Contacts of the helix formed by residues 28 - 45 (chain A) in PDB entry 2H8C
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG 2.5 29.0 + - - -
17A TYR 2.6 21.7 + - - -
18A TYR* 3.6 11.2 - - - +
19A ARG* 3.7 17.7 - - - +
27A VAL* 1.3 77.2 - - - +
29A ALA* 1.3 68.7 + - - +
30A GLU* 3.6 5.5 + - - -
31A GLY 2.9 17.8 + - - -
32A GLN* 3.0 11.6 + - - +
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Residues in contact with ALA 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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19A ARG* 3.9 9.4 - - - +
28A SER* 1.3 73.2 - - - +
30A GLU* 1.3 59.4 + - + +
32A GLN* 3.3 6.9 + - - +
33A ALA* 2.9 28.7 + - - +
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Residues in contact with GLU 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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12A PRO* 3.6 22.5 - - + +
16A ARG* 2.7 58.5 + - - +
28A SER* 3.1 10.4 + - - +
29A ALA* 1.3 79.9 - - + +
31A GLY* 1.3 56.3 + - - +
33A ALA* 3.4 9.2 - - + +
34A TYR* 3.0 28.8 + - - +
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Residues in contact with GLY 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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17A TYR* 3.6 36.2 + - - -
27A VAL* 4.4 4.9 - - - -
28A SER* 2.9 16.1 + - - -
30A GLU* 1.3 73.6 - - - +
32A GLN* 1.3 62.9 - - - -
34A TYR* 3.2 4.7 + - - +
35A ARG* 3.0 28.8 + - - +
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Residues in contact with GLN 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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27A VAL* 3.9 12.4 - - + +
28A SER 3.0 8.7 + - - +
29A ALA* 3.6 9.0 - - - +
31A GLY* 1.3 72.6 - - - +
33A ALA* 1.3 65.5 + - - +
35A ARG* 3.0 43.3 + - - +
36A ASP* 2.7 59.2 + - - +
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Residues in contact with ALA 33 (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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29A ALA 2.9 17.0 + - - +
30A GLU* 3.4 15.3 - - + +
32A GLN* 1.3 73.1 - - - +
34A TYR* 1.3 63.7 + - - +
36A ASP* 3.0 18.9 + - - +
37A ASN* 3.0 20.7 + - - +
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Residues in contact with TYR 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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8A LEU* 3.7 15.6 - - - +
9A PRO* 2.8 44.5 + - + -
10A TRP 3.7 4.7 - - - -
11A PRO* 3.3 25.5 - - + +
12A PRO* 3.5 22.4 - - + -
17A TYR* 3.6 22.0 - + + -
30A GLU 3.0 11.5 + - - +
31A GLY 3.5 7.2 - - - +
32A GLN 3.2 0.2 - - - -
33A ALA* 1.3 75.1 - - - +
35A ARG* 1.3 67.5 + - - +
37A ASN* 3.0 22.0 + - - +
38A VAL* 3.0 24.4 + - + +
77A ALA 4.2 7.9 - - - -
78A ALA* 5.0 1.9 - - - -
81A ALA* 3.7 22.0 - - + -
110A LEU* 3.9 9.0 - - - +
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Residues in contact with ARG 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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17A TYR* 3.9 8.7 + - - +
18A TYR* 5.8 1.2 - - - -
26A HIS* 5.7 1.4 + - - -
27A VAL* 3.3 35.1 - - - +
31A GLY 3.0 14.4 - - - +
32A GLN* 3.0 37.4 + - - +
34A TYR* 1.3 77.0 - - - +
36A ASP* 1.3 54.5 + - - +
38A VAL* 3.3 2.1 + - - +
39A ALA* 2.7 36.4 + - - +
80A ASP* 2.4 37.7 + - - +
81A ALA* 4.5 14.6 - - - +
84A LYS* 3.2 46.0 - - + +
85A ALA* 5.2 0.2 - - - +
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Residues in contact with ASP 36 (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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32A GLN* 2.7 47.2 + - - +
33A ALA* 3.2 13.0 + - - +
35A ARG* 1.3 73.2 - - - +
37A ASN* 1.3 54.8 + - - +
39A ALA* 3.1 9.4 - - - +
40A ARG* 2.7 37.6 + - + +
