Contacts of the helix formed by residues 21 - 34 (chain G) in PDB entry 6CNB
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 21 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1435A ASN 5.0 5.2 - - - +
1436A ILE* 5.0 8.8 - - - +
1440A ASP* 5.6 1.9 - - - +
19G HIS 3.6 1.9 + - - -
20G ARG* 1.3 80.3 - - - +
22G THR* 1.3 90.8 + - - +
23G ILE* 3.5 18.7 + - - +
24G SER* 3.4 14.7 + - - +
25G ALA* 3.3 15.6 + - - +
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Residues in contact with THR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434A THR* 3.3 28.8 + - - +
1435A ASN* 4.5 5.1 + - - +
1436A ILE* 5.4 4.5 - - + -
13G ILE* 5.4 6.7 - - + -
20G ARG 3.6 2.9 + - - -
21G ASP* 1.3 89.3 + - - +
23G ILE* 1.3 69.6 + - + +
25G ALA* 2.9 10.1 + - - +
26G ILE* 2.9 37.2 + - + +
54G VAL* 5.4 5.6 - - + -
68G ILE* 4.6 14.6 - - + -
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Residues in contact with ILE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436A ILE* 3.7 34.5 - - + -
1440A ASP* 5.4 11.7 - - + +
1441A LEU* 5.2 6.5 - - + -
21G ASP* 3.9 18.3 + - - +
22G THR* 1.3 76.6 - - + +
24G SER* 1.3 80.0 + - - +
26G ILE* 3.4 9.7 + - + +
27G THR* 2.9 34.3 + - - +
51G LEU* 4.0 21.8 - - + +
54G VAL* 5.4 4.9 - - + -
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Residues in contact with SER 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ARG* 4.0 19.7 - - - -
21G ASP* 3.4 15.3 + - - +
22G THR 3.2 0.8 - - - -
23G ILE* 1.3 91.6 - - - +
25G ALA* 1.3 51.5 + - - +
27G THR* 3.1 9.2 + - - -
28G HIS* 2.7 35.6 + - - +
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ILE* 4.2 22.2 - - + -
17G GLN* 4.4 26.0 - - + +
20G ARG* 4.4 8.2 - - - +
21G ASP 3.3 8.2 + - - +
22G THR* 2.9 11.7 + - - +
24G SER* 1.3 74.8 - - - +
26G ILE* 1.3 67.0 + - - +
28G HIS* 3.1 6.8 + - - +
29G GLN* 2.9 29.1 + - + +
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Residues in contact with ILE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 4.9 13.2 - - + +
13G ILE* 4.2 17.7 - - + -
22G THR* 2.9 30.6 + - + +
23G ILE* 3.6 10.3 - - + +
25G ALA* 1.3 74.4 - - - +
27G THR* 1.3 64.8 + - - +
29G GLN* 3.4 4.5 + - - +
30G LEU* 2.9 39.1 + - + +
51G LEU* 4.0 28.9 - - + -
54G VAL* 5.3 6.5 - - + -
68G ILE* 4.4 31.9 - - + -
70G VAL* 4.3 13.9 - - + -
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Residues in contact with THR 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 5.8 10.8 - - + -
23G ILE* 2.9 17.7 + - - +
24G SER* 3.3 11.1 - - - -
26G ILE* 1.3 76.0 - - - +
28G HIS* 1.3 63.9 + - - +
30G LEU* 3.1 11.0 + - - +
31G ASN* 2.9 39.7 + - - +
48G ILE* 4.6 19.1 - - + +
51G LEU* 4.8 8.9 - - - +
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Residues in contact with HIS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PRO* 4.9 16.9 - - + +
17G GLN* 5.3 9.0 + - - +
20G ARG* 5.1 14.9 + - - +
