +
35B GLY 3.3 0.2 - - - -
36B LEU* 1.3 75.5 - - - +
38B ALA* 1.3 55.6 + - - +
40B GLY* 3.3 6.9 + - - -
41B ALA 3.7 8.5 - - - +
42B SER* 5.0 1.8 - - - -
43B PRO* 3.8 23.3 - - + -
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Residues in contact with ALA 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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192A LYS* 4.0 6.4 + - - +
241A PRO* 3.9 22.4 - - + -
34B ASN 3.0 17.0 + - - +
35B GLY* 3.7 6.1 - - - +
36B LEU 3.3 0.2 - - - -
37B LEU* 1.3 73.5 - - - +
39B LEU* 1.3 64.7 + - - +
40B GLY 3.4 0.3 + - - -
249B LEU* 3.2 29.2 - - + +
252B LEU* 3.7 5.6 - - + -
253B SER* 3.0 28.7 + - - -
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Residues in contact with LEU 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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10B LEU* 4.4 20.0 - - + -
13B VAL* 4.1 14.1 - - + -
14B ARG* 3.0 33.1 + - - +
35B GLY 3.1 13.1 + - - +
36B LEU* 3.2 18.8 + - + +
38B ALA* 1.3 78.2 - - - +
40B GLY* 1.3 57.4 + - - +
41B ALA* 4.7 1.8 - - + -
203B VAL* 3.9 29.2 - - + -
206B ALA* 4.1 21.5 - - + -
207B PHE* 4.6 10.5 - - + -
224B SER* 5.7 4.0 - - - -
252B LEU* 3.3 30.2 + - + +
255B VAL* 5.8 2.0 - - + -
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Residues in contact with GLY 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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192A LYS* 4.3 9.2 - - - -
13B VAL* 4.0 9.2 - - - +
14B ARG* 4.2 11.7 - - - +
17B SER* 2.8 28.7 + - - -
36B LEU 3.0 2.0 + - - -
37B LEU 3.3 8.4 + - - -
38B ALA 3.2 2.4 - - - -
39B LEU* 1.3 78.8 - - - +
41B ALA* 1.3 62.8 + - - +
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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