Contacts of the strand formed by residues 36 - 41 (chain D) in PDB entry 1U3H
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 GLU 36 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C TYR* 3.5 33.2 + - + -
29D ARG* 3.3 26.7 + - - +
30D TYR 3.6 6.5 - - - +
31D ILE* 3.8 9.4 - - + +
34D ARG 3.9 3.2 + - - -
35D GLU* 1.3 71.3 - - - +
37D TYR* 1.3 57.9 + - - +
38D LEU 4.0 7.6 - - - +
39D ARG* 2.6 48.5 + - - +
50D VAL* 3.2 30.4 - - + +
51D THR* 3.3 10.0 - - - +
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Residues in contact with TYR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASN* 4.8 8.7 - - - +
73C LEU* 3.6 39.8 - - + +
9D VAL* 5.9 1.4 - - + +
30D TYR* 2.9 36.6 + + + +
31D ILE 3.7 9.4 + - - -
32D TYR* 3.6 33.4 - - + -
35D GLU* 3.3 4.7 + - - +
36D GLU* 1.3 74.0 - - - +
38D LEU* 1.3 90.2 + - + +
49D ALA* 3.6 1.6 - - - -
50D VAL* 2.7 27.3 + - - -
51D THR* 3.3 16.4 + - - +
53D LEU* 3.9 10.3 - - + -
54D GLY* 3.6 34.6 - - - +
57D ASP* 3.9 14.7 + - - -
61D TYR* 5.0 3.4 + - - -
4P TYR* 4.9 2.6 + - - -
7P SER* 5.9 0.5 - - - -
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Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ARG* 3.9 0.5 - - - -
30D TYR* 2.9 39.7 + - + +
36D GLU* 3.8 3.5 - - - +
37D TYR* 1.3 98.1 - - + +
39D ARG* 1.3 71.1 + - - +
47D TYR* 3.8 24.7 - - + +
48D ARG 3.4 16.2 - - - +
49D ALA* 3.9 6.3 - - + +
50D VAL* 3.7 3.4 - - - +
54D GLY* 5.1 0.7 - - - -
57D ASP* 3.7 21.1 - - + -
58D ALA* 4.6 10.1 - - - +
61D TYR* 3.4 41.7 - - + +
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 4.3 8.1 - - + -
28D THR 3.3 9.2 - - - +
29D ARG* 3.5 15.2 - - - +
36D GLU* 2.6 38.3 + - - +
38D LEU* 1.3 80.4 - - - +
40D PHE* 1.3 74.5 + - - +
41D ASP* 4.4 21.7 + - - +
46D GLU 3.7 1.2 - - - +
47D TYR* 3.6 5.8 - - - -
48D ARG* 3.1 34.2 + - - +
50D VAL* 3.5 24.6 - - + +
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 3.8 30.1 - + - -
27D VAL* 3.4 3.6 - - - -
28D THR* 2.9 42.3 + - - -
39D ARG* 1.3 80.6 - - - +
41D ASP* 1.3 60.9 + - - +
42D SER* 3.5 30.3 - - - -
45D GLY 4.0 4.9 - - - -
46D GLU 4.0 29.8 - - - -
47D TYR* 3.5 31.2 - + + -
68D LEU* 4.0 15.5 - - + -
71D THR* 3.7 25.1 - - + -
72D ARG* 4.0 22.2 - - + -
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Residues in contact with ASP 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ILE* 5.7 0.2 - - - +
25D ARG* 2.6 42.2 + - - +
26D TYR 3.6 2.9 - - - -
27D VAL* 4.0 9.9 - - - +
39D ARG* 4.1 21.5 + - - +
40D PHE* 1.3 82.1 - - - +
42D SER* 1.3 52.4 + - - +
43D ASP* 3.0 18.5 + - - +
44D VAL* 2.8 23.7 + - + +
45D GLY* 2.5 33.4 + - - -
46D GLU 3.8 5.2 + - - +
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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