Contacts of the helix formed by residues 39 - 51 (chain K) in PDB entry 6A5T
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 ASP 39 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995B ARG* 2.2 35.0 + - - -
998B ASP* 5.4 0.7 - - - -
34C ARG* 3.1 15.7 - - - +
39C GLU* 6.1 0.9 - - - +
165C LYS* 3.6 17.1 + - - +
9K LEU* 5.8 2.6 - - - +
38K GLU* 1.3 90.3 + - - +
40K HIS* 1.3 74.6 + - + +
41K THR* 3.0 6.3 - - - +
42K LEU 3.0 11.8 + - - +
43K ALA* 3.1 9.6 + - - -
63K VAL* 5.7 6.5 - - - +
69K ALA* 4.7 10.3 - - - +
70K ASN 5.2 0.2 + - - -
71K PHE* 3.6 13.7 - - - -
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Residues in contact with HIS 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B ASP* 4.9 2.2 - - - -
1076B HIS* 2.9 58.8 + + + +
34C ARG* 3.2 21.3 - - - +
39K ASP* 1.3 79.4 - - + +
41K THR* 1.3 62.2 + - - +
42K LEU 2.8 2.3 + - - -
43K ALA* 4.5 3.4 - - - -
44K ASN* 2.9 33.7 + - + +
61K TYR* 3.0 25.7 + + - -
63K VAL* 3.5 36.8 - - + +
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Residues in contact with THR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997B GLU* 5.2 0.7 + - - -
31C SER* 3.3 33.0 + - - +
34C ARG* 2.3 59.8 + - + +
35C THR* 3.7 23.6 - - - +
39C GLU* 4.8 17.7 - - - +
251C LEU* 4.7 12.0 - - + +
254C LYS* 5.2 4.0 - - - -
39K ASP* 3.0 5.3 - - - +
40K HIS* 1.3 71.0 - - - +
42K LEU* 1.3 60.1 + - - +
45K LEU* 4.1 4.0 - - - +
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Residues in contact with LEU 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LEU* 5.6 2.9 - - + -
254C LYS* 4.4 15.7 - - + -
255C LEU* 4.2 27.4 - - + -
258C VAL* 4.0 18.2 - - + -
35K PHE* 3.9 28.5 - - + -
38K GLU* 3.8 32.8 - - + +
39K ASP 3.0 7.6 + - - +
40K HIS 2.8 0.8 + - - -
41K THR* 1.3 82.7 - - - +
43K ALA* 1.3 67.5 + - - +
44K ASN 3.4 0.4 - - - -
45K LEU* 3.3 7.2 + - + +
46K LEU* 3.0 35.1 + - + +
71K PHE* 5.0 0.4 - - + -
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Residues in contact with ALA 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K PHE* 6.0 0.2 - - - -
39K ASP 3.1 8.1 + - - +
40K HIS* 4.3 2.5 - - - +
42K LEU* 1.3 80.1 - - - +
44K ASN* 1.3 64.6 + - - +
45K LEU 3.1 0.2 + - - -
46K LEU* 3.3 3.3 + - - +
47K ARG* 2.9 25.3 + - - +
61K TYR* 3.9 24.9 - - + -
63K VAL* 6.0 0.2 - - + -
71K PHE* 3.3 42.3 - - + -
73K MET* 4.0 7.2 - - + +
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Residues in contact with ASN 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076B HIS 2.5 30.4 + - - +
1077B THR* 3.2 23.3 - - - +
27C SER* 3.7 20.4 - - - +
30C ASN* 4.1 5.5 - - - +
31C SER* 5.0 3.3 + - - +
40K HIS* 2.9 19.6 + - - +
43K ALA* 1.3 76.6 - - - +
45K LEU* 1.3 57.0 + - - +
47K ARG* 3.2 22.2 + - - +
48K GLU* 3.0 27.0 + - - +
61K TYR* 4.0 15.7 - - - +
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Residues in contact with LEU 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN* 6.1 0.4 - - - +
27C SER* 3.5 26.2 - - - +
28C LEU* 3.5 22.2 - - + -
31C SER* 3.1 33.0 - - - +
251C LEU* 4.2 17.0 - - + -
255C LEU* 4.6 9.6 - - + -
40K HIS 4.2 0.6 + - - -
