Contacts of the helix formed by residues 26 - 38 (chain B) in PDB entry 1L9W
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 ASP 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG* 1.3 81.7 - - - +
27B ILE* 1.3 65.0 + - - +
28B ASN* 3.5 8.5 + - - +
29B SER* 3.0 49.5 + - - -
30B VAL* 3.1 11.8 + - - +
52B PHE* 3.7 12.1 - - - -
53B MET* 4.1 18.4 - - + +
54B ASP* 4.3 8.3 - - - +
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Residues in contact with ILE 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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26B ASP* 1.3 76.3 - - - +
28B ASN* 1.3 62.2 - - - +
30B VAL* 3.1 6.8 + - - +
31B LYS* 3.0 29.8 + - + +
52B PHE* 4.0 19.5 - - + -
54B ASP* 4.8 3.8 + - - +
60B SER* 4.3 23.3 - - - +
63B THR* 4.2 32.3 - - + -
64B ALA* 4.6 6.7 - - + +
67B VAL* 4.8 12.3 - - + +
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Residues in contact with ASN 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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26B ASP* 3.4 9.0 + - - +
27B ILE* 1.3 82.4 - - - +
29B SER* 1.3 61.4 + - - +
31B LYS* 3.9 11.9 - - - +
32B ALA* 3.1 21.3 + - - +
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Residues in contact with SER 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 3.8 5.5 - - - -
25B ARG* 3.7 16.7 + - - +
26B ASP* 3.0 33.7 + - - -
28B ASN* 1.3 77.0 - - - +
30B VAL* 1.3 60.4 + - - +
32B ALA* 3.3 5.7 + - - +
33B GLU* 2.9 35.2 + - - +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.5 4.8 - - + +
24B GLY* 4.1 22.9 - - - +
26B ASP 3.1 11.6 + - - +
27B ILE 3.1 8.3 + - - +
29B SER* 1.3 76.7 - - - +
31B LYS* 1.3 56.6 + - - +
33B GLU* 3.2 6.1 + - - +
34B ALA* 2.7 34.3 + - - +
47B TRP* 4.1 17.3 - - - +
52B PHE* 4.3 3.8 - - + -
64B ALA* 3.8 29.2 - - + +
67B VAL* 4.4 6.1 - - + -
68B ILE* 3.6 31.9 - - + -
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Residues in contact with LYS 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 ILE* 3.0 19.4 + - + +
28B ASN* 4.0 11.7 - - - +
30B VAL* 1.3 79.2 - - - +
32B ALA* 1.3 63.5 + - - +
34B ALA* 3.3 2.4 + - - +
35B LEU* 3.3 39.9 + - + +
67B VAL* 3.5 31.6 - - + -
129C ASP* 5.0 4.9 + - - +
130C TYR* 6.1 0.2 - - - +
133C ALA* 3.8 28.3 - - - +
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Residues in contact with ALA 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 ASN 3.1 15.5 + - - +
29B SER* 3.3 7.6 + - - +
31B LYS* 1.3 75.7 - - - +
33B GLU* 1.3 67.1 + - - +
35B LEU* 3.2 11.6 + - - +
36B ALA* 3.2 21.8 + - - +
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Residues in contact with GLU 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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22B LEU* 3.9 22.9 - - + -
23B MET 3.8 18.3 + - - +
24B GLY* 4.9 0.7 - - - -
29B SER* 2.9 26.6 + - - +
30B VAL 3.9 2.2 - - - +
32B ALA* 1.3 76.4 - - - +
34B ALA* 1.3 57.1 + - - +
36B ALA* 3.4 2.8 + - - +
37B TYR* 2.9 46.5 + - + +
229B LYS* 3.1 37.5 - - - +
230B GLN* 3.6 13.2 - - - +
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Residues in contact with ALA 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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22B LEU* 4.0 3.3 - - - +
30B VAL 2.7 20.3 + - - +
31B LYS 3.7 4.5 - - - +
32B ALA 3.2 0.2 - - - -
33B GLU* 1.3 74.7 - - - +
35B LEU* 1.3 59.8 + - + +
38B ARG* 3.5 23.0 + - - +
67B VAL* 4.3 9.6 - - + -
68B ILE* 4.3 17.7 - - + -
71B ALA* 3.9 20.9 - - + +
72B MET* 3.8 20.0 - - + +
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Residues in contact with LEU 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 LYS* 3.3 29.6 + - + +
32B ALA* 3.2 12.3 + - - +
34B ALA* 1.3 77.8 - - + +
36B ALA* 1.3 61.4 + - - +
38B ARG* 3.4 21.3 - - - +
39B GLU* 4.1 9.2 - - - +
71B ALA* 5.3 1.6 - - + -
129C ASP* 4.1 24.2 - - + +
132C HIS* 3.8 17.9 - - + +
133C ALA* 3.7 36.3 - - + +
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Residues in contact with ALA 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 ALA 3.2 12.9 + - - +
33B GLU* 4.1 4.5 - - - +
35B LEU* 1.3 76.0 - - - +
37B TYR* 1.3 64.9 + - + +
39B GLU* 3.0 21.5 + - - +
40B ALA* 4.1 2.9 + - - +
228B VAL* 5.5 2.3 - - - +
229B LYS* 3.7 26.2 - - - +
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Residues in contact with TYR 37 (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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20B VAL* 4.0 26.5 - - + -
21B SER 2.8 31.1 + - - -
22B LEU* 3.8 24.5 - - + -
33B GLU* 2.9 45.9 + - + +
34B ALA 3.7 0.2 + - - -
35B LEU 3.5 0.2 - - - -
36B ALA* 1.3 78.2 - - + +
38B ARG* 1.3 56.3 + - - +
40B ALA* 3.0 22.5 + - - +
42B PHE* 3.4 20.6 - + + -
45B LEU* 5.0 3.6 - - + -
72B MET* 4.2 19.5 - - + -
228B VAL* 3.8 35.9 + - + +
229B LYS* 4.5 6.1 + - + +
230B GLN* 4.3 17.2 + - - +
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Residues in contact with ARG 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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34B ALA 3.5 15.2 + - - +
35B LEU* 3.4 15.0 + - - +
37B TYR* 1.3 75.7 - - - +
39B GLU* 1.3 75.8 + - - +
40B ALA 3.4 5.0 + - - +
71B ALA* 3.1 24.2 + - - +
72B MET* 4.1 15.2 - - + -
132C HIS* 3.1 53.6 + - - +
135C ASN* 2.3 41.1 + - - +
137C TYR* 3.5 31.6 + - - -
167C ASP* 4.9 0.6 + - - -
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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