Contacts of the helix formed by residues 22 - 36 (chain A) in PDB entry 3KG2
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 ALA 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 PHE* 4.4 9.7 - - + +
19A PRO* 3.0 32.4 + - + +
21A GLY* 1.3 74.3 - - - +
23A ASP* 1.3 64.4 + - - +
25A GLU* 3.2 32.5 - - + +
26A TYR* 3.1 22.7 + - - +
76A PHE* 5.1 1.1 - - + -
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Residues in contact with ASP 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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21A GLY* 2.8 28.1 + - - +
22A ALA* 1.3 70.0 + - - +
24A GLN* 1.3 62.3 + - - +
25A GLU* 3.7 0.4 + - - -
26A TYR* 3.2 5.7 + - - +
27A SER* 2.8 33.4 + - - -
271A PRO* 3.7 31.2 - - + +
272A GLY* 5.3 0.9 - - - +
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Residues in contact with GLN 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 ALA 3.6 0.2 - - - -
23A ASP* 1.3 78.4 - - - +
25A GLU* 1.3 63.3 + - - +
27A SER* 3.6 1.9 - - - -
28A ALA* 2.9 29.3 + - - +
262A TRP* 3.7 16.1 - - + +
271A PRO 3.9 9.1 + - - +
272A GLY* 3.3 27.2 + - - +
275A THR* 4.4 3.4 + - - -
277A THR 4.0 5.9 + - - -
278A ILE* 3.6 26.7 - - - +
279A LYS* 3.4 22.2 + - - +
282A SER* 3.3 18.6 + - - +
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Residues in contact with GLU 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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18A PHE* 4.0 3.1 - - + -
21A GLY 4.5 0.7 - - - +
22A ALA* 3.2 35.7 - - + -
23A ASP 3.7 0.3 + - - -
24A GLN* 1.3 80.6 + - - +
26A TYR* 1.3 58.2 + - - +
28A ALA* 3.4 1.6 + - - +
29A PHE 2.9 20.4 + - - -
76A PHE* 4.2 22.0 - - + -
279A LYS* 5.0 2.3 - - - +
281A THR* 2.8 28.4 + - - +
282A SER* 3.5 23.9 + - - +
285A THR* 3.3 21.3 - - - +
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Residues in contact with TYR 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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18A PHE* 3.7 33.6 - + + -
22A ALA 3.1 18.1 + - - +
23A ASP* 3.7 4.7 - - - +
25A GLU* 1.3 73.8 - - - +
27A SER* 1.3 61.9 + - - +
29A PHE* 3.0 12.6 + + - +
30A ARG* 2.8 60.0 + - + +
47A ILE* 3.5 46.1 - - + +
49A ASN* 5.8 0.2 - - - -
271A PRO* 6.1 3.1 - - + -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP 2.8 18.9 + - - -
24A GLN 3.6 4.9 - - - -
26A TYR* 1.3 77.3 - - - +
28A ALA* 1.3 57.1 + - - +
30A ARG* 3.3 9.1 + - - +
31A VAL* 3.1 32.2 + - - +
262A TRP* 4.1 13.0 - - - -
270A TYR* 3.8 19.2 - - - -
271A PRO* 3.1 40.6 + - - +
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Residues in contact with ALA 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 GLN 2.9 18.1 + - - +
25A GLU 3.6 3.8 - - - +
27A SER* 1.3 74.5 - - - +
29A PHE* 1.3 65.0 + - - +
31A VAL* 3.5 2.6 + - - +
32A GLY* 3.1 20.1 + - - -
258A PHE* 5.4 0.2 - - + -
262A TRP* 3.8 21.0 - - + -
278A ILE* 4.6 2.9 - - + -
282A SER* 3.4 31.0 - - - +
285A THR* 4.5 2.0 - - - -
286A TYR* 3.9 18.0 - - + +
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Residues in contact with PHE 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 ILE* 4.6 11.4 - - + -
15A GLY 5.7 0.2 - - - -