41K THR 4.1 4.9 - - - +
42K LEU* 3.3 11.1 + - + +
43K ALA 3.1 0.6 - - - -
44K ASN* 1.3 77.3 - - - +
46K LEU* 1.3 68.6 + - - +
47K ARG 3.3 0.2 + - - -
48K GLU* 3.3 2.6 + - - +
49K GLU* 3.0 23.8 + - + +
94K ILE* 4.1 28.5 - - + -
98K LEU* 5.2 0.4 - - + -
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Residues in contact with LEU 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C LEU* 4.4 16.8 - - + -
258C VAL* 4.8 8.3 - - + -
35K PHE* 4.2 25.6 - - + -
42K LEU* 3.0 35.3 + - + +
43K ALA* 3.9 3.6 - - - +
45K LEU* 1.3 76.6 - - - +
47K ARG* 1.3 63.9 + - - +
49K GLU* 3.4 2.3 + - - +
50K LEU* 2.9 26.4 + - - +
73K MET* 3.9 15.3 - - + -
87K LEU* 4.4 25.8 - - + -
90K ALA* 4.6 8.5 - - + -
91K CYS* 4.8 5.2 - - - -
94K ILE* 3.9 22.0 - - + -
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Residues in contact with ARG 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A GLU* 4.3 32.1 + - - +
548A MET* 5.1 5.1 - - + +
549A ASN* 3.8 35.8 - - - +
1077B THR* 4.3 11.9 - - - +
27C SER* 5.8 0.2 - - - -
43K ALA 2.9 20.8 + - - +
44K ASN* 3.2 26.1 + - - +
46K LEU* 1.3 71.3 - - - +
48K GLU* 1.3 67.4 + - - +
50K LEU* 2.5 31.3 + - - +
51K ALA* 2.8 15.3 + - + +
59K VAL* 4.3 21.8 - - + +
60K ALA* 4.3 5.8 - - - +
61K TYR* 3.9 17.3 - - + -
73K MET* 3.9 10.6 - - + +
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Residues in contact with GLU 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A GLU* 4.9 11.4 - - - +
25C ASN* 3.0 46.2 + - - +
26C LEU* 4.3 1.9 + - - -
27C SER* 2.2 47.8 + - - +
44K ASN* 3.0 9.7 + - - +
45K LEU 4.1 0.4 - - - +
47K ARG* 1.3 88.1 - - - +
49K GLU* 1.3 55.7 + - - +
51K ALA* 2.6 34.7 + - + -
52K LEU* 3.4 18.4 + - + +
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Residues in contact with GLU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN* 4.9 5.6 + - - +
45K LEU 3.0 10.4 + - - +
46K LEU 3.8 2.9 - - - +
48K GLU* 1.3 79.3 - - - +
50K LEU* 1.3 61.7 + - - +
51K ALA 3.5 0.3 + - - -
52K LEU* 3.8 16.1 + - - +
53K TYR* 2.9 49.6 + - - -
90K ALA* 3.7 23.1 - - + -
93K SER* 4.1 7.8 + - - -
94K ILE* 3.6 32.5 - - + +
97K LYS* 3.3 25.3 + - - -
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Residues in contact with LEU 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K LEU 2.9 15.1 + - - +
47K ARG 2.5 16.4 + - - +
49K GLU* 1.3 74.1 - - - +
51K ALA* 1.3 58.4 + - - -
52K LEU 3.3 1.4 + - - -
53K TYR* 3.9 11.0 + - + -
56K VAL* 3.1 52.2 - - + +
59K VAL* 3.9 23.1 - - + +
73K MET* 4.6 7.9 - - - -
75K LEU* 4.1 21.3 - - + -
86K ALA* 4.5 13.0 - - + +
87K LEU* 3.8 24.7 - - + -
90K ALA* 4.3 19.7 - - + -
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Residues in contact with ALA 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A TYR* 6.0 2.5 - - + -
545A GLU* 4.6 20.3 - - + +
548A MET* 4.5 21.1 - - + -
47K ARG* 2.8 13.3 + - + +
48K GLU* 2.6 25.0 + - + +
50K LEU* 1.3 73.4 - - - +
52K LEU* 1.3 64.9 + - + +
53K TYR 3.5 1.9 - - - +
56K VAL* 5.3 0.2 - - - -
59K VAL* 5.2 2.7 - - + -
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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