Contacts of the helix formed by residues 38 - 48 (chain H) in PDB entry 6YOV
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G PHE* 4.5 9.0 - + + -
27G PRO* 4.2 22.9 - - + -
30G ARG* 3.9 20.0 - - - -
31G VAL* 5.5 4.9 - - + -
34G LEU* 3.1 29.8 - - + +
56G LEU* 5.9 2.3 - - + +
36H GLU* 4.9 4.7 - - + +
37H SER* 1.3 84.0 - - - +
39H SER* 1.3 59.5 + - - +
40H ILE 3.1 2.9 - - - -
41H TYR* 2.9 18.1 + + + -
42H VAL* 2.8 40.7 + - + +
64H ASN* 3.0 18.4 + - - +
67H VAL* 3.5 37.4 - - + +
68H ASN* 3.4 28.2 + - - -
71H PHE* 5.3 5.0 - - - -
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Residues in contact with SER 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H SER* 3.5 15.1 + - - -
38H TYR* 1.3 77.1 - - - +
40H ILE* 1.3 66.4 + - - +
42H VAL* 4.5 0.9 - - - -
43H TYR* 3.1 11.6 + - - +
60H MET* 2.9 39.6 - - - +
64H ASN* 3.5 14.8 + - - -
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Residues in contact with ILE 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H SER 5.6 0.7 - - - +
38H TYR* 4.8 0.9 - - - -
39H SER* 1.3 85.2 + - - +
41H TYR* 1.3 98.4 + - + +
43H TYR* 3.7 10.8 - - + +
44H LYS* 3.1 49.7 + - + +
201H PTD 5.8 0.2 - - + -
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Residues in contact with TYR 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLN* 3.1 33.4 - - + +
26G PHE* 3.9 20.9 - - + -
27G PRO* 3.5 44.3 - - + +
30G ARG* 4.2 19.0 + - - -
37H SER 4.7 1.3 - - - -
38H TYR* 2.9 21.8 + - + +
40H ILE* 1.3 98.1 - - + +
42H VAL* 1.3 61.3 + - - +
44H LYS* 3.3 6.8 + - + +
45H VAL* 2.9 36.0 + - - +
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Residues in contact with VAL 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 5.1 2.0 - - + -
60G THR* 4.3 15.5 - - + -
64G LEU* 3.6 19.3 - - + +
38H TYR* 2.8 30.6 + - + +
39H SER* 4.8 0.7 - - - -
41H TYR* 1.3 77.0 - - - +
43H TYR* 1.3 63.3 + - - +
45H VAL* 3.3 4.7 + - - -
46H LEU* 3.0 20.8 + - - +
55H ILE* 4.7 0.9 - - + -
60H MET* 3.9 22.4 - - + +
63H MET* 3.8 40.6 - - + +
64H ASN* 4.9 1.3 - - - +
67H VAL* 4.7 7.9 - - + -
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Residues in contact with TYR 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H SER 3.1 17.6 + - - +
40H ILE* 3.7 13.9 - - + +
41H TYR 3.2 0.2 - - - -
42H VAL* 1.3 80.4 - - - +
44H LYS* 1.3 74.6 + - + +
46H LEU* 3.3 8.1 + - + +
47H LYS* 3.2 38.0 + - + +
53H THR 5.9 1.6 - - - -
54H GLY* 5.7 4.9 - - - -
55H ILE* 4.2 23.6 - - + -
60H MET* 3.8 9.6 - - + +
113L ARG* 5.5 18.3 + - + -
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Residues in contact with LYS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G GLN* 5.3 15.7 - - + +
40H ILE* 3.1 34.9 + - + +
41H TYR* 3.7 9.2 - - + +
42H VAL 3.3 0.2 - - - -
43H TYR* 1.3 85.9 - - + +
45H VAL* 1.3 66.2 + - + +
47H LYS* 3.2 26.8 + - + +
48H GLN* 3.1 26.9 + - + +
201H PTD 1.3 81.0 - - + +
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Residues in contact with VAL 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLN* 4.7 8.5 - - + -
26G PHE* 4.1 12.8 - - + -
57G GLU* 4.1 27.6 - - + +
60G THR* 4.3 3.1 - - + -
61G ALA* 3.6 41.1 - - + +
64G LEU* 3.8 9.0 - - + -
41H TYR 2.9 21.2 + - - +
42H VAL 3.3 4.5 + - - +
44H LYS* 1.3 75.2 - - - +
46H LEU* 1.3 64.7 + - - +
48H GLN* 3.1 24.5 + - - +
49H VAL* 3.6 12.3 - - + +
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G LEU* 3.7 29.8 - - + +
79G ILE* 3.5 26.9 - - + -
42H VAL 3.0 13.1 + - - +
43H TYR* 3.5 11.4 - - + +
45H VAL* 1.3 76.9 - - - +
47H LYS* 1.3 58.0 + - - +
49H VAL* 2.9 6.4 + - + +
50H HIS* 2.8 42.4 + - + +
53H THR* 3.7 24.7 - - + +
54H GLY* 3.8 16.2 - - - +
55H ILE* 3.8 26.7 - - + -
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Residues in contact with LYS 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H TYR* 3.2 23.4 + - + +
44H LYS* 3.2 34.2 + - - +
46H LEU* 1.3 80.2 - - + +
48H GLN* 1.3 65.6 + - + +
49H VAL 3.1 1.2 + - - -
50H HIS 4.0 2.5 - - - +
51H PRO* 3.3 42.4 - - + +
53H THR 5.5 2.2 - - - +
201H PTD 1.3 72.1 - - - +
113L ARG* 5.9 2.2 - - - +
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Residues in contact with GLN 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G GLN* 3.6 39.1 + - - +
57G GLU* 5.0 3.1 - - - +
44H LYS* 3.1 17.4 + - - +
45H VAL* 3.6 17.0 - - - +
46H LEU 3.1 0.8 - - - -
47H LYS* 1.3 82.1 - - + +
49H VAL* 1.3 62.4 - - + +
51H PRO* 5.2 0.7 - - - -
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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