Contacts of the helix formed by residues 37 - 49 (chain H) in PDB entry 6IY3
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 37 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G PHE* 3.7 35.4 - + + -
26G PRO* 4.5 5.6 - - + -
29G ARG* 4.4 17.0 - - + -
30G VAL* 4.8 12.9 - - + +
33G LEU* 3.3 28.5 - - + +
55G LEU* 5.6 2.1 - - + +
36H SER* 1.3 78.0 - - - +
38H ALA* 1.3 62.3 + - - +
39H ILE 3.5 1.6 - - - -
40H TYR* 3.4 18.5 + + + -
41H VAL* 3.0 31.6 + - + +
59H MET* 5.1 0.2 - - - -
63H ASN* 3.6 22.6 + - - +
66H VAL* 3.6 28.0 - - + -
67H ASN* 3.7 23.8 + - - -
70H PHE* 5.0 9.5 - - - -
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Residues in contact with ALA 38 (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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36H SER* 3.3 16.9 + - - +
37H TYR* 1.3 78.0 - - - +
39H ILE* 1.3 62.5 + - + +
40H TYR 3.3 0.2 + - - -
42H TYR* 3.0 24.5 + - - +
59H MET* 3.3 38.2 - - + +
63H ASN* 6.1 1.3 - - + -
123J C 5.9 2.0 - - - +
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Residues in contact with ILE 39 (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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36H SER 5.4 0.2 - - - +
38H ALA* 1.3 79.2 - - + +
40H TYR* 1.3 86.5 + - + +
42H TYR* 3.7 7.9 - - + +
43H LYS* 2.9 44.8 + - - +
122J T 3.8 30.7 - - + +
123J C 3.6 28.0 - - + +
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Residues in contact with TYR 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLN* 3.1 26.8 - - - +
25G PHE* 4.5 17.7 - - + -
26G PRO* 3.5 46.6 - - + +
29G ARG* 3.6 20.2 + - - -
36H SER 4.3 0.7 - - - -
37H TYR* 3.9 21.1 - + - +
38H ALA 3.2 0.6 - - - -
39H ILE* 1.3 95.4 - - + +
41H VAL* 1.3 64.0 + - - +
43H LYS* 3.3 13.6 + - + +
44H VAL* 3.1 30.4 + - - +
122J T 2.7 43.0 + - - -
123J C 5.2 0.4 - - - -
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 4.9 2.9 - - + -
59G THR* 4.3 20.2 - - + +
63G LEU* 3.8 20.2 - - + +
37H TYR* 3.0 29.3 + - + +
38H ALA 3.7 3.1 - - - +
40H TYR* 1.3 75.0 - - - +
42H TYR* 1.3 58.0 + - - +
44H VAL* 3.3 1.4 + - - -
45H LEU* 3.0 27.0 + - - +
54H ILE* 4.2 5.6 - - + -
59H MET* 3.8 22.7 - - + -
62H MET* 3.9 36.3 - - + +
63H ASN 5.0 0.4 - - - +
66H VAL* 4.9 3.4 - - + -
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Residues in contact with TYR 42 (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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38H ALA 3.0 17.3 + - - +
39H ILE* 3.7 9.6 - - + +
40H TYR 3.3 0.2 - - - -
41H VAL* 1.3 77.9 - - - +
43H LYS* 1.3 58.5 + - - +
45H LEU* 3.4 8.7 + - + +
46H LYS* 2.9 69.1 + - + +
54H ILE* 4.0 24.5 - - + -
59H MET* 4.1 5.8 - - + -
19I T 3.2 48.3 + - - -
20I C 3.8 18.7 + - - -
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Residues in contact with LYS 43 (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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24G GLN* 3.2 39.0 - - + +
39H ILE* 2.9 39.7 + - - +
40H TYR* 3.6 12.2 - - + +
41H VAL 3.2 0.4 - - - -
42H TYR* 1.3 76.3 - - - +
44H VAL* 1.3 61.2 + - - +
46H LYS* 3.3 7.6 + - + +
47H GLN* 3.0 30.8 + - + +
122J T 5.6 3.0 + - - -
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Residues in contact with VAL 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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24G GLN* 4.1 21.8 - - + -
25G PHE* 4.4 10.8 - - + -
56G GLU* 4.2 19.1 - - + +
59G THR* 4.3 11.4 - - + +
60G ALA* 3.8 39.5 - - + +
63G LEU* 4.8 2.0 - - + -
40H TYR 3.1 16.4 + - - +
41H VAL 3.3 4.2 + - - +
43H LYS* 1.3 76.4 - - - +
45H LEU* 1.3 61.6 + - - +
47H GLN* 3.2 11.9 + - - +
48H VAL* 3.0 25.3 + - + +
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Residues in contact with LEU 45 (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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63G LEU* 4.0 25.5 - - + +
78G ILE* 4.0 22.0 - - + -
41H VAL 3.0 16.1 + - - +
42H TYR* 3.5 13.2 - - + +
43H LYS 3.2 0.2 - - - -
44H VAL* 1.3 76.7 - - - +
46H LYS* 1.3 59.3 + - + +
48H VAL* 4.0 8.3 - - + -
49H HIS* 2.9 43.2 + - + +
52H THR* 4.0 18.6 - - - +
53H GLY 4.1 3.1 - - - +
54H ILE* 3.7 43.7 - - + +
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Residues in contact with LYS 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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42H TYR* 2.9 62.4 + - + +
43H LYS* 3.3 7.4 + - + +
45H LEU* 1.3 75.9 - - - +
47H GLN* 1.3 65.0 + - - +
49H HIS 4.0 3.6 - - - +
50H PRO* 4.0 36.0 + - + +
51H ASP 4.5 2.2 + - - -
52H THR 2.6 32.8 + - - +
53H GLY* 4.3 2.6 - - - -
19I T 5.4 0.8 + - - -
20I C 5.4 3.5 + - - -
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Residues in contact with GLN 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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24G GLN* 3.0 38.8 - - - +
56G GLU* 4.6 8.2 + - - +
43H LYS* 3.0 17.2 + - + +
44H VAL* 3.5 12.6 - - - +
45H LEU 3.2 0.4 - - - -
46H LYS* 1.3 80.7 - - - +
48H VAL* 1.3 66.5 + - + +
49H HIS 3.5 0.5 + - - -
50H PRO* 4.5 8.1 - - - +
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ALA* 4.6 24.7 - - + +
63G LEU* 4.4 16.6 - - + -
64G GLU* 4.5 11.4 - - + +
44H VAL* 3.0 19.0 + - + +
45H LEU* 3.7 11.2 - - + +
47H GLN* 1.3 82.1 - - + +
49H HIS* 1.3 86.1 + - + +
50H PRO* 4.3 2.2 - - - +
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Residues in contact with HIS 49 (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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63G LEU 4.1 10.8 - - - -
64G GLU* 4.0 13.0 + - - +
67G GLY* 3.8 36.1 - - - -
68G ASN* 4.1 7.0 + - - -
71G ARG* 3.9 26.0 + - - -
45H LEU* 2.9 27.8 + - + +
46H LYS* 4.0 2.1 - - - +
47H GLN 3.4 0.2 - - - -
48H VAL* 1.3 96.7 + - + +
50H PRO* 1.3 70.0 - - - +
51H ASP* 3.3 5.3 + - - +
52H THR* 3.5 34.4 + - - +
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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