Contacts of the helix formed by residues 41 - 56 (chain B) in PDB entry 5BNG
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 THR 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ALA* 4.5 0.2 - - - -
39B GLY 5.4 1.1 - - - +
40B LEU* 1.3 75.7 - - - +
42B ILE* 1.3 66.7 + - - +
43B LEU* 3.8 7.5 + - - +
44B GLN* 2.8 41.9 + - - +
45B VAL* 3.0 25.6 + - - +
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Residues in contact with ILE 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 GLU* 5.1 8.3 - - - +
31B LYS* 4.5 9.6 - - + +
32B LYS* 4.0 24.9 - - + +
35B ALA* 4.0 20.9 - - + -
41B THR* 1.3 75.3 - - - +
43B LEU* 1.3 52.7 + - - +
45B VAL* 3.1 5.8 + - - +
46B ASN* 2.8 59.3 + - - +
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Residues in contact with LEU 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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41B THR* 3.3 7.3 - - - +
42B ILE* 1.3 79.4 - - - +
44B GLN* 1.3 58.5 + - + +
46B ASN* 3.7 12.5 - - + +
47B ASN* 3.1 56.4 + - - +
7M C 3.3 26.7 - - + +
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Residues in contact with GLN 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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40B LEU* 3.4 34.8 - - + +
41B THR* 2.8 50.3 + - - +
43B LEU* 1.3 80.6 - - + +
45B VAL* 1.3 60.6 + - - +
47B ASN* 4.2 2.1 - - - +
48B TRP* 3.3 24.3 + - - +
5M G 4.7 0.4 + - - -
6M A 2.8 43.3 + - - +
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Residues in contact with VAL 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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13B MET* 4.0 14.8 - - + -
31B LYS* 3.8 31.0 - - + +
34B LEU* 4.4 6.1 - - + -
35B ALA* 3.9 30.7 - - + +
38B THR* 4.6 2.0 - - - +
40B LEU* 4.4 9.9 - - + -
41B THR 3.0 18.1 + - - +
42B ILE* 3.5 7.4 - - - +
44B GLN* 1.3 75.7 - - - +
46B ASN* 1.3 65.3 + - - +
48B TRP* 3.5 6.1 + - - +
49B PHE* 3.2 40.1 + - + -
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Residues in contact with ASN 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 LYS* 3.5 36.5 - - - +
42B ILE* 2.8 37.6 + - - +
43B LEU* 3.7 14.1 - - + +
44B GLN 3.4 0.2 - - - -
45B VAL* 1.3 79.2 - - - +
47B ASN* 1.3 66.8 + - - +
48B TRP 3.4 0.2 + - - -
49B PHE* 3.6 4.1 + - - +
50B ILE* 3.2 31.7 + - + +
53B ARG* 5.7 0.2 + - - -
29L G 5.9 0.2 - - - -
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Residues in contact with ASN 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 LEU* 3.1 41.8 + - - +
44B GLN* 4.3 2.9 - - - +
46B ASN* 1.3 76.2 - - - +
48B TRP* 1.3 62.9 + - - +
50B ILE* 3.3 13.6 + - - +
51B ASN* 2.5 42.6 + - - +
5M G 6.1 1.1 - - + -
6M A 4.8 20.0 + - + +
7M C 3.9 37.4 + - - +
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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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10B THR* 4.4 13.9 - - + +
13B MET* 3.4 72.2 - - + +
14B ARG* 3.9 19.1 - - + -
17B LEU* 4.4 9.4 - - + -
40B LEU* 6.0 5.2 - - + -
44B GLN 3.3 18.0 + - - +
45B VAL 3.8 0.4 - - - +
46B ASN 3.3 0.4 - - - -
47B ASN* 1.3 79.8 - - - +
49B PHE* 1.3 70.3 + + - +
51B ASN* 3.3 6.1 + - - +
52B ALA* 2.8 56.4 + - + +
56B ILE* 4.6 6.1 - - + -
5M G 3.5 42.6 + - - -
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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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13B MET* 3.3 36.3 - - + -
