Contacts of the helix formed by residues 22 - 39 (chain A) in PDB entry 3T2D
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 HIS 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.6 42.0 - + + +
21A VAL* 1.3 77.6 - - - +
23A PRO* 1.3 71.8 - - + +
24A LYS* 3.0 51.1 + - + +
25A MET* 2.9 35.8 + - + +
26A LEU 3.8 1.6 + - - -
84A ILE* 4.9 0.7 - - + -
88A PHE* 3.6 32.3 - + - -
90A LEU* 3.8 23.8 - - + -
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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
----------------------------------------------------------
15A PHE* 4.3 11.2 - - + -
21A VAL* 3.8 5.6 - - + +
22A HIS* 1.3 98.1 - - + +
24A LYS* 1.3 62.6 + - + +
26A LEU* 3.1 16.3 + - + +
27A GLU* 3.0 33.7 + - + +
289A ILE* 4.5 19.7 - - + -
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Residues in contact with LYS 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 HIS* 3.0 29.2 + - + +
23A PRO* 1.3 79.7 - - + +
25A MET* 1.3 56.1 + - - +
27A GLU* 3.7 22.5 + - - +
28A TYR* 2.9 30.7 + - - +
84A ILE* 4.0 22.1 - - + +
88A PHE* 4.1 17.5 - - + -
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Residues in contact with MET 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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12A VAL* 3.6 39.3 - - + +
13A GLY* 3.4 23.3 - - - +
21A VAL* 4.2 4.0 - - + -
22A HIS* 2.9 27.1 + - + +
24A LYS* 1.3 77.0 - - - +
26A LEU* 1.3 62.8 + - - +
28A TYR* 3.4 2.4 + - - +
29A ALA* 3.0 24.1 + - - +
54A ILE* 3.8 18.9 - - + +
80A VAL* 3.8 20.6 - - + +
84A ILE* 3.7 22.2 - - + -
85A ALA* 4.5 2.0 - - + +
90A LEU* 3.5 23.1 - - + -
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Residues in contact with LEU 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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21A VAL* 4.0 15.7 - - + -
22A HIS 4.5 0.4 - - - +
23A PRO* 3.1 14.2 + - + +
25A MET* 1.3 73.7 - - - +
27A GLU* 1.3 61.3 + - - +
29A ALA* 3.4 2.0 + - - +
30A ALA* 2.9 30.1 + - - +
47A VAL* 3.8 25.2 - - + +
48A TYR* 4.0 19.5 - - - -
49A ASN* 3.7 22.4 - - - +
54A ILE* 4.1 22.0 - - + -
287A ILE* 3.9 19.6 - - + +
288A ALA 3.9 6.5 - - - +
289A ILE* 3.9 23.8 - - + -
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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
----------------------------------------------------------
23A PRO* 3.0 26.6 + - + +
24A LYS* 3.8 31.5 + - + +
26A LEU* 1.3 77.3 - - + +
28A TYR* 1.3 61.4 + - - +
30A ALA* 3.4 2.6 + - - +
31A ALA* 3.0 25.0 + - - +
285A ARG* 3.4 41.1 + - - +
287A ILE* 3.9 14.1 - - + -
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Residues in contact with TYR 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 LYS 2.9 18.4 + - - +
25A MET 3.8 3.6 - - - +
27A GLU* 1.3 72.9 - - - +
29A ALA* 1.3 66.8 + - - +
31A ALA* 3.2 7.5 + - + +
32A LYS* 3.0 29.1 + - + +
76A THR* 4.8 0.9 - - + -
79A GLU* 2.7 49.1 + - + +
80A VAL* 3.7 18.4 - - + -
83A GLN* 3.9 25.2 - - + +
84A ILE* 4.1 25.4 - - + -
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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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25A MET 3.0 18.3 + - - +
26A LEU* 3.8 3.8 - - - +
28A TYR* 1.3 77.7 - - - +
30A ALA* 1.3 61.4 + - - +
32A LYS* 3.2 2.6 + - - +
33A LEU* 3.0 27.9 + - - +
47A VAL* 4.0 9.0 - - + -
54A ILE* 5.1 4.5 - - + -
56A LEU* 3.9 19.7 - - + -
76A THR* 3.8 26.0 - - + +
77A PHE* 6.3 0.7 - - + -
80A VAL* 4.2 5.1 - - + +
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Residues in contact with ALA 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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26A LEU 2.9 18.3 + - - +
27A GLU* 3.8 3.8 - - - +
