Contacts of the helix formed by residues 20 - 37 (chain B) in PDB entry 1URV
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 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B GLU* 4.9 1.1 - - - -
19B LEU* 1.3 78.2 - - - +
21B GLU* 1.3 65.6 + - - +
22B ALA* 3.3 11.8 + - - +
23B GLU* 3.1 36.3 + - - -
24B ARG* 2.9 24.4 + - - +
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Residues in contact with GLU 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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18B GLU* 5.2 0.6 + - - -
20B SER* 1.3 73.7 + - - +
22B ALA* 1.3 60.7 + - - +
24B ARG* 3.2 33.8 + - - +
25B LYS* 2.9 53.3 + - + +
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Residues in contact with ALA 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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20B SER* 3.3 8.8 + - - +
21B GLU* 1.3 80.6 - - - +
23B GLU* 1.3 57.8 + - + +
25B LYS* 3.6 8.4 + - - +
26B ALA* 3.0 27.2 + - - +
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Residues in contact with GLU 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 LEU* 4.0 10.3 - - + -
20B SER* 3.1 37.5 + - - +
21B GLU 3.3 0.6 - - - -
22B ALA* 1.3 75.6 - - + +
24B ARG* 1.3 66.2 + - - +
26B ALA* 3.3 2.7 + - - +
27B VAL* 3.1 29.5 + - - +
146B GLU* 5.5 2.4 - - - +
149B ARG* 5.4 3.5 - - - +
150B ALA* 3.8 25.4 + - + -
153B LYS* 3.3 43.5 + - - +
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Residues in contact with ARG 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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18B GLU* 4.2 19.8 + - - -
19B LEU* 4.5 12.0 + - + +
20B SER 2.9 16.1 + - - +
21B GLU* 3.3 41.1 + - - +
23B GLU* 1.3 73.6 - - - +
25B LYS* 1.3 66.9 + - - +
27B VAL* 3.2 3.5 + - - +
28B GLN* 3.0 45.5 + - - +
96B LEU* 3.5 27.8 + - + +
97B HIS* 3.4 49.0 + - - +
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Residues in contact with LYS 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 GLU* 2.9 37.6 + - + +
22B ALA* 3.8 8.1 - - - +
24B ARG* 1.3 77.4 - - + +
26B ALA* 1.3 57.1 + - - +
28B GLN* 3.8 11.9 + - - +
29B ALA* 2.9 32.6 + - - +
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Residues in contact with ALA 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 ALA 3.0 19.0 + - - +
23B GLU* 3.5 7.6 - - - +
24B ARG 3.2 0.4 - - - -
25B LYS* 1.3 76.6 - - - +
27B VAL* 1.3 56.3 + - - +
29B ALA* 3.4 4.9 + - - +
30B MET* 3.1 26.5 + - - +
146B GLU* 4.7 4.0 - - + +
147B THR* 3.9 26.0 + - - +
150B ALA* 3.8 16.4 - - + -
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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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19B LEU* 4.2 8.7 - - + -
23B GLU 3.1 20.2 + - - +
24B ARG 3.8 3.8 - - - +
26B ALA* 1.3 72.4 - - - +
28B GLN* 1.3 62.4 + - - +
30B MET* 3.4 6.4 + - - +
31B TRP* 2.9 27.4 + - - +
93B VAL* 4.3 6.1 - - + -
96B LEU* 3.9 17.0 - - + -
147B THR* 5.3 1.1 - - - -
150B ALA* 3.6 34.1 - - + +
151B TRP* 3.7 19.2 - - + +
154B LEU* 3.7 28.5 - - + -
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Residues in contact with GLN 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 ARG* 3.0 47.7 + - - +
25B LYS* 3.9 11.0 - - - +
27B VAL* 1.3 77.4 - - - +
29B ALA* 1.3 57.1 + - - +
31B TRP* 3.9 1.4 - - - +
32B ALA* 3.1 27.9 + - - +
93B VAL* 2.8 43.7 + - + +
94B GLU* 4.1 12.9 + - - +
96B LEU* 4.0 4.9 - - + +
97B HIS* 4.9 1.8 - - - +