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Residues in contact with ASN 37 (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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9A PRO* 4.9 16.9 - - + +
33A ALA* 3.0 16.9 + - - +
34A TYR* 3.0 15.9 + - + +
36A ASP* 1.3 74.1 - - - +
38A VAL* 1.3 56.0 + - + +
40A ARG* 2.8 11.4 + - - +
41A ILE* 2.6 47.9 + - + +
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Residues in contact with VAL 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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8A LEU* 4.1 22.4 - - + -
9A PRO* 5.0 0.7 - - + -
34A TYR* 3.0 30.5 + - + +
35A ARG 3.4 6.3 - - - +
37A ASN* 1.3 73.6 - - + +
39A ALA* 1.3 56.6 + - - +
41A ILE* 2.8 13.7 + - + +
42A ILE* 2.7 44.2 + - + +
81A ALA* 3.5 44.6 - - + +
82A LEU* 4.1 6.5 - - + -
85A ALA* 3.9 8.1 - - + -
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Residues in contact with ALA 39 (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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35A ARG 2.7 18.1 + - - +
36A ASP* 3.1 15.7 - - - +
38A VAL* 1.3 71.4 - - - +
40A ARG* 1.3 57.6 + - - +
42A ILE* 3.9 0.7 - - - +
43A LYS* 2.8 56.1 + - - +
84A LYS 5.9 0.4 - - - -
85A ALA* 3.9 21.2 - - + +
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Residues in contact with ARG 40 (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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36A ASP 2.7 18.6 + - - +
37A ASN* 2.8 13.4 + - - +
39A ALA* 1.3 71.5 - - - +
41A ILE* 1.3 64.7 + - + +
43A LYS* 3.9 12.5 - - - +
44A ASN* 3.1 44.8 + - - +
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Residues in contact with ILE 41 (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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6A ILE* 5.6 4.5 - - + -
7A THR 4.2 15.9 - - - +
8A LEU* 4.1 10.3 - - + -
9A PRO* 3.9 29.8 - - + -
37A ASN* 2.6 29.6 + - + +
38A VAL* 2.8 12.9 + - - +
40A ARG* 1.3 68.1 - - + +
42A ILE* 1.3 71.1 + - + +
44A ASN* 2.8 20.9 + - - +
45A ALA* 2.9 15.6 + - + +
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Residues in contact with ILE 42 (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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6A ILE* 3.4 36.8 - - + -
8A LEU* 5.2 0.9 - - + -
38A VAL* 2.7 27.9 + - + +
39A ALA 3.9 3.1 - - - +
41A ILE* 1.3 77.9 - - + +
43A LYS* 1.3 57.8 + - - +
45A ALA* 3.1 7.6 + - + +
47A LEU* 2.6 42.9 + - + +
48A ASP* 3.3 31.0 - - + +
82A LEU* 4.1 12.3 - - + -
85A ALA* 3.7 31.2 - - + +
87A PHE* 4.7 5.8 - - + +
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Residues in contact with LYS 43 (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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39A ALA* 2.8 49.2 + - - +
40A ARG* 4.0 14.0 - - - +
42A ILE* 1.3 74.3 - - + +
44A ASN* 1.3 64.7 + - - +
46A MET* 3.4 17.2 + - - +
48A ASP* 3.7 27.1 - - + +
85A ALA* 5.7 3.4 - - - +
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Residues in contact with ASN 44 (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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40A ARG* 3.1 33.6 + - - +
41A ILE* 2.8 12.3 + - + +
43A LYS* 1.3 77.1 - - - +
45A ALA* 1.3 53.4 + - - +
46A MET* 2.6 26.4 + - - +
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Residues in contact with ALA 45 (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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6A ILE* 5.5 3.6 - - + -
41A ILE* 2.9 15.9 + - + +
42A ILE* 3.1 9.8 + - + +
44A ASN* 1.3 72.6 - - - +
46A MET* 1.3 59.2 + - - +
47A LEU* 2.8 39.7 + - + +
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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