Contacts of the helix formed by residues 38 - 50 (chain D) in PDB entry 6R93
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 TYR 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C PHE* 4.0 27.4 - + + -
27C PRO* 4.7 12.3 - - + -
30C ARG* 4.9 7.5 - - - -
31C VAL* 4.5 13.5 - - + +
34C LEU* 3.4 28.3 - - + +
56C LEU* 5.4 2.0 - - + +
36D GLU* 4.3 13.9 - - - -
37D SER* 1.3 78.8 + - - +
39D SER* 1.3 62.1 + - - -
40D ILE 3.4 2.2 - - - -
41D TYR* 3.1 22.5 + + + +
42D VAL* 3.0 32.7 + - + +
60D MET* 5.0 0.4 - - - -
64D ASN* 3.5 24.9 + - - +
67D VAL* 3.9 32.2 - - + +
68D ASN* 4.4 15.7 + - - -
71D PHE* 5.6 5.7 - - - +
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Residues in contact with SER 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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37D SER* 2.8 27.6 + - - -
38D TYR* 1.3 74.9 - - - +
40D ILE* 1.3 75.3 + - - +
41D TYR 3.2 0.2 + - - -
42D VAL 3.3 1.0 + - - -
43D TYR* 3.0 22.2 + - - +
60D MET* 3.3 38.8 - - - +
64D ASN* 5.8 0.2 - - - +
122J T 5.8 0.4 - - - -
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Residues in contact with ILE 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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38D TYR 3.4 1.0 - - - -
39D SER* 1.3 85.4 - - - +
41D TYR* 1.3 67.5 + - + +
43D TYR* 3.4 7.5 + - + +
44D LYS* 3.0 39.9 + - + +
121J G 5.1 11.0 - - + +
122J T 3.6 44.6 + - + +
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Residues in contact with TYR 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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25C GLN* 3.4 21.2 - - - +
26C PHE* 3.7 26.5 - - + -
27C PRO* 3.6 38.4 - - + +
30C ARG* 4.3 8.5 - - - -
37D SER 4.1 14.6 - - - -
38D TYR* 3.1 24.6 + + - +
40D ILE* 1.3 83.6 - - + +
42D VAL* 1.3 66.2 + - - +
44D LYS* 3.3 15.0 + - + +
45D VAL* 3.0 28.6 + - - +
121J G 2.6 58.0 + - - -
122J T 4.9 3.1 - - - -
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Residues in contact with VAL 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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26C PHE* 4.6 5.6 - - + -
60C THR* 4.5 18.6 - - + -
64C LEU* 3.8 20.6 - - + +
38D TYR* 3.0 23.0 + - + +
41D TYR* 1.3 75.3 - - - +
43D TYR* 1.3 58.0 + - - +
45D VAL* 3.3 6.5 + - - +
46D LEU* 2.9 28.4 + - + +
55D ILE* 4.9 2.9 - - + -
60D MET* 3.5 34.3 - - + -
63D MET* 4.5 26.5 - - + -
64D ASN 5.6 0.4 - - - +
67D VAL* 5.4 2.9 - - + -
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Residues in contact with TYR 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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39D SER 3.0 16.4 + - - +
40D ILE* 3.7 8.7 - - + +
42D VAL* 1.3 78.0 - - - +
44D LYS* 1.3 58.3 + - + +
46D LEU* 3.4 9.7 + - + +
47D LYS* 2.9 57.4 + - + +
53D THR 5.3 0.9 - - - -
54D GLY* 4.5 3.6 - - - -
55D ILE* 3.9 22.9 - - + -
60D MET* 3.8 7.8 - - + +
20I T 2.6 59.8 + - + -
21I T 4.0 14.8 - - - -
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Residues in contact with LYS 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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25C GLN* 3.5 63.2 + - + +
40D ILE* 3.0 32.8 + - + +
41D TYR* 3.3 13.9 + - + +
43D TYR* 1.3 76.9 - - + +
45D VAL* 1.3 62.4 + - - +
47D LYS* 3.2 8.5 + - - +
48D GLN* 3.0 21.9 + - - +
121J G 5.7 1.6 + - - +
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Residues in contact with VAL 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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25C GLN* 4.4 9.2 - - + -
26C PHE* 4.2 11.2 - - + -
57C GLU* 3.8 31.9 - - + +
60C THR* 4.2 4.7 - - - +
61C ALA* 3.8 39.5 - - + +
64C LEU* 4.5 5.6 - - + -
41D TYR 3.0 20.9 + - - +
42D VAL* 3.7 5.6 - - - +
44D LYS* 1.3 75.4 - - - +
46D LEU* 1.3 64.0 + - - +
48D GLN* 3.0 10.1 + - - +
49D VAL* 2.9 24.1 + - + +
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Residues in contact with LEU 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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64C LEU* 3.5 30.2 - - + +
79C ILE* 4.3 14.6 - - + -
42D VAL* 2.9 18.5 + - + +
43D TYR* 3.6 13.2 - - + +
45D VAL* 1.3 76.5 - - - +
47D LYS* 1.3 53.5 + - - +
49D VAL* 3.2 2.6 + - + -
50D HIS* 2.7 55.0 + - + +
53D THR* 4.0 18.6 - - + +
54D GLY* 3.8 23.1 - - - +
55D ILE* 3.9 26.7 - - + -
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Residues in contact with LYS 47 (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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43D TYR* 2.9 46.9 + - + +
44D LYS* 3.2 6.9 + - - +
46D LEU* 1.3 77.2 - - - +
48D GLN* 1.3 61.7 + - - +
50D HIS 4.1 2.5 - - - -
51D PRO* 3.1 52.3 + - + +
53D THR 4.0 16.1 + - - +
54D GLY* 5.8 0.2 - - - -
21I T 4.9 10.1 + - - -
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Residues in contact with GLN 48 (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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25C GLN* 5.9 7.9 - - + +
44D LYS 3.0 13.2 + - - +
45D VAL* 3.0 13.0 + - + +
47D LYS* 1.3 81.2 - - - +
49D VAL* 1.3 80.2 + - - +
51D PRO* 4.8 3.3 - - - +
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Residues in contact with VAL 49 (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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61C ALA* 3.9 28.7 - - + +
64C LEU* 5.6 2.2 - - + -
65C GLU* 3.7 36.0 - - + +
45D VAL* 2.9 16.3 + - + +
46D LEU* 4.1 3.8 - - - +
48D GLN* 1.3 95.5 - - - +
50D HIS* 1.3 78.4 + - + +
51D PRO* 4.1 4.5 - - - +
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Residues in contact with HIS 50 (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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64C LEU 3.9 18.2 - - - -
65C GLU* 3.2 39.5 + - - -
68C GLY* 4.2 9.7 - - - -
69C ASN* 4.2 0.6 + - - -
72C ARG* 3.6 25.4 + - - -
46D LEU* 2.7 28.0 + - + +
47D LYS* 4.1 1.4 - - - -
49D VAL* 1.3 91.0 + - + +
51D PRO* 1.3 70.9 - - - +
52D ASP* 3.1 6.2 + - - +
53D THR* 3.6 32.5 + - - +
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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