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Residues in contact with ALA 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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25B LYS 2.9 18.6 + - - +
26B ALA* 3.8 5.6 - - - +
27B VAL 3.2 0.2 - - - -
28B GLN* 1.3 75.2 - - - +
30B MET* 1.3 63.2 + - - +
32B ALA* 3.8 6.8 + - - +
33B ARG* 3.8 14.0 + - - +
142B ASP* 5.6 1.9 - - - +
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Residues in contact with MET 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 ALA 3.1 13.8 + - - +
27B VAL* 3.7 9.2 - - - +
29B ALA* 1.3 73.4 - - - +
31B TRP* 1.3 61.5 + - - +
33B ARG* 2.9 31.0 + - + +
34B LEU* 3.1 38.0 + - + +
135B VAL* 3.9 9.4 - - + -
139B PHE* 3.3 30.1 - - + -
142B ASP* 3.3 29.4 - - + +
143B PHE* 3.6 24.0 - - + -
147B THR* 3.9 13.0 - - + -
151B TRP* 4.6 14.8 - - + -
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Residues in contact with TRP 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 2.9 18.8 + - - +
28B GLN 3.9 2.9 - - - +
30B MET* 1.3 76.7 - - - +
32B ALA* 1.3 55.2 + - - +
34B LEU* 3.2 28.5 + - + +
35B TYR* 2.7 54.3 + + + +
86B MET* 3.4 45.8 - - + -
89B LEU* 3.5 28.7 - - + -
90B ASN* 2.8 37.9 + - - +
93B VAL* 3.7 33.0 - - + -
94B GLU* 4.9 4.3 - - - -
131B ILE* 6.4 0.9 - - + -
151B TRP* 3.8 19.5 - + + -
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Residues in contact with ALA 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 GLN 3.1 17.9 + - - +
29B ALA* 4.0 8.5 - - - +
30B MET 3.2 0.2 - - - -
31B TRP* 1.3 78.5 - - - +
33B ARG* 1.3 60.3 + - - +
35B TYR* 4.1 6.4 - - - +
36B ALA* 3.2 23.0 + - - +
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Residues in contact with ARG 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 ALA 3.8 7.9 + - - +
30B MET* 2.9 19.3 + - + +
32B ALA* 1.3 78.8 - - - +
34B LEU* 1.3 62.5 + - - +
35B TYR 3.6 0.2 + - - -
36B ALA* 3.8 13.2 + - - +
37B ASN* 4.3 4.0 + - - +
139B PHE* 3.5 32.7 - - + -
142B ASP* 3.6 38.1 + - + +
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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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30B MET* 3.1 37.2 - - + +
31B TRP* 3.2 41.3 + - + +
33B ARG* 1.3 75.9 - - - +
35B TYR* 1.3 61.6 + - - +
37B ASN* 3.3 22.0 + - - +
38B SER* 3.4 3.5 + - - -
41B VAL* 3.7 22.1 - - + +
45B ILE* 5.9 1.6 - - + -
86B MET* 4.4 2.9 - - + +
131B ILE* 5.7 1.1 - - + -
135B VAL* 3.8 21.8 - - + -
139B PHE* 3.3 30.3 - - + -
151B TRP* 4.2 11.0 - - + -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B TRP* 2.7 42.9 + + + +
32B ALA* 4.2 5.6 - - - +
33B ARG 3.3 0.4 - - - -
34B LEU* 1.3 70.3 - - - +
36B ALA* 1.3 67.3 + - - +
37B ASN 3.1 2.5 - - - -
38B SER* 3.0 40.6 + - - +
86B MET* 4.0 8.7 - - + -
87B GLY* 5.0 5.3 - - - -
90B ASN* 3.6 45.9 + - + +
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Residues in contact with ALA 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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32B ALA 3.2 17.2 + - - +
33B ARG* 3.8 9.6 - - - +
34B LEU 3.3 0.2 - - - -
35B TYR* 1.3 78.1 - - - +
37B ASN* 1.3 58.8 + - + +
38B SER 3.8 0.9 + - - -
39B GLU* 4.9 2.8 - - - +
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Residues in contact with ASN 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 ARG 5.0 3.4 - - - +
34B LEU 3.3 7.6 + - - +
35B TYR 3.1 0.2 - - - -
36B ALA* 1.3 78.9 - - + +
38B SER* 1.3 64.6 + - - +
39B GLU* 3.1 7.5 + - - +
40B ASP* 3.2 43.4 + - - +
41B VAL* 3.2 24.5 + - + +
139B PHE* 5.9 2.2 - - + -
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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