16A GLY* 5.5 3.4 - - - -
18A PHE* 3.4 26.2 - + + -
25A GLU 2.9 14.9 + - - +
26A TYR* 3.0 22.4 + + - +
28A ALA* 1.3 78.9 - - - +
30A ARG* 1.3 60.4 + - + +
32A GLY 3.5 0.5 + - - -
33A MET* 3.1 40.8 + - + +
45A PRO* 3.8 33.9 - - + -
47A ILE* 4.0 10.5 - - + -
74A PHE* 3.7 31.6 - + + -
285A THR* 3.6 9.2 - - + +
289A VAL* 3.8 26.8 - - + +
292A MET* 5.4 2.9 - - - -
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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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26A TYR* 2.8 53.6 + - + +
27A SER* 3.5 10.3 - - - +
28A ALA 3.2 0.2 - - - -
29A PHE* 1.3 75.3 - - + +
31A VAL* 1.3 66.5 + - - +
33A MET* 3.0 21.2 + - - +
34A VAL* 3.2 17.1 + - + +
269A GLU* 2.8 34.8 + - - +
270A TYR* 3.8 34.5 + - + +
271A PRO* 5.0 2.4 - - - +
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Residues in contact with VAL 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 SER 3.1 17.3 + - - +
28A ALA* 3.9 6.3 - - - +
29A PHE 3.5 0.2 - - - -
30A ARG* 1.3 75.0 - - - +
32A GLY* 1.3 57.7 + - - +
34A VAL* 3.2 9.5 + - + +
35A GLN* 2.9 30.0 + - + +
258A PHE* 4.2 13.2 - - + -
262A TRP* 3.8 11.2 - - + -
265A LEU* 3.7 29.8 - - + -
270A TYR* 4.0 13.0 - - + -
286A TYR* 4.2 15.5 - - + -
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Residues in contact with GLY 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 ALA 3.1 13.4 + - - -
29A PHE 3.9 2.5 - - - -
30A ARG 3.1 0.4 - - - -
31A VAL* 1.3 74.7 - - - +
33A MET* 1.3 64.5 + - - +
36A PHE* 3.0 33.7 + - - +
286A TYR* 3.7 21.9 - - - -
289A VAL* 3.4 17.2 - - - +
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Residues in contact with MET 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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14A ILE* 5.1 1.6 - - - -
29A PHE* 3.1 37.1 + - + +
30A ARG* 3.0 12.0 + - - +
32A GLY* 1.3 75.8 - - - +
34A VAL* 1.3 60.7 + - + +
36A PHE 4.0 1.0 - - - -
37A SER* 3.2 27.4 + - - -
43A LEU* 3.3 49.6 - - + +
45A PRO* 3.6 21.8 - - + -
289A VAL* 3.8 17.0 - - - +
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Residues in contact with VAL 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 ARG* 3.2 15.1 + - + +
31A VAL* 3.6 9.4 - - + +
32A GLY 3.1 0.2 - - - -
33A MET* 1.3 78.7 - - + +
35A GLN* 1.3 63.5 + - - +
36A PHE 3.2 0.4 - - - -
37A SER* 3.0 21.9 + - - +
270A TYR* 4.9 11.7 - - - +
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Residues in contact with GLN 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 VAL* 2.9 19.5 + - + +
34A VAL* 1.3 78.6 - - - +
36A PHE* 1.3 76.3 + - + +
37A SER 3.5 1.8 + - - +
286A TYR* 3.3 28.7 - - + +
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Residues in contact with PHE 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 GLY* 3.0 27.7 + - - +
33A MET* 4.0 4.5 - - - -
35A GLN* 1.3 87.5 - - + +
37A SER* 1.3 58.8 + - - +
38A THR* 3.8 3.9 + - - +
43A LEU* 5.7 3.1 - - - +
286A TYR* 3.4 47.3 - + - -
289A VAL* 4.1 2.7 - - + -
290A GLN* 3.4 61.9 - - + -
293A THR* 3.7 38.4 + - + +
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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