Contacts of the helix formed by residues 26 - 40 (chain B) in PDB entry 3K4H
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 PRO 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B GLN 3.6 6.2 - - - +
25B ASN* 1.3 93.2 - - - +
27B PHE* 1.3 63.8 + - - +
28B PHE 3.2 0.8 + - - -
29B PRO* 3.5 13.1 - - + +
30B GLU* 3.4 21.0 + - - +
200B ASP* 5.7 0.2 - - - +
202B LEU* 4.2 14.1 - - + +
228B ASN* 5.9 1.1 - - - +
230B ALA* 4.6 14.1 - - + +
231B LEU* 6.2 0.4 - - + -
232B LEU* 3.5 37.0 - - + -
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Residues in contact with PHE 27 (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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25B ASN* 2.7 24.9 + - - +
26B PRO* 1.3 70.9 - - - +
28B PHE* 1.3 91.3 + + + +
30B GLU* 3.3 3.1 + - - -
31B VAL* 2.8 41.1 + - + +
76B LEU 4.3 7.9 - - - -
98B ILE* 3.8 13.9 - - + -
228B ASN* 4.5 10.7 + - - +
247B ILE* 3.6 33.4 - - + +
250B LEU* 4.1 7.6 - - + -
1D GLC 3.8 35.0 - - - +
2D GLC 3.4 38.8 - - - -
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Residues in contact with PHE 28 (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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15B MSE 6.3 1.6 - - + -
16B PRO* 4.1 24.5 - - + -
22B ALA* 3.0 46.4 - - + -
23B PHE* 4.7 5.6 - - + +
25B ASN* 3.3 6.0 + - + +
26B PRO 3.2 0.6 - - - -
27B PHE* 1.3 96.6 - + + +
29B PRO* 1.3 74.5 - - + +
30B GLU 3.1 1.1 - - - -
31B VAL* 3.0 3.4 + - + -
32B ILE* 2.9 31.7 + - + +
76B LEU* 3.9 42.6 - - + -
77B TYR* 4.7 10.8 - + + -
1D GLC 4.4 17.3 - - - -
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Residues in contact with PRO 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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23B PHE 4.7 7.2 - - - +
24B GLN 5.8 0.4 - - - -
25B ASN 3.4 15.7 - - - +
26B PRO* 3.5 13.5 - - + +
28B PHE* 1.3 90.3 - - + +
30B GLU* 1.3 57.0 + - - +
32B ILE* 3.2 8.5 + - + +
33B ARG* 2.9 32.4 + - + +
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Residues in contact with GLU 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 PRO 3.4 9.5 + - - +
27B PHE* 3.3 9.3 + - - +
28B PHE 3.1 1.2 - - - -
29B PRO* 1.3 79.8 - - - +
31B VAL* 1.3 63.4 + - - +
33B ARG* 2.5 55.2 + - - +
34B GLY 3.4 5.2 + - - -
231B LEU* 5.4 8.1 - - - +
247B ILE* 3.8 26.9 - - + +
248B TYR* 3.7 17.9 + - - +
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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
----------------------------------------------------------
27B PHE* 2.8 27.9 + - + +
28B PHE* 3.0 20.4 + - + +
30B GLU* 1.3 78.1 - - - +
32B ILE* 1.3 62.4 + - + +
34B GLY 3.3 2.8 + - - -
35B ILE* 3.1 28.1 + - + +
76B LEU* 4.2 21.3 - - + -
98B ILE* 3.7 28.7 - - + -
247B ILE* 3.6 15.7 - - + +
250B LEU* 4.6 0.7 - - + -
251B GLY* 3.4 25.9 - - - +
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Residues in contact with ILE 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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13B LEU* 3.7 31.9 - - + -
15B MSE 4.1 15.0 - - + -
28B PHE* 2.9 22.4 + - + +
29B PRO* 3.5 8.7 - - + +
31B VAL* 1.3 74.8 - - + +
33B ARG* 1.3 65.0 + - - +
35B ILE* 3.2 6.5 + - + -
36B SER* 2.8 27.1 + - - -
46B LEU* 4.4 11.2 - - + -
48B MSE 5.4 7.4 - - + -
76B LEU* 3.7 23.8 - - + -
