Contacts of the helix formed by residues 22 - 36 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 4.4 9.7 - - + +
19B PRO* 3.0 32.4 + - + +
21B GLY* 1.3 73.7 - - - +
23B ASP* 1.3 64.1 + - - +
25B GLU* 3.2 32.3 - - + +
26B TYR* 3.1 22.7 + - - +
76B PHE* 5.1 1.6 - - + -
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Residues in contact with ASP 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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21B GLY* 2.8 28.4 + - - +
22B ALA* 1.3 69.9 + - - +
24B GLN* 1.3 62.0 + - - +
25B GLU* 3.7 0.4 + - - -
26B TYR* 3.2 6.0 + - - +
27B SER* 2.8 33.1 + - - -
271B PRO* 3.7 32.5 - - + +
272B GLY* 5.8 0.4 - - - -
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 1.3 79.8 - - - +
25B GLU* 1.3 62.3 + - - +
27B SER* 3.6 1.2 - - - -
28B ALA* 2.9 29.1 + - - +
262B TRP* 3.7 16.6 - - + +
271B PRO 3.9 8.5 + - - +
272B GLY* 3.3 26.8 + - - +
275B THR* 4.4 3.8 + - - -
277B THR 4.0 5.1 + - - -
278B ILE* 3.6 27.1 - - - +
279B LYS* 3.4 23.0 + - - +
282B SER* 3.3 18.4 + - - +
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 4.0 3.8 - - + -
21B GLY 4.5 0.9 - - - +
22B ALA* 3.2 35.5 - - + -
23B ASP 3.7 0.2 + - - -
24B GLN* 1.3 80.1 + - - +
26B TYR* 1.3 57.2 + - - +
28B ALA* 3.4 1.9 + - - +
29B PHE 2.9 21.0 + - - -
76B PHE* 4.2 22.4 - - + -
279B LYS* 5.0 2.1 - - - +
281B THR* 2.8 29.8 + - - +
282B SER* 3.5 23.9 + - - +
285B THR* 3.3 20.0 - - - +
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Residues in contact with TYR 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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18B PHE* 3.7 33.6 - + + -
22B ALA 3.1 19.4 + - - +
23B ASP* 3.7 4.3 - - - +
25B GLU* 1.3 74.3 - - - +
27B SER* 1.3 61.9 + - - +
29B PHE* 2.9 12.1 + + - +
30B ARG* 2.8 60.6 + - + +
47B ILE* 3.5 45.7 - - + +
271B PRO* 6.1 3.8 - - + -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP 2.8 19.6 + - - -
24B GLN 3.6 4.9 - - - -
26B TYR* 1.3 78.1 - - - +
28B ALA* 1.3 56.0 + - - +
30B ARG* 3.3 8.8 + - - +
31B VAL* 3.1 32.4 + - - +
262B TRP* 4.1 13.5 - - - -
270B TYR* 4.0 19.0 - - - -
271B PRO* 3.1 40.2 + - - +
273B ALA* 4.4 0.2 - - - -
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN 2.9 18.3 + - - +
25B GLU 3.7 4.0 - - - +
27B SER* 1.3 73.7 - - - +
29B PHE* 1.3 64.9 + - - +
31B VAL* 3.9 2.8 - - - +
32B GLY* 3.1 19.9 + - - -
258B PHE* 5.4 0.4 - - + -
262B TRP* 3.7 20.6 - - + -
278B ILE* 4.6 3.1 - - + -
282B SER* 3.4 30.1 - - - +
285B THR* 4.5 2.0 - - - -
286B TYR* 3.9 19.2 - - + +
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Residues in contact with PHE 29 (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 ILE* 4.6 12.1 - - + -
15B GLY 5.6 0.4 - - - -
16B GLY* 5.5 3.4 - - - -
18B PHE* 3.4 25.4 - + + -
25B GLU 2.9 15.2 + - - +
26B TYR* 2.9 23.1 + + - +
28B ALA* 1.3 78.1 - - - +
30B ARG* 1.3 59.5 + - + +
32B GLY 3.6 0.7 + - - -
33B MET* 3.1 40.4 + - + +
45B PRO* 3.8 33.2 - - + -
47B ILE* 4.0 10.8 - - + -
74B PHE* 3.7 32.8 - + + -
285B THR* 3.6 10.5 - - + +
289B VAL* 3.8 26.8 - - + +
292B MET* 5.4 2.7 - - - -
