Contacts of the helix formed by residues 12 - 26 (chain B) in PDB entry 4H7Y
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 ASN 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ALA* 3.1 13.1 + - - +
11B ASN* 1.3 74.9 - - - +
13B PRO* 1.3 74.6 - - + +
14B GLU* 3.2 14.6 + - - +
15B ASP* 2.7 52.9 + - - +
16B TRP* 3.2 20.2 + - - -
49B LEU* 3.8 6.3 - - - -
54B TYR* 4.1 4.5 - - + +
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Residues in contact with PRO 13 (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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12B ASN* 1.3 88.0 - - + +
14B GLU* 1.3 62.1 + - - +
16B TRP* 3.6 0.7 - - - +
17B LEU* 2.8 31.9 + - - +
49B LEU* 3.8 19.0 - - + -
54B TYR* 3.4 48.5 - - + -
57B ASN* 3.4 25.1 - - - +
59B SER* 3.8 2.0 - - - -
60B PHE* 3.5 21.1 - - + +
63B ILE* 3.7 2.5 - - + +
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Residues in contact with GLU 14 (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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12B ASN* 3.5 14.7 - - - +
13B PRO* 1.3 84.8 - - - +
15B ASP* 1.3 64.3 + - - +
17B LEU* 3.9 2.4 - - - +
18B SER* 3.0 27.1 + - - -
57B ASN* 2.9 28.4 + - - +
59B SER* 3.7 19.4 + - - +
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Residues in contact with ASP 15 (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 ALA* 3.1 32.5 - - + +
12B ASN* 2.7 35.5 + - - +
14B GLU* 1.3 75.2 - - - +
16B TRP* 1.3 61.8 + - - +
18B SER* 3.4 8.1 + - - -
19B LEU* 3.1 25.3 + - + +
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Residues in contact with TRP 16 (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 ALA 4.4 5.3 + - - -
11B ASN* 3.1 35.3 + - - +
12B ASN 3.2 25.5 + - - +
13B PRO 3.6 7.4 - - - +
15B ASP* 1.3 75.2 - - - +
17B LEU* 1.3 65.8 + - - +
19B LEU* 3.2 26.1 + - + +
20B LEU* 2.9 32.2 + - + +
41B ARG* 3.6 32.1 - - + -
44B GLN 4.0 5.6 - - - -
45B ALA* 3.4 40.8 - - + -
48B ALA* 3.9 9.2 - - + +
49B LEU* 3.9 12.8 - - + -
63B ILE* 3.9 13.7 - - + -
47C GLU* 3.2 32.1 - - - -
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Residues in contact with LEU 17 (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 PRO 2.8 20.8 + - - +
14B GLU 3.9 3.4 - - - +
16B TRP* 1.3 73.0 - - - +
18B SER* 1.3 57.3 + - - +
20B LEU* 3.2 6.2 + - + -
21B LEU* 2.9 66.0 + - + +
42B TYR* 4.7 8.1 - - - +
59B SER* 3.8 20.6 - - - +
62B ARG* 3.6 44.4 - - + +
63B ILE* 4.0 21.0 - - + +
66B ARG* 5.3 1.8 - - + -
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Residues in contact with SER 18 (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 GLU 3.0 17.8 + - - -
15B ASP* 3.6 9.8 + - - -
16B TRP 3.2 0.2 - - - -
17B LEU* 1.3 77.7 - - - +
19B LEU* 1.3 62.4 + - - +
21B LEU* 4.0 5.4 - - - +
22B LYS* 3.1 24.6 + - - +
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Residues in contact with LEU 19 (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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15B ASP* 3.1 15.2 + - + +
16B TRP* 3.2 36.5 + - + +
18B SER* 1.3 79.7 - - - +
20B LEU* 1.3 69.1 + - + +
22B LYS* 3.5 11.5 + - + +
23B LEU* 2.9 30.7 + - + +
41B ARG* 3.7 39.0 - - + +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 2.9 28.5 + - + +
17B LEU* 3.7 5.2 - - + +
19B LEU* 1.3 80.8 - - + +
21B LEU* 1.3 59.3 + - - +
23B LEU* 3.2 7.2 + - + +
24B GLU* 2.9 32.7 + - - +
38B LEU* 4.2 0.9 - - - +
41B ARG* 3.6 46.2 - - + +
42B TYR* 3.7 46.2 - - + +
45B ALA* 3.8 23.1 - - + -
63B ILE* 4.0 11.0 - - + -
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Residues in contact with LEU 21 (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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28A VAL* 5.1 0.8 - - + +
29A PRO* 4.2 20.9 - - + -
17B LEU* 2.9 47.0 + - + +
18B SER* 4.1 5.6 - - - +
20B LEU* 1.3 73.0 - - - +
22B LYS* 1.3 65.8 + - - +
24B GLU* 3.2 13.9 + - + +
25B LYS* 3.0 32.6 + - + +
42B TYR* 4.1 14.6 - - - +
66B ARG* 5.3 4.0 - - + -
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Residues in contact with LYS 22 (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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18B SER 3.1 18.7 + - - +
19B LEU* 3.6 10.1 - - + +
20B LEU 3.3 0.2 - - - -
21B LEU* 1.3 77.7 - - - +
23B LEU* 1.3 63.0 + - - +
25B LYS* 3.2 9.0 + - + +
26B ASN* 3.0 43.7 + - - +
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Residues in contact with LEU 23 (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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19B LEU* 2.9 18.9 + - + +
20B LEU* 3.6 7.0 - - + +
22B LYS* 1.3 75.4 - - - +
24B GLU* 1.3 57.5 + - - +
26B ASN* 3.2 12.1 + - + +
27B SER* 2.5 39.7 + - - +
37B LYS* 4.4 30.3 - - + +
38B LEU* 3.7 24.0 - - + +
41B ARG* 3.7 40.8 - - + -
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Residues in contact with GLU 24 (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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28A VAL* 4.0 16.0 - - + +
29A PRO* 3.7 15.7 - - - +
30A LEU* 4.1 2.6 + - - +
20B LEU 2.9 22.0 + - - +
21B LEU* 3.5 13.0 - - + +
22B LYS 3.2 0.2 - - - -
23B LEU* 1.3 76.6 - - - +
25B LYS* 1.3 62.4 + - - +
27B SER* 3.1 18.7 + - - -
28B VAL* 4.1 6.1 - - - +
38B LEU* 3.5 30.3 - - + +
42B TYR* 2.5 26.2 + - - +
66B ARG* 2.9 38.9 + - - -
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Residues in contact with LYS 25 (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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25A LYS* 4.6 18.6 + - + +
28A VAL* 3.7 36.8 + - + +
29A PRO* 5.8 0.9 - - - -
21B LEU* 3.0 23.5 + - + +
22B LYS* 3.2 11.4 + - + +
24B GLU* 1.3 76.4 - - - +
26B ASN* 1.3 64.4 + - - +
27B SER 3.2 1.3 + - - -
28B VAL* 3.7 16.7 + - - +
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Residues in contact with ASN 26 (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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22B LYS* 3.0 40.4 + - - +
23B LEU* 3.5 13.7 - - + +
24B GLU 3.1 0.2 - - - -
25B LYS* 1.3 81.0 - - - +
27B SER* 1.3 56.6 + - - +
28B VAL 3.4 8.4 + - - +
34B LEU* 5.3 3.8 - - - +
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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