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Residues in contact with ARG 33 (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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29B PRO* 2.9 17.6 + - + +
30B GLU* 2.5 53.9 + - - +
31B VAL 3.2 0.4 - - - -
32B ILE* 1.3 75.2 - - - +
34B GLY* 1.3 55.9 + - - +
36B SER* 2.8 22.2 + - - -
37B SER* 2.9 17.5 + - - -
248B TYR* 3.6 36.9 - - + +
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Residues in contact with GLY 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 GLU 3.4 3.8 + - - -
31B VAL 3.3 3.9 + - - -
32B ILE 3.3 0.4 - - - -
33B ARG* 1.3 75.1 - - - +
35B ILE* 1.3 65.9 + - - +
37B SER* 3.3 2.1 + - - -
38B PHE 3.0 20.8 + - - -
248B TYR* 3.3 38.9 - - - -
252B TYR* 3.4 17.9 - - - -
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Residues in contact with ILE 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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11B LEU* 5.1 1.1 - - + -
13B LEU* 4.0 12.3 - - + -
31B VAL* 3.1 23.3 + - + +
32B ILE* 3.2 10.7 + - + +
34B GLY* 1.3 75.6 - - - +
36B SER* 1.3 57.5 + - - +
39B ALA* 2.9 30.4 + - + +
46B LEU* 3.9 25.1 - - + -
74B ILE* 3.8 33.2 - - + -
76B LEU* 3.8 29.6 - - + -
98B ILE* 4.8 1.1 - - + -
251B GLY* 3.4 21.1 - - - +
254B ALA* 5.2 0.2 - - + -
255B ALA* 4.0 8.8 - - + +
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Residues in contact with SER 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 ILE* 2.8 19.1 + - - -
33B ARG* 2.8 22.5 + - - -
35B ILE* 1.3 73.1 - - - +
37B SER* 1.3 59.9 + - - +
39B ALA* 3.4 4.3 - - - +
40B HIS* 2.9 33.9 + - - +
46B LEU* 3.8 22.9 - - - -
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG 3.2 13.9 - - - -
34B GLY 3.5 5.4 - - - -
36B SER* 1.3 83.6 + - - +
38B PHE* 1.3 60.3 + - - +
40B HIS* 3.6 16.7 - - - +
41B VAL* 4.0 9.5 - - - +
248B TYR* 2.4 34.7 + - - -
252B TYR* 3.8 8.3 - - - -
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Residues in contact with PHE 38 (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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264A ASN* 6.2 0.2 - - - -
34B GLY 3.0 10.5 + - - +
37B SER* 1.3 72.1 + - - +
39B ALA* 1.3 74.1 + - - +
40B HIS 2.9 2.0 - - - -
41B VAL* 2.8 31.4 + - + +
42B GLU* 3.7 21.5 + - + -
252B TYR* 3.5 55.3 - + + +
255B ALA* 3.7 8.7 - - + -
256B LYS* 3.5 61.5 - - + -
259B VAL* 3.7 24.2 - - + -
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Residues in contact with ALA 39 (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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11B LEU* 4.9 6.7 - - + -
35B ILE 2.9 20.4 + - - +
36B SER* 3.1 10.1 + - - +
38B PHE* 1.3 83.1 - - - +
40B HIS* 1.3 56.4 + - - +
42B GLU* 3.3 3.7 + - - +
43B GLY 3.0 8.5 + - - -
44B TYR* 2.9 52.6 + - + +
46B LEU* 4.0 15.7 - - + -
255B ALA* 5.1 1.3 - - + -
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Residues in contact with HIS 40 (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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36B SER 2.9 16.1 + - - +
37B SER* 3.6 12.3 - - - +
38B PHE 2.9 0.2 + - - -
39B ALA* 1.3 75.4 - - - +
41B VAL* 1.3 73.3 + - + +
43B GLY* 3.3 12.7 + - - +
44B TYR 4.9 2.2 - - - -
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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