Contacts of the strand formed by residues 37 - 46 (chain D) in PDB entry 1HE1
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 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA 5.7 0.2 - - - -
101B PHE* 3.8 19.5 - + - -
102B LYS* 4.0 41.0 - - + +
105B VAL* 3.7 31.0 - - + -
106B LEU* 4.3 14.4 - - + +
35D THR* 3.7 2.6 - - - -
36D VAL* 1.3 86.8 + - + +
38D ASP* 1.3 83.8 + - - +
39D ASN* 4.7 4.5 - - + -
56D TRP* 3.5 31.4 - + - -
57D ASP 3.8 9.0 - - - -
58D THR* 5.1 0.4 - - - +
67D LEU* 4.6 2.5 - - + -
70D LEU* 5.4 1.3 - - + -
71D SER* 3.4 28.3 - - - -
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Residues in contact with ASP 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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102B LYS* 3.0 24.3 + - - +
33D ILE* 5.8 4.7 - - - +
35D THR* 4.5 5.4 - - + -
37D PHE* 1.3 91.5 - - - +
39D ASN* 1.3 76.0 + - - +
40D TYR* 3.6 32.2 + - - +
56D TRP* 3.7 4.2 - - - +
57D ASP* 2.9 36.8 + - + +
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Residues in contact with ASN 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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98B ALA* 5.0 11.8 - - - +
102B LYS* 4.7 6.2 + - - +
37D PHE* 4.7 10.8 - - + -
38D ASP* 1.3 88.0 + - - +
40D TYR* 1.3 83.9 + - - +
54D GLY* 4.4 1.4 - - - -
55D LEU 2.6 31.8 + - - +
56D TRP* 3.7 35.1 - - + +
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Residues in contact with TYR 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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17D THR* 3.9 10.7 - - - +
20D LEU* 3.8 32.5 - - + -
21D ILE* 3.9 25.7 - - + +
24D THR* 4.4 17.5 - - + +
35D THR* 4.9 1.2 + - - -
38D ASP* 3.6 35.0 + - + +
39D ASN* 1.3 87.2 + - - +
41D SER* 1.3 66.0 + - - +
54D GLY* 3.7 0.5 - - - -
55D LEU* 2.8 39.3 + - + +
57D ASP* 2.6 40.2 + - + -
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Residues in contact with SER 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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24D THR* 4.1 14.7 - - - +
39D ASN* 5.7 0.4 - - - -
40D TYR* 1.3 79.6 - - - +
42D ALA* 1.3 62.9 + - - +
43D ASN* 6.2 0.2 - - - -
53D LEU 3.1 13.9 - - - -
54D GLY* 4.6 3.1 - - - -
55D LEU* 4.6 1.1 - - - +
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Residues in contact with ALA 42 (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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23D TYR* 4.4 18.6 - - + +
24D THR* 4.1 22.4 - - + +
41D SER* 1.3 78.0 - - - +
43D ASN* 1.3 68.7 + - - +
44D VAL* 5.5 1.8 - - + -
52D ASN 3.8 1.0 - - - -
53D LEU* 2.8 39.8 + - + +
55D LEU* 4.9 1.1 - - + -
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Residues in contact with ASN 43 (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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41D SER* 6.2 0.2 - - - -
42D ALA* 1.3 78.4 - - - +
44D VAL* 1.3 60.0 + - - +
51D VAL 3.4 5.6 - - - +
52D ASN* 2.8 30.5 + - - +
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Residues in contact with VAL 44 (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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23D TYR* 3.9 22.9 - - + +
42D ALA* 5.2 2.5 - - + +
43D ASN* 1.3 76.3 - - - +
45D MET* 1.3 82.8 + - - +
46D VAL* 4.0 6.7 - - + -
49D LYS 3.6 0.7 - - - +
50D PRO* 3.5 1.9 - - - +
51D VAL* 2.7 45.6 + - + +
53D LEU* 4.7 9.2 - - + -
166D LYS* 6.3 2.0 - - - -
170D ASP* 4.7 5.4 - - - +
173D ILE* 3.5 31.2 - - + -
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Residues in contact with MET 45 (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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44D VAL* 1.3 83.6 - - - +
46D VAL* 1.3 64.6 - - - +
47D ASP 4.3 0.2 - - - -
48D GLY* 3.5 35.7 - - - +
49D LYS 3.4 3.6 - - - -
50D PRO* 3.5 33.7 - - + -
166D LYS* 5.9 1.9 + - - -
170D ASP* 4.7 2.3 - - - +
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Residues in contact with VAL 46 (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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44D VAL* 4.0 7.0 - - + -
45D MET* 1.3 79.7 - - - +
47D ASP* 1.3 86.0 + - - +
48D GLY 3.1 1.1 - - - -
49D LYS* 2.9 27.6 + - - +
51D VAL* 5.0 1.8 - - + -
170D ASP* 3.7 31.2 - - - +
173D ILE* 3.6 42.6 - - + -
174D ARG* 3.8 21.8 - - + +
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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