Contacts of the helix formed by residues 22 - 38 (chain A) in PDB entry 2H7B
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 SER 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLY 3.3 6.4 - - - +
19A ASN* 3.7 9.8 - - - +
20A ASP 3.0 5.5 + - - -
21A ILE* 1.3 90.4 + - - +
23A PRO* 1.3 73.4 - - - +
24A GLU* 4.1 15.5 + - - -
25A ILE* 2.8 21.7 - - - +
26A GLY* 3.1 21.7 + - - -
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Residues in contact with PRO 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASN* 4.5 8.5 - - - +
22A SER* 1.3 88.1 - - - +
24A GLU* 1.3 78.6 + - + +
27A GLU* 2.8 30.9 + - - +
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 4.1 17.1 + - - -
23A PRO* 1.3 83.1 - - + +
25A ILE* 1.3 76.3 + - - +
27A GLU* 3.0 25.2 - - - +
28A ARG* 3.1 26.7 + - - +
53A ALA 3.6 16.8 - - - +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.2 34.1 - - + -
22A SER* 2.8 30.1 - - - +
24A GLU* 1.3 82.8 + - - +
26A GLY* 1.3 57.8 + - - +
28A ARG* 4.3 3.1 - - - -
29A VAL* 2.7 61.9 + - + +
50A LEU* 5.1 0.7 - - + -
53A ALA* 3.4 32.7 + - + +
54A THR* 3.3 31.4 - - + -
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN 5.6 0.3 - - - +
18A GLY* 3.0 28.8 - - - -
19A ASN* 4.0 5.4 - - - -
22A SER 3.1 10.0 + - - -
23A PRO 3.5 0.2 - - - -
24A GLU 3.0 3.2 + - - -
25A ILE* 1.3 87.3 - - - +
27A GLU* 1.3 63.0 + - - -
28A ARG 3.0 0.2 + - - -
29A VAL* 3.6 1.4 - - - +
30A ARG* 3.0 28.2 + - - +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASN* 4.4 2.8 + - - +
23A PRO* 2.8 21.3 + - - +
24A GLU* 3.0 26.9 - - - +
26A GLY* 1.3 70.5 - - - -
28A ARG* 1.3 62.1 + - + +
30A ARG* 3.0 24.1 - - - +
31A THR* 2.5 41.1 + - - +
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.1 29.7 + - - +
25A ILE 3.6 3.4 - - - +
26A GLY 3.0 0.4 - - - -
27A GLU* 1.3 86.8 - - - +
29A VAL* 1.3 68.6 + - - +
31A THR* 2.9 6.3 + - + -
32A LEU* 2.8 32.5 + - + +
49A LYS* 3.8 37.7 - - + +
52A GLU* 3.5 40.5 + - - -
53A ALA* 3.2 31.8 + - + +
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.3 43.5 - - + +
15A GLN* 3.6 18.8 - - + +
18A GLY* 4.8 4.5 - - - -
25A ILE* 2.7 52.8 + - + +
26A GLY* 3.6 4.9 - - - +
28A ARG* 1.3 72.4 - - - +
30A ARG* 1.3 59.5 + - - +
32A LEU* 4.0 3.3 - - - +
33A VAL* 2.9 37.0 + - + +
50A LEU* 5.0 12.6 - - + -
54A THR* 4.9 4.5 - - + -
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 4.6 15.5 - - + +
19A ASN* 3.0 32.6 - - - +
26A GLY 3.0 15.0 + - - +
27A GLU* 3.0 36.0 + - - +
29A VAL* 1.3 81.2 - - - +
31A THR* 1.3 61.1 + - - +
33A VAL* 4.4 2.2 - - - -
34A LEU* 2.8 58.2 + - + +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 2.5 28.9 + - - +
28A ARG* 2.9 7.1 + - - -
30A ARG* 1.3 78.7 + - - +
32A LEU* 1.3 67.8 + - + +
34A LEU* 5.2 1.1 - - - -
35A GLY* 2.7 34.5 + - - -
41A LEU* 4.5 6.6 - - + +
49A LYS* 5.1 9.4 - - - +
92A LEU* 4.7 3.4 - - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 2.8 27.8 + - + +
29A VAL* 4.0 1.8 - - - +
31A THR* 1.3 78.3 - - + +
33A VAL* 1.3 70.2 + - - +
35A GLY 3.1 1.0 + - - -
36A LEU* 2.9 27.8 + - - +
41A LEU* 3.9 13.7 - - + +
46A PHE* 3.0 43.3 - - + +
49A LYS* 3.5 37.9 - - + -
50A LEU* 3.1 37.2 - - + +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.3 29.6 - - + -
14A LEU* 4.1 3.1 - - + -
15A GLN* 3.1 33.2 - - + +
29A VAL* 2.9 44.1 + - + +
30A ARG* 3.9 3.6 - - - +
32A LEU* 1.3 75.3 - - - +
34A LEU* 1.3 66.6 + - - +
35A GLY 3.0 0.2 + - - -
36A LEU* 3.1 11.1 - - + +
37A VAL* 2.8 26.9 + - + +
46A PHE* 4.5 13.2 - - + -
50A LEU* 5.4 1.3 - - + -
66A LEU* 5.8 0.9 - - + -
73A LEU* 4.1 7.6 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 2.9 29.8 - - - +
30A ARG* 2.8 42.0 + - + +
31A THR* 5.5 0.4 - - - -
33A VAL* 1.3 75.5 - - - +
35A GLY* 1.3 61.7 + - - +
37A VAL* 3.3 6.2 + - - -
38A ASN* 2.7 31.5 + - - +
77A LEU* 3.6 21.5 - - + -
91A TYR* 3.9 28.3 - - + +
92A LEU* 3.2 27.4 - - + +
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR 2.7 25.7 + - - -
32A LEU 3.4 0.7 - - - -
33A VAL 3.0 1.4 + - - -
34A LEU* 1.3 73.4 - - - +
36A LEU* 1.3 55.4 + - - -
37A VAL 2.9 0.2 + - - -
39A SER* 2.4 56.0 + - - +
41A LEU* 3.5 12.1 - - - -
92A LEU* 3.5 2.9 - - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU 2.9 17.7 + - - +
33A VAL* 3.1 9.0 - - - +
35A GLY* 1.3 69.9 - - - -
37A VAL* 1.3 75.9 + - + +
39A SER 3.9 4.7 - - - +
41A LEU* 3.2 33.8 - - + +
42A THR 4.7 3.4 - - - +
43A ILE* 5.2 1.3 - - - -
46A PHE* 3.1 54.3 - - + -
66A LEU* 4.0 16.4 - - + -
70A LEU* 3.3 46.2 - - + +
73A LEU* 5.1 0.2 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 2.8 29.4 - - + +
34A LEU* 3.3 10.1 - - - +
35A GLY 2.9 1.6 + - - -
36A LEU* 1.3 91.7 - - + +
38A ASN* 1.3 74.9 + - - +
70A LEU* 4.5 5.9 - - - +
73A LEU* 3.9 22.0 - - + -
74A GLN* 3.6 30.0 - - + +
77A LEU* 3.4 25.4 - - + -
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Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 2.7 28.1 + - - +
37A VAL* 1.3 93.4 - - - +
39A SER* 1.3 68.5 + - - +
77A LEU* 3.4 27.0 - - - +
88A PRO 4.0 10.1 - - - +
89A ALA* 5.3 9.7 - - - +
92A LEU* 4.1 19.3 - - + +
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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