Contacts of the helix formed by residues 30 - 43 (chain B) in PDB entry 5UHE
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 PHE 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG 4.7 1.3 - - - -
41A THR* 4.0 26.5 - - + -
44A SER* 4.4 6.3 - - - -
45A SER* 3.1 37.0 - - - -
214A THR* 4.5 11.7 - - + -
215A LEU* 4.4 8.5 - - + -
218A LEU* 6.0 9.2 - - + -
26B LEU* 3.4 17.0 - - + +
27B GLU* 2.9 41.9 + - + +
28B PRO 4.9 1.6 - - - -
29B GLY* 1.3 78.1 - - - +
31B GLY* 1.3 65.6 + - - +
32B TYR 3.3 1.8 - - - -
33B THR* 3.5 31.5 - - + -
34B LEU* 3.1 25.5 + - + +
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Residues in contact with GLY 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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26B LEU* 3.8 10.8 - - - -
30B PHE* 1.3 78.9 - - - +
32B TYR* 1.3 56.9 + - - +
34B LEU* 3.3 2.9 + - - +
35B GLY* 2.9 23.7 + - - -
178B VAL* 3.7 29.2 - - - +
190B ASP* 3.2 17.9 + - - +
192B LEU* 4.0 9.5 - - - +
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Residues in contact with TYR 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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40A ARG* 3.9 18.8 - - - +
29B GLY* 4.5 1.2 + - - -
30B PHE 3.3 0.2 - - - -
31B GLY* 1.3 71.7 - - - +
33B THR* 1.3 65.4 + - - +
34B LEU 3.1 2.0 - - - -
35B GLY* 3.1 15.0 + - - +
36B ASN* 3.9 6.4 + - - +
37B SER 5.4 0.2 + - - -
176B TYR* 5.2 11.2 - + - -
178B VAL* 3.5 44.9 + - + +
190B ASP* 4.6 7.4 - - - -
727C GLU* 5.3 2.5 - - - -
903C ASP* 5.2 2.7 - - - -
1014C ARG* 3.1 88.5 + - + +
1015C SER* 5.9 0.4 - - - -
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Residues in contact with THR 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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37A SER* 3.5 38.1 + - - +
40A ARG* 2.7 34.6 + - + +
41A THR* 3.9 0.9 - - - +
215A LEU* 4.9 4.6 - - + +
219A PHE* 5.3 1.7 - - - -
29B GLY 2.4 27.5 + - - -
30B PHE* 3.5 36.3 - - + -
31B GLY 3.3 0.2 - - - -
32B TYR* 1.3 80.2 - - - +
34B LEU* 1.3 55.9 + - - +
37B SER* 3.5 12.5 + - - -
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Residues in contact with LEU 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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218A LEU* 5.3 14.8 - - + +
219A PHE* 3.4 44.2 - - + -
23B ILE* 4.2 19.7 - - + -
26B LEU* 4.0 22.0 - - + -
30B PHE* 3.1 18.3 + - + +
31B GLY 3.9 2.7 - - - +
33B THR* 1.3 76.6 - - - +
35B GLY* 1.3 67.2 + - - +
37B SER* 3.3 7.0 + - - -
38B LEU* 3.3 24.8 - - + +
192B LEU* 3.9 16.7 - - + +
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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 GLY 2.9 15.9 + - - -
32B TYR 3.1 6.9 + - - -
34B LEU* 1.3 82.0 - - - +
36B ASN* 1.3 62.1 + - - -
37B SER 3.0 2.1 + - - -
38B LEU* 3.0 9.9 + - - +
39B ARG* 3.5 9.2 + - - +
176B TYR* 3.7 28.3 - - - +
192B LEU* 4.4 7.0 - - - -
194B LEU* 5.8 1.6 - - - +
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Residues in contact with ASN 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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33A THR* 3.2 7.3 + - - -
32B TYR 3.9 6.7 + - - +
35B GLY* 1.3 71.5 - - - +
37B SER* 1.3 60.5 + - - +
38B LEU 3.4 0.2 - - - -
39B ARG* 3.7 15.2 + - - -
40B ARG* 3.3 31.9 + - - +
176B TYR* 3.3 30.9 + - - +
1015C SER* 3.0 37.5 + - - +
1017C GLU* 3.2 34.2 + - - +
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Residues in contact with SER 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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30A PHE* 4.2 6.9 - - - -
33A THR* 3.2 19.9 + - - -
34A LEU* 5.2 5.4 - - - -