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Residues in contact with ARG 30 (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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26B TYR* 2.8 53.0 + - + +
27B SER* 3.5 10.3 - - - +
29B PHE* 1.3 77.2 - - + +
31B VAL* 1.3 67.4 + - - +
33B MET* 3.0 21.5 + - - +
34B VAL* 3.2 16.7 + - + +
269B GLU* 2.8 35.2 + - - +
270B TYR* 3.8 34.9 + - + +
271B PRO* 5.0 2.2 - - - +
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Residues in contact with VAL 31 (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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27B SER 3.1 17.3 + - - +
28B ALA* 3.9 6.1 - - - +
30B ARG* 1.3 74.3 - - - +
32B GLY* 1.3 57.1 + - - +
34B VAL* 3.2 9.6 + - + +
35B GLN* 2.9 29.4 + - + +
258B PHE* 4.2 12.6 - - + -
262B TRP* 3.8 11.4 - - + -
265B LEU* 3.7 29.6 - - + -
270B TYR* 4.0 13.0 - - + -
286B TYR* 4.2 15.7 - - + -
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Residues in contact with GLY 32 (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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28B ALA 3.1 13.6 + - - -
29B PHE 3.6 2.2 + - - -
30B ARG 3.1 0.2 - - - -
31B VAL* 1.3 75.8 - - - +
33B MET* 1.3 62.7 + - - +
36B PHE* 3.0 34.9 + - - +
286B TYR* 3.7 22.0 - - - -
289B VAL* 3.4 18.2 - - - +
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Residues in contact with MET 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 5.1 1.6 - - - -
29B PHE* 3.1 36.9 + - + +
30B ARG* 3.0 12.9 + - - +
32B GLY* 1.3 75.4 - - - +
34B VAL* 1.3 60.0 + - + +
36B PHE 4.0 1.0 - - - -
37B SER* 3.2 27.2 + - - -
43B LEU* 3.3 51.1 - - + +
45B PRO* 3.6 21.8 - - + -
289B VAL* 3.8 16.8 - - - +
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Residues in contact with VAL 34 (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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30B ARG* 3.2 15.4 + - + +
31B VAL* 3.6 9.4 - - + +
32B GLY 3.1 0.6 - - - -
33B MET* 1.3 78.7 - - + +
35B GLN* 1.3 64.3 + - - +
36B PHE 3.2 0.4 - - - -
37B SER* 3.0 21.9 + - - +
270B TYR* 4.9 11.0 - - - +
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Residues in contact with GLN 35 (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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31B VAL* 2.9 18.6 + - + +
32B GLY 4.2 2.0 - - - +
34B VAL* 1.3 78.7 - - - +
36B PHE* 1.3 74.0 + - + +
37B SER 3.5 1.8 + - - +
286B TYR* 3.3 28.9 + - + +
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Residues in contact with PHE 36 (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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32B GLY* 3.0 26.9 + - - +
33B MET 4.0 4.0 - - - -
35B GLN* 1.3 89.9 - - + +
37B SER* 1.3 58.2 + - - +
38B THR* 3.8 3.5 + - - +
41B PHE* 5.9 0.2 - - - -
43B LEU* 5.7 3.1 - - - +
286B TYR* 3.5 46.7 - + - -
289B VAL* 4.1 2.5 - - + -
290B GLN* 3.5 61.5 - - + -
293B THR* 3.7 39.0 + - + +
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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