24G SER 2.7 20.0 + - - +
25G ALA* 3.6 8.3 - - - +
27G THR* 1.3 75.7 - - - +
29G GLN* 1.3 68.1 + - + +
31G ASN* 3.3 8.3 + - + +
32G ASN* 2.8 66.4 + - - +
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Residues in contact with GLN 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 3.8 21.3 - - + -
12G ARG 3.8 21.7 - - - +
13G ILE* 4.0 12.3 - - + -
14G PRO* 4.1 16.2 - - - +
17G GLN* 4.2 15.4 - - - +
25G ALA* 2.9 19.2 + - + +
26G ILE 3.9 0.4 - - - +
28G HIS* 1.3 82.4 + - - +
30G LEU* 1.3 58.5 + - - +
32G ASN* 3.1 20.4 + - - +
33G LYS* 2.8 29.2 + - - +
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Residues in contact with LEU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ASP* 5.1 3.8 - - + +
11G VAL* 3.7 27.1 - - + -
26G ILE* 2.9 38.4 + - + +
27G THR* 3.5 1.6 - - - +
29G GLN* 1.3 76.4 - - - +
31G ASN* 1.3 57.7 + - - +
33G LYS* 2.9 9.0 + - + +
34G PHE* 2.8 44.1 + - + +
48G ILE* 3.5 33.7 - - + -
51G LEU* 4.8 3.1 - - + -
70G VAL* 4.9 0.9 - - + -
72G PHE* 3.5 41.5 - - + -
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Residues in contact with ASN 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 5.3 3.2 - - - +
54D GLU* 5.4 0.5 - - - +
55D LEU* 3.8 32.1 - - + +
27G THR* 2.9 32.0 + - - +
28G HIS* 3.7 10.5 - - + +
30G LEU* 1.3 74.2 - - - +
32G ASN* 1.3 64.7 + - - +
33G LYS 3.2 0.5 + - - -
34G PHE* 3.3 4.5 + - - +
35G ALA* 3.3 30.2 + - + +
47G THR* 2.7 31.1 + - - -
48G ILE* 3.4 15.8 + - - +
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Residues in contact with ASN 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PRO* 4.3 16.0 + - - +
28G HIS* 2.8 55.2 + - - +
29G GLN* 3.3 23.1 + - - +
31G ASN* 1.3 76.3 - - - +
33G LYS* 1.3 59.5 + - - +
34G PHE 5.2 0.3 - - - -
35G ALA* 5.7 0.2 - - - +
37G LYS* 5.6 5.0 + - - +
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Residues in contact with LYS 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 4.3 5.3 - - + +
6A VAL 2.5 33.3 + - - +
7A SER* 3.8 17.2 - - - +
8A GLU* 4.3 7.7 + - - +
1D MET 5.6 0.2 - - - +
9G ASP* 3.1 29.4 - - - +
10G LEU 5.7 2.0 - - - +
11G VAL* 5.8 2.5 - - + -
29G GLN 2.8 11.5 + - - +
30G LEU* 2.9 13.4 + - + +
32G ASN* 1.3 79.3 - - - +
34G PHE* 1.3 85.0 + - + +
37G LYS* 4.1 12.5 - - - +
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Residues in contact with PHE 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.7 25.4 - - + -
7A SER* 5.6 0.4 - - - -
1D MET 5.8 3.8 - - - -
7G ILE* 3.5 32.3 - - + -
9G ASP* 4.1 17.7 - - + -
30G LEU* 2.8 25.2 + - + +
31G ASN* 3.3 1.1 + - - +
32G ASN 5.2 0.2 - - - -
33G LYS* 1.3 102.9 - - + +
35G ALA* 1.3 64.0 + - - +
36G ASN 3.1 0.9 + - - -
37G LYS* 2.6 44.3 + - - +
39G ILE* 6.1 6.5 - - + -
45G CYS* 4.5 23.1 - - + -
47G THR* 6.3 0.2 - - - -
48G ILE* 4.3 15.5 - - + -
72G PHE* 3.8 12.6 - + - -
74G ALA* 5.2 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