Contacts of the helix formed by residues 40 - 46 (chain A) in PDB entry 1SHC
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 1.3 75.1 - - - +
41A PRO* 1.3 93.9 - - + +
43A ASP* 4.2 6.5 - - - +
44A LYS* 3.1 35.2 + - + +
50A VAL* 3.1 11.7 - - + +
52A TYR* 3.2 34.9 - + - -
185A GLY* 4.4 9.7 + - - -
189A ASP* 3.2 29.6 + - + +
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Residues in contact with PRO 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.2 10.8 - - + -
40A HIS* 1.3 103.0 - - + +
42A ASN* 1.3 56.3 + - - +
45A VAL* 3.0 32.4 + - - +
50A VAL* 3.4 1.2 - - + +
52A TYR* 3.3 6.7 - - - +
189A ASP* 2.8 55.9 - - + +
192A SER* 4.4 5.6 - - - -
193A THR* 3.0 32.8 - - + +
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 4.9 11.5 - - - +
37A GLY 4.3 1.8 + - - +
38A TRP* 4.2 30.1 - - + +
39A LEU* 3.8 4.9 + - + +
41A PRO* 1.3 80.1 - - - +
43A ASP* 1.3 72.3 + - - +
44A LYS 3.0 2.7 + - - -
45A VAL* 3.0 14.3 + - - +
46A MET* 3.2 21.1 + - - +
192A SER* 5.1 4.0 + - - +
196A GLN* 2.5 44.0 + - + +
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 5.5 3.1 + - - -
37A GLY* 3.3 34.6 + - - +
38A TRP 4.8 0.2 - - - +
39A LEU 3.3 12.7 + - - +
40A HIS* 3.6 6.5 + - - +
42A ASN* 1.3 83.1 + - - +
44A LYS* 1.3 60.5 + - + +
46A MET* 3.8 4.0 + - - +
47A GLY* 3.1 19.6 + - - -
48A PRO* 5.2 0.2 - - - +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 3.1 21.4 + - + +
42A ASN 3.1 0.4 - - - -
43A ASP* 1.3 78.4 - - + +
45A VAL* 1.3 65.8 + - - +
46A MET 3.0 1.6 - - - -
47A GLY* 2.8 11.4 + - - +
48A PRO* 4.3 13.7 - - + -
49A GLY* 2.8 32.5 + - - +
50A VAL* 3.0 49.8 - - + +
51A SER* 5.2 4.9 - - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO 3.0 26.1 + - - +
42A ASN* 3.0 8.4 + - - +
44A LYS* 1.3 75.7 - - - +
46A MET* 1.3 65.0 + - + +
47A GLY 3.8 2.8 - - - +
50A VAL 4.3 0.2 - - - +
126A VAL* 3.8 22.4 - - + +
127A SER* 3.8 1.4 - - - +
128A THR* 2.7 48.4 + - + +
193A THR* 3.5 22.0 - - + +
196A GLN* 3.8 35.9 - - + +
197A ALA 4.3 4.9 - - - +
200A LEU* 4.7 3.4 - - + -
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Residues in contact with MET 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN* 3.2 22.2 + - - +
43A ASP* 4.2 3.8 - - - +
44A LYS 3.0 0.2 - - - -
45A VAL* 1.3 82.4 - - + +
47A GLY* 1.3 69.7 + - - +
128A THR* 3.7 28.5 + - + +
196A GLN* 5.4 2.0 - - - +
200A LEU* 4.5 12.6 - - + -
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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