16B TRP* 3.6 28.9 - + + -
17B LEU* 4.1 15.7 - - + -
24B PRO 4.1 10.1 - - - -
26B PRO* 4.3 12.6 - - + -
31B LYS* 6.1 0.2 - - + -
34B LEU* 3.4 30.5 - - + -
45B VAL* 3.2 25.3 + - + -
46B ASN* 4.1 4.3 - - - +
47B ASN 3.4 0.4 - - - -
48B TRP* 1.3 93.9 - + - +
50B ILE* 1.3 58.4 + - - +
52B ALA* 2.9 2.0 + - - +
53B ARG* 2.7 59.4 + - - +
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Residues in contact with ILE 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 ASN* 3.2 27.4 - - + +
47B ASN* 3.3 17.4 + - - +
49B PHE* 1.3 75.8 - - - +
51B ASN* 1.3 62.2 + - - +
53B ARG* 3.4 23.4 + - - +
54B ARG* 3.5 20.2 + - - +
29L G 4.4 16.6 - - + +
30L C 3.5 49.3 + - + +
31L T 3.7 17.5 - - + +
7M C 6.3 1.6 - - - +
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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 ASN* 2.5 41.4 + - - +
48B TRP* 3.7 5.7 - - - +
50B ILE* 1.3 79.0 - - - +
52B ALA* 1.3 64.3 + - - +
53B ARG 3.2 0.2 - - - -
54B ARG* 2.8 36.3 + - - +
55B ARG* 3.1 59.3 + - - +
5M G 4.7 11.0 + - + +
6M A 3.6 16.0 + - - -
7M C 4.5 4.9 - - - +
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Residues in contact with ALA 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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17B LEU* 4.2 7.4 - - + -
48B TRP* 2.8 49.8 + - + +
49B PHE* 2.9 5.4 + - - +
51B ASN* 1.3 73.8 - - - +
53B ARG* 1.3 54.6 + - - +
55B ARG* 4.6 1.3 - - - -
56B ILE* 2.5 57.9 + - + +
57B VAL* 3.3 2.4 + - - -
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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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17B LEU* 4.9 3.1 - - + -
24B PRO* 3.0 45.1 + - + +
25B TYR* 3.7 40.8 - - - +
26B PRO* 3.7 5.9 - - - +
31B LYS* 6.1 0.6 - - - +
46B ASN 5.7 0.2 + - - -
49B PHE* 2.7 34.6 + - - +
50B ILE* 3.4 33.0 - - - +
52B ALA* 1.3 73.4 - - - +
54B ARG* 1.3 54.6 + - + +
57B VAL* 3.2 16.4 + - + +
58B GLN* 2.7 40.6 + - + +
29L G 4.3 10.7 + - - -
30L C 2.9 32.0 + - - +
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Residues in contact with ARG 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 ILE* 3.5 14.6 + - - +
51B ASN* 2.8 39.6 + - - +
53B ARG* 1.3 78.8 - - + +
55B ARG* 1.3 69.2 + - + +
58B GLN* 4.0 14.3 - - + +
59B PRO* 4.0 11.8 - - - +
30L C 5.7 0.2 - - - -
31L T 3.3 48.6 + - - +
32L G 2.7 48.9 + - - -
33L T 3.3 15.1 + - - +
6M A 3.4 0.8 - - - +
7M C 5.0 1.0 - - - +
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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* 3.1 48.4 + - - +
52B ALA* 4.2 2.9 - - - +
54B ARG* 1.3 93.3 - - + +
56B ILE* 1.3 64.9 + - + +
59B PRO* 3.5 16.7 - - - +
33L T 3.3 23.4 + - - +
34L C 4.9 0.2 - - - +
4M T 3.8 50.4 + - - +
5M G 3.3 34.6 + - - -
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Residues in contact with ILE 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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14B ARG* 5.4 8.3 - - + -
17B LEU* 3.7 21.8 - - + -
18B PHE* 3.5 37.9 - - + -
21B LEU* 5.8 0.4 - - + -
48B TRP* 4.6 11.2 - - + -
52B ALA* 2.5 31.6 + - + +
55B ARG* 1.3 83.1 - - + +
57B VAL* 1.3 63.1 + - + +
59B PRO* 3.6 4.9 - - - +
60B MET* 3.4 23.0 + - - +
4M T 6.1 0.4 - - - +
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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