37A SER* 3.2 29.3 + - - -
219A PHE* 4.4 11.3 - - - -
32B TYR 5.4 0.2 + - - -
33B THR 3.5 9.4 + - - -
34B LEU* 3.3 12.8 + - - -
36B ASN* 1.3 77.1 - - - +
38B LEU* 1.3 57.3 + - - +
39B ARG 3.5 0.3 + - - -
40B ARG 3.7 0.3 + - - -
41B THR* 2.7 33.4 + - - -
215B LEU* 4.1 3.8 - - - +
219B PHE* 6.1 1.1 - - - -
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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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219A PHE* 4.7 7.0 - - + -
222A ALA* 5.6 6.5 - - + -
23B ILE* 4.6 14.8 - - + -
34B LEU* 3.3 35.4 - - + +
35B GLY* 3.0 5.1 + - - +
37B SER* 1.3 81.0 + - - +
39B ARG* 1.3 60.3 + - - +
41B THR* 3.8 2.1 - - - -
42B LEU* 3.3 24.2 + - + +
192B LEU* 5.2 3.4 - - + -
194B LEU* 4.3 23.3 - - + -
208B LEU* 4.4 23.6 - - + -
211B ALA* 4.8 13.2 - - + +
212B GLY* 4.9 3.8 - - - -
215B LEU* 3.8 21.5 - - + -
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Residues in contact with ARG 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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35B GLY 3.5 8.0 + - - +
36B ASN* 4.0 14.5 + - - +
37B SER 3.2 0.4 - - - -
38B LEU* 1.3 77.0 - - - +
40B ARG* 1.3 82.8 + - - +
41B THR 3.0 5.8 + - - -
42B LEU* 3.4 2.9 + - - +
43B LEU* 3.2 37.4 + - + +
173B LYS* 3.0 22.0 - - - +
174B VAL* 2.8 46.1 + - + -
176B TYR* 4.1 26.9 - - + -
194B LEU* 5.2 2.0 - - + +
619D ILE* 3.8 6.5 - - - +
623D ASP* 2.8 34.6 + - - -
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Residues in contact with ARG 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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28A PRO 5.3 1.1 - - - -
29A GLY* 2.7 45.5 + - - +
30A PHE* 3.2 21.3 - - + -
33A THR* 3.8 12.8 - - + -
36B ASN* 3.3 24.0 + - - +
37B SER 3.7 1.5 + - - +
38B LEU 3.6 0.2 - - - -
39B ARG* 1.3 100.6 - - - +
41B THR* 1.3 57.0 + - - +
43B LEU* 4.2 5.4 - - - -
44B SER* 3.2 40.0 - - - +
1017C GLU* 3.5 34.2 + - - +
623D ASP* 3.9 36.4 + - - +
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Residues in contact with THR 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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30A PHE* 3.3 9.7 - - - -
37B SER 2.7 22.5 + - - -
38B LEU 3.8 5.6 - - - -
39B ARG 3.0 0.6 - - - -
40B ARG* 1.3 76.6 - - - +
42B LEU* 1.3 61.9 + - - +
43B LEU 3.2 1.3 - - - -
45B SER* 2.6 47.8 + - - +
46B ILE* 4.1 0.3 - - - +
211B ALA* 3.3 36.1 - - + +
214B THR* 4.2 3.6 - - + +
215B LEU* 3.1 32.1 - - + +
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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
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38B LEU* 3.3 18.6 + - + +
39B ARG 3.4 4.8 + - - +
41B THR* 1.3 79.7 - - - +
43B LEU* 1.3 60.5 + - - +
44B SER 3.7 0.2 + - - -
46B ILE* 4.1 11.3 - - + +
169B SER* 3.5 4.5 + - - -
171B VAL* 3.3 37.9 - - + +
174B VAL* 4.4 9.2 - - + -
194B LEU* 4.5 6.1 - - + -
196B VAL* 4.0 27.8 - - + -
207B ALA* 3.1 44.0 - - + +
208B LEU* 4.0 18.2 - - + +
211B ALA* 3.2 18.8 - - + -
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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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39B ARG* 3.2 57.7 + - + +
40B ARG* 4.6 4.9 - - - +
41B THR 3.2 0.4 - - - -
42B LEU* 1.3 77.6 - - - +
44B SER* 1.3 64.8 + - - +
145B GLY* 3.4 12.0 - - - -
169B SER* 3.2 17.6 + - - -
171B VAL* 4.0 30.3 - - + +
172B LEU 4.3 9.4 - - - +
173B LYS* 4.4 1.8 - - + +
174B VAL* 4.2 20.0 - - + +
619D ILE* 5.6 1.8 - - + -
620D MET* 4.0 20.8 - - + +
623D ASP* 4.0 9.0 - - + +
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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