29A ALA* 1.3 74.8 - - - +
31A ALA* 1.3 56.9 + - - +
33A LEU 3.4 0.5 + - - -
34A LYS* 2.9 30.2 + - - +
45A TYR* 3.7 14.6 + - + +
47A VAL* 3.9 15.4 - - + +
285A ARG* 4.1 11.2 - - - +
286A ARG 4.7 0.2 - - - +
287A ILE* 3.8 25.4 - - + -
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Residues in contact with ALA 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 3.0 17.4 + - - +
28A TYR* 3.2 6.7 + - + +
30A ALA* 1.3 75.9 - - - +
32A LYS* 1.3 62.1 + - - +
34A LYS* 3.3 10.0 + - - +
35A GLU* 3.1 21.0 + - - +
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Residues in contact with LYS 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 TYR* 3.0 24.0 + - + +
29A ALA 3.2 5.1 + - - +
31A ALA* 1.3 76.4 - - - +
33A LEU* 1.3 61.3 + - - +
35A GLU* 3.2 9.5 + - + +
36A ALA* 3.0 20.4 + - - +
39A ARG* 5.3 5.0 + - - +
72A LEU* 4.2 12.9 - - + +
75A GLU* 2.6 37.5 + - - -
76A THR* 3.5 35.4 - - + +
79A GLU* 3.0 35.6 + - - +
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Residues in contact with LEU 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 3.0 16.8 + - - +
30A ALA 3.9 0.2 - - - +
32A LYS* 1.3 72.2 - - - +
34A LYS* 1.3 60.1 + - - +
36A ALA* 3.2 4.3 + - - +
37A GLN* 2.8 29.5 + - - +
42A ILE* 3.7 5.4 - - + +
45A TYR* 3.7 38.3 - - + -
47A VAL* 3.8 22.2 - - + -
56A LEU* 4.2 26.5 - - + -
58A MET* 4.1 13.7 - - + -
72A LEU* 3.8 33.7 - - + -
76A THR* 4.0 14.4 - - + +
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Residues in contact with LYS 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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30A ALA 2.9 14.0 + - - +
31A ALA* 3.5 10.1 - - - +
33A LEU* 1.3 74.8 - - - +
35A GLU* 1.3 58.1 + - - +
37A GLN* 3.3 13.9 + - - +
38A LYS* 2.9 27.6 + - + +
45A TYR* 3.3 27.2 - - - +
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Residues in contact with GLU 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 ALA 3.1 12.8 + - - +
32A LYS* 3.2 12.1 + - + +
34A LYS* 1.3 78.5 - - - +
36A ALA* 1.3 61.2 + - - +
38A LYS* 3.2 31.3 + - - +
39A ARG* 3.1 57.4 + - - +
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Residues in contact with ALA 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 LYS 3.0 12.7 + - - +
33A LEU* 3.2 8.9 + - - +
35A GLU* 1.3 75.4 - - - +
37A GLN* 1.3 60.9 + - - +
39A ARG* 3.3 17.9 + - - +
40A GLY 3.1 4.5 + - - -
41A VAL* 2.9 34.2 + - + +
42A ILE* 4.2 4.7 - - + -
72A LEU* 3.6 38.4 - - + -
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Residues in contact with GLN 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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33A LEU 2.8 14.0 + - - +
34A LYS* 3.4 21.0 - - - +
36A ALA* 1.3 74.9 - - - +
38A LYS* 1.3 67.1 + - - +
40A GLY* 3.0 14.4 + - - -
42A ILE* 3.5 20.4 - - + +
43A ILE 2.9 28.8 + - - +
44A ASP* 3.6 22.0 + - - +
45A TYR* 3.8 15.5 + - + -
313A TYR* 4.4 8.6 - - + -
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Residues in contact with LYS 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 LYS* 2.9 14.5 + - + +
35A GLU* 3.2 33.3 + - - +
37A GLN* 1.3 77.8 + - - +
39A ARG* 1.3 61.8 + - + +
40A GLY 3.2 0.6 + - - -
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Residues in contact with ARG 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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32A LYS* 5.3 5.1 + - - +
35A GLU* 3.1 39.5 + - - +
36A ALA* 3.3 31.1 + - - +
37A GLN 3.2 0.2 - - - -
38A LYS* 1.3 77.2 - - + +
40A GLY* 1.3 59.7 + - - +
41A VAL* 3.6 24.3 + - + +
72A LEU* 5.3 5.7 - - - +
75A GLU* 5.9 1.0 + - - -
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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