Contacts of the helix formed by residues 18 - 33 (chain B) in PDB entry 2UUG
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 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B GLN 3.7 4.2 - - - +
17B GLN* 1.3 92.1 - - + +
19B TYR* 1.3 64.4 + - + +
20B PHE 3.1 0.5 + - - -
21B LEU* 3.2 8.5 + - + +
22B ASN* 3.0 37.1 + - - +
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Residues in contact with TYR 19 (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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14B GLU* 2.8 41.0 + - - +
17B GLN* 3.5 24.7 - - + -
18B PRO* 1.3 80.0 - - + +
20B PHE* 1.3 70.9 + + + +
22B ASN* 3.7 5.7 + - - +
23B THR* 2.5 37.1 + - - -
139B LEU 4.5 0.7 - - - +
140B GLY* 3.6 31.4 - - - -
143B THR* 3.7 24.4 - - + +
144B PHE* 3.5 19.9 + - + +
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU 3.6 16.6 - - - +
15B LYS* 3.5 46.9 - - + -
17B GLN 3.3 4.4 + - - +
18B PRO 3.2 0.8 - - - -
19B TYR* 1.3 94.7 - + + +
21B LEU* 1.3 65.8 + - + +
23B THR* 3.3 7.1 + - + -
24B LEU* 3.1 66.2 + - + +
45B PHE* 4.2 10.8 - + - -
140B GLY 5.7 0.4 - - - -
141B TRP* 4.3 7.2 - + - -
144B PHE* 3.8 50.3 - + + -
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Residues in contact with LEU 21 (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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15B LYS 3.0 24.2 - - - +
16B GLN* 3.7 26.0 - - + +
17B GLN 3.2 8.9 + - - +
18B PRO* 3.2 6.8 + - + +
20B PHE* 1.3 80.6 - - + +
22B ASN* 1.3 64.7 + - - +
24B LEU* 3.7 11.0 + - + +
25B GLN* 3.3 25.4 + - - +
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Residues in contact with ASN 22 (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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18B PRO* 3.0 28.8 + - - +
19B TYR* 4.0 5.2 - - - +
21B LEU* 1.3 75.4 - - - +
23B THR* 1.3 62.1 + - - +
25B GLN* 3.5 21.9 + - - +
26B THR* 2.7 35.5 + - - +
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Residues in contact with THR 23 (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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19B TYR 2.5 24.9 + - - -
20B PHE* 3.4 10.6 - - + -
22B ASN* 1.3 76.4 - - - +
24B LEU* 1.3 64.5 + - - +
26B THR* 3.0 17.4 + - - -
27B VAL* 3.1 14.6 + - - +
139B LEU* 2.7 41.0 + - + +
140B GLY* 3.7 8.7 - - - -
141B TRP* 4.0 38.6 - - + +
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Residues in contact with LEU 24 (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 PHE* 3.1 51.7 + - + +
21B LEU* 4.0 13.7 - - + +
23B THR* 1.3 75.9 - - + +
25B GLN* 1.3 58.1 + - - +
27B VAL* 3.4 7.5 + - - +
28B ALA* 3.1 26.7 + - - +
45B PHE* 3.9 14.8 - - + -
141B TRP* 3.6 28.9 - - + -
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Residues in contact with GLN 25 (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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21B LEU 3.3 15.0 + - - +
22B ASN* 3.7 26.4 + - - +
24B LEU* 1.3 76.5 - - - +
26B THR* 1.3 62.7 + - - +
28B ALA* 4.2 8.1 - - + +
29B SER* 3.1 26.8 + - - -
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Residues in contact with THR 26 (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 ASN* 2.7 27.0 + - - +
23B THR* 3.0 8.0 + - - -
25B GLN* 1.3 77.8 - - - +
27B VAL* 1.3 65.9 + - - +
29B SER* 3.1 7.7 - - - -
30B GLU* 3.1 36.2 + - + +
139B LEU* 4.1 28.1 - - + +
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Residues in contact with VAL 27 (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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23B THR 3.1 12.6 + - - +
24B LEU* 3.6 8.1 - - - +
26B THR* 1.3 74.3 - - - +
28B ALA* 1.3 66.1 + - - +
30B GLU* 3.2 2.8 + - - -
31B ARG* 3.0 52.6 + - - +
37B ILE* 3.7 17.1 - - + +
44B VAL* 5.9 0.2 - - + -
127B THR* 3.7 29.4 - - + +
136B HIS* 3.9 12.8 - - + +
139B LEU* 4.3 8.1 - - + -
141B TRP* 4.1 15.0 - - + -
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Residues in contact with ALA 28 (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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24B LEU 3.1 14.2 + - - +
25B GLN* 4.2 8.5 - - - +
27B VAL* 1.3 79.7 - - - +
29B SER* 1.3 62.0 + - - +
31B ARG* 3.3 9.4 + - - +
32B GLN* 3.0 42.4 + - - +
41B GLN* 4.6 15.0 - - - +
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Residues in contact with SER 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 3.1 23.0 + - - -
26B THR* 3.1 11.2 - - - -
28B ALA* 1.3 76.0 - - - +
30B GLU* 1.3 64.5 + - - +
32B GLN* 3.2 12.0 + - - +
33B SER* 2.9 27.1 + - - -
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Residues in contact with GLU 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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26B THR* 3.1 23.0 + - + +
27B VAL 3.2 1.8 + - - +
29B SER* 1.3 81.5 - - - +
31B ARG* 1.3 62.4 + - - +
33B SER* 3.2 15.1 + - - -
34B GLY 3.4 0.2 + - - -
35B VAL* 3.1 34.4 + - + +
37B ILE* 3.3 18.6 - - + +
129B ARG* 3.3 38.5 + - - +
136B HIS* 2.9 29.4 + - - -
139B LEU* 6.1 0.2 - - - +
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Residues in contact with ARG 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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27B VAL* 3.0 38.0 + - - +
28B ALA* 3.5 10.5 - - - +
29B SER 3.2 0.4 - - - -
30B GLU* 1.3 75.6 - - - +
32B GLN* 1.3 62.3 + - + +
34B GLY* 3.3 13.2 + - - -
35B VAL 3.7 11.1 - - - +
37B ILE* 3.1 42.9 + - + +
38B TYR 4.4 0.6 - - - -
39B PRO 2.4 32.5 + - - -
40B PRO* 3.5 0.8 - - - +
41B GLN* 3.3 53.9 - - - +
44B VAL* 4.0 11.7 - - - +
127B THR* 4.6 0.6 - - - +
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Residues in contact with GLN 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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28B ALA* 3.0 29.0 + - - +
29B SER* 3.2 7.8 + - - +
31B ARG* 1.3 74.1 - - + +
33B SER* 1.3 63.4 + - - +
34B GLY* 3.1 3.5 + - - -
41B GLN* 5.9 1.6 - - - +
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Residues in contact with SER 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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29B SER* 2.9 18.4 + - - -
30B GLU* 3.2 15.2 + - - -
32B GLN* 1.3 77.5 - - - +
34B GLY* 1.3 57.5 - - - +
35B VAL* 4.3 10.4 - - - +
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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