Contacts of the helix formed by residues 38 - 46 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.7 23.3 - - - -
17D GLN* 3.1 18.9 + - + -
18D ARG* 3.9 2.5 - - - -
22D LEU 3.1 18.6 + - - -
23D LEU 3.4 24.5 - - - -
24D CYS* 3.9 13.2 - - - -
25D ASP* 3.3 6.3 - - - +
26D CYS* 4.7 0.4 - - - -
37D ALA* 1.3 74.8 - - - +
39D LYS* 1.3 65.8 + - - +
40D ALA* 4.3 2.0 - - + +
41D VAL* 3.1 17.8 + - + +
42D LEU* 3.1 23.9 + - - +
78D TYR* 2.7 33.7 + + - +
171D THR* 3.5 29.4 - - + -
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Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASP* 2.8 48.6 + - - +
26D CYS* 4.0 8.3 - - + -
37D ALA 4.1 0.2 - - - -
38D HIS* 1.3 72.0 - - - +
40D ALA* 1.3 57.8 + - - +
42D LEU* 3.3 3.6 + - - -
43D ALA* 2.8 31.4 + - - +
53D PHE* 3.4 47.6 - - + -
60D VAL* 4.4 15.7 - - - +
154D LEU* 4.2 21.2 - - + +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASP* 5.0 1.4 + - - -
38D HIS* 3.2 2.3 - - + +
39D LYS* 1.3 81.0 - - - +
41D VAL* 1.3 56.7 + - - +
43D ALA 3.4 0.3 + - - -
44D ALA* 2.9 28.9 + - - +
145D LEU* 4.0 12.6 - - + -
148D LEU* 3.6 7.6 - - + +
154D LEU* 4.1 16.7 - - + +
169D HIS* 3.8 34.1 - - + +
171D THR* 4.8 10.5 - - + -
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 5.7 0.7 - - + -
14D LEU* 3.8 33.9 - - + -
38D HIS* 3.1 22.9 + - + +
40D ALA* 1.3 74.4 - - - +
42D LEU* 1.3 68.1 + - + +
44D ALA* 3.0 7.3 + - - +
45D CYS* 2.9 36.5 + - - -
77D MET 4.8 3.1 - - - +
78D TYR* 3.7 40.6 - - + +
141D VAL* 5.0 5.8 - - + -
145D LEU* 4.6 6.1 - - + -
171D THR* 4.8 5.4 - - + -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D CYS* 4.2 10.3 - - - -
28D PHE* 3.7 35.7 - - + -
37D ALA* 3.8 22.4 - - + -
38D HIS 3.1 15.2 + - - +
39D LYS 3.5 7.4 - - - +
41D VAL* 1.3 79.1 - - - +
43D ALA* 1.3 56.5 + - - +
45D CYS* 3.0 2.3 + - - +
46D SER* 2.9 33.8 + - - -
49D PHE* 4.0 29.4 - - + -
53D PHE* 4.1 7.6 - - + -
74D LEU* 4.0 8.7 - - + -
77D MET* 3.7 23.6 - - - -
78D TYR* 4.3 8.5 - - + -
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS 2.8 20.2 + - - +
40D ALA 3.7 3.8 - - - +
42D LEU* 1.3 72.8 - - - +
44D ALA* 1.3 61.9 + - - +
46D SER 3.4 13.5 + - - +
47D GLU* 5.1 0.2 - - - -
49D PHE* 4.2 1.3 - - - +
50D LYS* 3.5 43.5 - - + +
53D PHE* 4.0 3.4 - - + -
144D ASN* 5.3 0.7 - - - +
148D LEU* 4.0 10.5 - - + -
154D LEU* 3.6 23.1 - - + -
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA 2.9 18.5 + - - +
41D VAL* 3.0 7.4 + - - +
43D ALA* 1.3 78.9 - - - +
45D CYS* 1.3 59.9 + - - +
141D VAL* 3.9 30.4 - - + +
144D ASN* 3.0 40.4 + - + +
145D LEU* 3.9 15.5 - - + +
148D LEU* 4.2 3.6 - - + +
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Residues in contact with CYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D VAL* 2.9 23.5 + - - +
42D LEU 3.0 3.1 + - - +
44D ALA* 1.3 77.4 - - - +
46D SER* 1.3 60.6 + - - +
47D GLU 4.2 0.8 + - - -
76D PHE* 5.7 1.0 - - - -
77D MET* 3.6 50.5 - - + -
101D MET* 4.2 12.7 - - + +
137D HIS* 3.8 11.1 - - + -
141D VAL* 3.7 26.5 - - - -
144D ASN* 5.6 0.4 - - - -
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Residues in contact with SER 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU 2.9 13.2 + - - +
43D ALA 3.4 8.6 - - - +
44D ALA 3.6 1.0 - - - -
45D CYS* 1.3 81.3 - - - +
47D GLU* 1.3 63.5 + - - +
48D TYR* 3.3 13.2 + - - +
49D PHE* 3.2 30.8 + - - -
50D LYS 3.1 18.2 + - - -
77D MET* 4.2 8.7 - - - -
99D LEU* 3.7 8.8 + - - +
100D GLN 5.5 0.3 + - - -
101D MET* 4.2 10.6 - - - +
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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