Contacts of the helix formed by residues 38 - 46 (chain B) in PDB entry 4U2M
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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 3.7 24.0 - - - -
17B GLN* 3.1 19.0 + - + -
18B ARG* 3.9 2.5 - - - -
22B LEU 3.1 17.2 + - - -
23B LEU 3.4 20.6 - - - +
24B CYS* 3.9 13.4 - - - -
25B ASP* 3.3 5.6 - - - +
37B ALA* 1.3 75.0 - - - +
39B LYS* 1.3 66.8 + - - +
40B ALA* 4.4 4.3 - - + +
41B VAL* 3.7 16.5 - - + +
42B LEU* 3.1 23.0 + - - +
78B TYR* 2.7 33.0 + + - +
171B THR* 3.0 31.2 - - + +
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Residues in contact with LYS 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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25B ASP* 2.8 44.7 + - - +
26B CYS* 4.0 6.5 - - + +
37B ALA 4.1 0.6 + - - -
38B HIS* 1.3 70.5 - - - +
40B ALA* 1.3 59.2 + - - +
41B VAL 3.2 0.2 + - - -
42B LEU* 3.3 2.8 + - - +
43B ALA* 2.8 31.7 + - - +
53B PHE* 3.8 47.3 - - + -
56B GLN 4.6 1.8 + - - -
57B LYS* 4.0 22.0 - - - +
60B VAL* 3.5 36.7 - - - +
154B LEU* 4.2 21.6 - - + +
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Residues in contact with ALA 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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25B ASP* 5.0 1.6 + - - -
38B HIS* 3.2 4.1 - - + +
39B LYS* 1.3 78.9 - - - +
41B VAL* 1.3 60.3 + - + +
43B ALA 3.5 0.2 + - - -
44B ALA* 3.0 28.6 + - - +
145B LEU* 3.6 13.3 - - + +
148B LEU* 3.6 7.7 - - + +
154B LEU* 4.1 18.5 - - + +
169B HIS* 3.8 33.9 - - + +
171B THR* 6.1 4.0 - - - -
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Residues in contact with VAL 41 (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* 5.7 0.9 - - + -
14B LEU* 3.9 32.5 - - + -
38B HIS* 3.1 23.0 + - + +
40B ALA* 1.3 76.7 - - + +
42B LEU* 1.3 67.1 + - + +
44B ALA* 3.0 15.0 + - - +
45B CYS* 3.1 26.4 + - - -
77B MET* 4.8 5.2 - - + +
78B TYR* 3.6 42.0 - - + +
141B VAL* 4.9 5.4 - - + -
145B LEU* 4.6 7.9 - - + -
171B THR* 4.9 1.8 - - + -
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Residues in contact with LEU 42 (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 CYS* 4.2 3.8 - - + -
28B PHE* 3.6 35.4 - - + -
37B ALA* 3.8 25.4 - - + -
38B HIS 3.1 11.1 + - - +
39B LYS 3.6 7.2 - - - +
41B VAL* 1.3 77.0 - - - +
43B ALA* 1.3 58.5 + - - +
45B CYS* 3.0 2.6 + - - +
46B SER* 2.9 32.9 + - - -
49B PHE* 3.8 28.0 - - + -
53B PHE* 3.9 16.6 - - + -
74B LEU* 3.9 8.1 - - + -
77B MET* 3.7 23.1 - - - -
78B TYR* 4.2 10.1 - - + -
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Residues in contact with ALA 43 (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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39B LYS 2.8 20.4 + - - +
40B ALA 3.7 4.0 - - - +
42B LEU* 1.3 73.4 - - - +
44B ALA* 1.3 60.3 + - - +
45B CYS 3.4 0.7 + - - -
46B SER 3.5 12.6 + - - +
47B GLU* 5.2 0.2 - - - -
49B PHE* 4.1 2.2 - - - +
50B LYS* 3.6 43.3 - - + +
148B LEU* 4.0 11.1 - - + +
154B LEU* 3.6 23.6 - - + -
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Residues in contact with ALA 44 (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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40B ALA 3.0 17.6 + - - +
41B VAL* 3.0 7.6 + - - +
43B ALA* 1.3 78.1 - - - +
45B CYS* 1.3 58.7 + - - +
141B VAL* 3.9 23.8 - - + +
144B ASN* 3.0 48.2 + - + +
145B LEU* 4.0 14.1 - - + +
148B LEU* 4.2 4.5 - - + +
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Residues in contact with CYS 45 (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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41B VAL* 3.1 17.1 + - - +
42B LEU 3.0 7.0 + - - +
44B ALA* 1.3 79.8 - - - +
46B SER* 1.3 58.3 + - - +
77B MET* 3.7 45.1 - - + -
101B MET* 3.9 19.7 - - + +
137B HIS* 3.8 10.3 - - + -
141B VAL* 3.7 28.3 - - - -
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Residues in contact with SER 46 (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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42B LEU 2.9 11.2 + - - +
43B ALA 3.5 9.1 - - - +
44B ALA 3.7 1.2 - - - -
45B CYS* 1.3 80.5 - - - +
47B GLU* 1.3 62.7 + - - +
48B TYR* 3.3 3.8 + - - +
49B PHE* 3.3 28.0 + - - -
50B LYS 3.0 19.1 + - - -
77B MET* 4.3 8.1 - - - -
99B LEU* 3.0 27.9 + - - +
100B GLN 5.9 0.2 - - - -
101B MET* 4.3 6.3 - - - -
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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