Contacts of the helix formed by residues 41 - 56 (chain B) in PDB entry 6A8R
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 PRO 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B ARG* 5.5 3.1 - - - +
6B THR* 4.8 4.9 - - + -
35B ALA* 4.7 0.4 - - + -
39B GLY 4.1 4.0 - - - +
40B LEU* 1.3 91.6 - - + +
42B GLU* 1.3 67.4 + - - +
43B SER* 4.1 10.3 - - - +
44B ARG* 2.8 40.4 + - + +
45B ILE* 3.1 9.0 + - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 4.2 13.7 - - - +
31B ARG* 2.6 58.1 + - + -
32B GLU* 3.9 23.2 - - + +
35B ALA* 3.7 19.7 - - + +
40B LEU 3.5 2.2 + - - -
41B PRO* 1.3 72.0 - - - +
43B SER* 1.3 72.8 + - - +
45B ILE* 3.1 7.4 + - - +
46B GLN* 3.0 24.6 + - - +
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 4.3 7.6 + - - -
41B PRO* 4.1 8.3 - - - +
42B GLU* 1.3 88.8 + - - +
44B ARG* 1.3 97.8 + - - +
46B GLN* 3.5 7.6 + - - +
47B ILE* 3.4 19.2 + - - +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 2.9 50.1 - - - +
6B THR* 3.1 25.8 - - + +
8B VAL* 6.3 0.4 - - + -
40B LEU* 4.7 12.3 - - + -
41B PRO* 2.8 38.3 + - + +
43B SER* 1.3 106.4 + - - +
45B ILE* 1.3 60.4 + - - +
47B ILE* 2.8 42.5 + - - +
48B TRP* 2.9 28.3 + - - +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.3 9.6 - - + -
31B ARG* 3.5 22.4 - - + +
34B LEU* 3.5 13.0 - - + +
35B ALA* 3.1 46.2 - - + +
38B THR* 4.0 4.0 - - - +
40B LEU* 3.9 23.8 - - + +
41B PRO 3.1 7.0 + - - +
42B GLU* 3.1 8.1 + - - +
44B ARG* 1.3 73.3 - - - +
46B GLN* 1.3 64.8 + - - +
48B TRP* 3.1 6.8 + - - +
49B PHE* 3.0 48.0 + - + -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ARG* 3.4 50.5 + - - +
42B GLU* 3.0 12.6 + - - +
43B SER* 3.7 10.9 - - - +
44B ARG 3.3 0.4 - - - -
45B ILE* 1.3 76.6 - - - +
47B ILE* 1.3 63.8 + - + +
49B PHE* 3.3 4.7 + - - +
50B GLN* 3.0 45.6 + - + +
53B ARG* 5.8 1.6 + - - -
14F C 4.4 13.2 + - - -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B SER 3.4 5.4 + - - +
44B ARG* 2.8 54.1 - - - +
45B ILE 3.3 0.4 - - - -
46B GLN* 1.3 75.3 - - + +
48B TRP* 1.3 68.0 + - - +
50B GLN* 3.2 21.9 + - - +
51B ASN* 2.9 40.6 + - - +
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Residues in contact with TRP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.9 14.6 - - + +
13B THR* 4.4 16.9 + - + +
16B LEU* 3.6 62.4 - - + +
17B LEU* 3.8 18.6 - - + -
20B PHE* 3.9 22.0 - + + -
40B LEU* 6.1 0.9 - - + -
44B ARG 2.9 18.7 + - - +
45B ILE* 3.1 8.0 + - - +
47B ILE* 1.3 79.1 - - - +
49B PHE* 1.3 78.2 + + - +
51B ASN* 3.4 5.5 + - - +
52B ARG* 3.0 52.9 + - + +
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.2 9.2 - - + -
19B ALA* 4.1 11.7 - - + -
20B PHE* 3.7 26.0 - + - -
23B ASP 3.5 16.4 - - - -
24B ARG 3.6 8.5 - - - -
26B PRO* 3.4 36.3 - - + -
31B ARG* 5.9 0.4 - - - -
34B LEU* 3.9 20.0 - - + -
45B ILE* 3.0 48.8 + - + +
46B GLN* 3.8 5.4 - - - +
48B TRP* 1.3 90.1 - + - +
50B GLN* 1.3 65.1 + - - +
52B ARG* 3.3 2.8 + - - +
53B ARG* 2.9 42.4 + - - +
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 3.0 44.4 + - + +
47B ILE* 3.5 21.8 - - - +
49B PHE* 1.3 76.9 - - - +
51B ASN* 1.3 65.5 + - - +
53B ARG* 3.3 27.5 + - - +
54B ALA* 3.1 21.7 + - - +
14F C 6.3 1.4 - - - -
15F A 5.0 22.8 + - + +
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 2.9 37.0 + - - +
48B TRP* 3.9 5.5 - - - +
50B GLN* 1.3 76.7 - - - +
52B ARG* 1.3 66.4 + - - +
54B ALA* 3.3 5.6 + - - +
55B ARG* 2.9 63.1 + - - +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR* 6.0 1.8 - - - +
17B LEU* 3.2 33.1 - - - +
20B PHE* 3.3 37.2 - - + -
48B TRP* 3.0 43.3 + - + +
49B PHE 3.7 1.3 - - - +
50B GLN 3.2 0.4 - - - -
51B ASN* 1.3 76.4 - - - +
53B ARG* 1.3 64.3 + - - +
55B ARG* 4.5 1.1 - - - +
56B HIS* 2.9 82.6 + - - +
58B GLY 4.6 1.2 + - - -
59B GLN 4.8 5.1 - - - -
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.9 16.6 - - + -
24B ARG* 2.7 38.6 + - + +
25B PHE* 3.3 46.5 - - - +
26B PRO* 4.8 0.4 - - - +
46B GLN* 5.3 1.8 + - - -
49B PHE* 2.9 40.1 + - - +
50B GLN* 3.7 26.2 - - - +
51B ASN 3.2 0.4 - - - -
52B ARG* 1.3 77.5 - - - +
54B ALA* 1.3 60.7 + - - +
55B ARG 3.6 0.2 + - - -
57B PRO* 3.7 22.0 - - - +
14F C 4.6 10.1 + - - -
15F A 2.9 38.1 + - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN 3.1 16.2 + - - +
51B ASN* 3.7 7.9 - - - +
52B ARG 3.2 0.2 - - - -
53B ARG* 1.3 79.3 - - - +
55B ARG* 1.3 64.4 + - + +
57B PRO* 4.8 1.8 - - - +
15F A 5.1 18.4 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ASN* 2.9 49.7 + - - +
52B ARG* 4.9 1.1 - - - -
54B ALA* 1.3 85.8 - - + +
56B HIS* 1.3 63.8 + - + +
57B PRO* 3.6 5.6 - - - +
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 4.1 0.7 - - - -
52B ARG* 2.9 62.6 + - - +
55B ARG* 1.3 78.9 - - + +
57B PRO* 1.3 65.2 - - - +
58B GLY 2.6 32.9 + - - +
59B GLN* 3.5 30.5 + - + +
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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