Contacts of the helix formed by residues 25 - 38 (chain A) in PDB entry 1UZL
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 ARG 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY 4.0 4.9 + - - +
23A GLY 3.5 1.2 - - - -
24A ASN* 1.3 91.2 + - - +
26A GLY* 1.3 71.2 + - - +
27A ILE 3.4 0.2 + - - -
28A GLY* 3.2 7.8 + - - -
29A LEU* 3.1 17.5 + - - +
189A ASP* 4.9 16.4 - - - -
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 1.3 77.9 - - - +
27A ILE* 1.3 63.5 + - - -
29A LEU* 3.2 9.7 + - - +
30A ALA* 3.1 19.9 + - - +
188A THR* 5.5 11.0 - - - -
189A ASP* 6.0 3.6 - - - -
214A PRO* 4.7 7.4 - - - +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG 3.4 0.2 + - - -
26A GLY* 1.3 71.7 - - - -
28A GLY* 1.3 58.1 + - - +
30A ALA* 3.2 2.5 + - - +
31A ILE* 2.9 47.7 + - + +
88A ASN* 4.2 9.0 - - - +
138A ILE* 4.6 5.6 - - + -
141A VAL* 4.5 11.2 - - + -
183A PRO* 4.9 7.2 - - + -
186A ILE* 3.7 40.6 - - + -
188A THR* 4.3 17.1 - - + +
214A PRO* 4.3 16.4 - - + +
217A VAL* 4.1 22.2 - - + -
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.8 1.4 - - - +
22A GLY 3.4 20.4 + - - -
23A GLY* 3.6 9.4 - - - -
25A ARG 3.2 4.2 + - - -
27A ILE* 1.3 79.1 - - - +
29A LEU* 1.3 55.4 + - - +
31A ILE* 3.3 4.0 + - - +
32A ALA* 2.9 30.5 + - - +
88A ASN* 3.6 21.4 - - - +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY 3.4 14.2 + - - +
24A ASN 4.0 13.0 - - - +
25A ARG* 3.1 20.9 + - - +
26A GLY* 3.4 11.9 - - - +
28A GLY* 1.3 73.8 - - - +
30A ALA* 1.3 64.6 + - - +
32A ALA* 3.3 0.7 + - - -
33A GLN* 3.0 56.6 + - + +
52A PRO* 3.6 32.5 - - + -
55A LEU* 4.8 1.3 - - + -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY 3.1 8.8 + - - +
27A ILE 3.2 7.2 + - - +
29A LEU* 1.3 75.3 - - - +
31A ILE* 1.3 63.0 + - - +
33A GLN* 3.5 8.3 + - - +
34A ARG* 3.1 24.1 + - - +
214A PRO* 3.7 41.7 - - + +
215A ALA* 4.4 2.7 - - - +
218A ALA* 3.5 5.6 - - + +
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Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.3 5.2 - - + -
27A ILE* 2.9 38.5 + - + +
28A GLY* 3.6 4.9 - - - +
30A ALA* 1.3 75.9 - - + +
32A ALA* 1.3 64.4 + - - +
34A ARG* 3.1 3.5 + - - +
35A LEU* 3.0 34.0 + - + +
86A VAL* 4.0 11.0 - - + -
88A ASN* 3.8 18.4 - - - +
138A ILE* 4.0 9.4 - - + -
217A VAL* 4.6 2.2 - - + -
218A ALA* 3.8 24.9 - - + +
221A VAL* 3.7 40.8 - - + -
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.2 9.9 - - + -
23A GLY 3.8 3.6 - - - +
28A GLY 2.9 17.2 + - - +
29A LEU 3.9 1.6 - - - +
31A ILE* 1.3 76.6 - - - +
33A GLN* 1.3 62.0 + - - +
35A LEU* 3.4 0.8 + - - +
36A ALA* 3.0 24.4 + - - +
42A VAL* 3.7 17.8 - - + +
44A VAL* 3.6 30.5 - - + -
55A LEU* 3.7 13.6 - - + +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.0 50.2 + - + +
30A ALA* 4.1 6.3 - - - +
32A ALA* 1.3 74.7 - - - +
34A ARG* 1.3 57.4 + - - +
36A ALA* 3.6 6.7 + - - +
37A ALA* 3.1 27.5 + - - +
52A PRO* 5.1 6.1 - - - +
53A LYS 5.6 2.3 - - - +
55A LEU* 4.6 11.2 - - + -
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 3.1 18.3 + - - +
31A ILE 3.1 4.2 + - - +
33A GLN* 1.3 75.2 - - - +
35A LEU* 1.3 61.8 + - + +
37A ALA* 3.2 6.6 + - - -
38A ASP* 2.8 50.6 + - - +
215A ALA 5.0 2.2 + - - -
218A ALA* 3.8 19.1 - - + +
219A GLY* 3.7 8.9 - - - +
222A SER* 3.3 34.0 + - - +
9B ALA* 4.8 9.9 + - - +
10B LYS* 3.5 53.3 - - - +
11B PRO* 4.2 0.4 - - - +
228B ASP* 2.7 43.4 + - - -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.6 27.4 - - + -
20A VAL* 4.2 3.1 - - + -
31A ILE* 3.0 37.2 + - + +
32A ALA 4.0 0.9 - - - +
34A ARG* 1.3 76.9 - - + +
36A ALA* 1.3 61.3 + - - +
38A ASP* 3.2 26.4 - - - +
40A HIS* 3.1 31.4 + - + +
42A VAL* 3.7 15.3 - - + -
84A VAL* 5.0 2.2 - - + -
86A VAL* 4.1 14.1 - - + -
218A ALA 5.9 0.2 - - - +
221A VAL* 4.3 2.5 - - + +
222A SER* 3.9 23.1 - - - +
225A ALA* 3.9 17.7 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA 3.0 17.4 + - - +
33A GLN* 3.7 6.7 - - - +
35A LEU* 1.3 75.1 - - - +
37A ALA* 1.3 58.7 + - - +
39A GLY* 3.1 9.9 + - - -
40A HIS 4.0 4.5 - - - +
42A VAL* 3.4 16.4 - - + +
54A GLY 5.2 2.2 - - - +
55A LEU* 4.0 16.8 - - + -
1248A CS 3.0 25.0 - - - -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLN 3.1 18.2 + - - +
34A ARG* 3.2 9.2 + - - +
36A ALA* 1.3 71.0 - - - +
38A ASP* 1.3 63.1 + - - +
39A GLY* 3.1 3.8 + - - -
1249A CS 2.9 27.3 - - - -
10B LYS* 6.2 4.5 - - + +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.3 23.1 - - + -
34A ARG* 2.8 42.7 + - - +
35A LEU* 3.2 23.9 - - - +
37A ALA* 1.3 76.5 - - - +
39A GLY* 1.3 56.3 + - - +
40A HIS* 4.0 13.2 + - + +
222A SER* 2.6 31.2 + - - +
10B LYS* 5.0 5.9 + - - +
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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