Contacts of the helix formed by residues 37 - 47 (chain A) in PDB entry 1Y9A
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 CYS 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PRO* 1.3 74.0 - - - +
38A THR* 1.3 73.6 + - - +
39A SER* 3.4 13.7 - - - +
40A ASP* 3.0 23.0 + - - +
41A THR 3.7 2.4 + - - -
59A HIS* 3.6 11.4 - - + +
60A GLU* 3.1 15.7 - - - +
150A ASP* 3.7 2.2 - - - -
151A MET* 4.0 14.8 - - - -
334A LEU* 4.1 7.2 - - - +
337A MET* 4.1 5.4 - - - -
346A LYS* 3.9 3.1 - - - +
1000A ZN 2.3 34.8 - - - -
1001A CAC 3.5 2.2 - - - -
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Residues in contact with THR 38 (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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37A CYS* 1.3 77.6 - - - +
39A SER* 1.3 61.0 + - - +
41A THR* 2.8 42.1 - - - +
42A HIS* 3.1 17.8 + - - -
177A PRO* 5.9 4.7 - - + -
337A MET* 3.6 27.5 - - + +
340A LYS* 4.0 25.8 - - - +
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A CYS* 3.0 8.2 - - - -
38A THR* 1.3 81.2 + - - +
40A ASP* 1.3 57.3 + - - +
42A HIS* 3.0 18.4 + - - -
43A THR* 3.0 12.1 + - - -
59A HIS* 4.1 7.2 - - - -
110A TRP* 4.5 3.4 - - - -
267A TYR* 3.3 40.8 - - - +
1000A ZN 3.8 1.1 - - - -
1001A CAC 2.5 33.8 + - - +
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Residues in contact with ASP 40 (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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37A CYS* 3.0 14.8 + - - +
39A SER* 1.3 75.6 - - - +
41A THR* 1.3 57.2 + - - +
43A THR* 3.7 7.3 + - - -
44A VAL* 2.8 41.3 + - - +
45A TRP* 5.0 0.2 - - - -
57A LEU* 3.7 20.4 - - + +
58A GLY* 2.9 31.5 + - - -
59A HIS* 3.6 10.1 - - - -
110A TRP* 4.9 0.9 - - - -
113A SER* 2.6 28.9 + - - +
120A PHE* 4.5 4.7 - - - -
334A LEU* 4.0 16.3 - - + +
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Residues in contact with THR 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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37A CYS 3.7 1.0 + - - -
38A THR* 2.8 30.0 - - - +
40A ASP* 1.3 75.4 - - - +
42A HIS* 1.3 77.6 + - + +
45A TRP* 3.1 40.6 + - + +
46A ALA 3.8 0.5 + - - -
334A LEU* 4.6 3.1 - - - +
337A MET* 3.8 12.4 + - - +
338A LYS* 3.7 31.9 + - + +
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Residues in contact with HIS 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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38A THR* 3.9 24.4 + - - -
39A SER* 3.0 7.5 + - - +
41A THR* 1.3 83.4 - - + +
43A THR* 1.3 67.7 + - - +
46A ALA* 3.0 25.6 + - - +
47A GLY 3.2 7.4 + - - -
48A ALA* 3.2 14.4 + - + -
266A ASN* 5.1 4.0 + - - -
267A TYR* 3.5 56.5 + + + +
269A GLY* 4.3 12.0 - - - -
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Residues in contact with THR 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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6A MET* 3.5 24.7 - - + +
39A SER 3.0 15.1 + - - -
40A ASP* 3.8 9.3 + - - +
41A THR 3.3 0.2 - - - -
42A HIS* 1.3 81.8 - - - +
44A VAL* 1.3 62.9 + - + +
47A GLY* 3.3 17.0 + - - -
48A ALA 3.9 3.1 + - - +
49A ILE* 3.6 26.8 - - + +
50A GLY 4.5 1.7 - - - +
52A ARG* 5.0 3.6 - - + -
55A MET* 4.5 6.1 - - + -
57A LEU* 5.4 0.9 - - + -
110A TRP* 4.4 4.2 - - - -
113A SER 4.2 14.6 + - - +
267A TYR* 2.7 27.1 + - - -
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Residues in contact with VAL 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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6A MET* 3.8 22.0 - - + -
9A ILE* 3.4 10.4 - - - +
10A GLY 2.8 19.8 + - - +
11A ARG 4.0 17.7 - - - +
12A ILE* 3.7 21.1 - - + -
40A ASP 2.8 24.9 + - - +
43A THR* 1.3 76.4 - - - +
45A TRP* 1.3 88.3 + - + +
57A LEU* 3.9 31.9 - - + -
334A LEU* 5.3 0.4 - - + -
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Residues in contact with TRP 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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9A ILE* 4.2 7.4 - - - +
10A GLY* 3.5 33.4 + - - +
12A ILE* 4.1 16.8 - - + -
41A THR* 3.1 37.6 + - + +
44A VAL* 1.3 98.8 - - + +
46A ALA* 1.3 60.4 + - - +
334A LEU* 4.3 15.7 - - + -
335A MET* 3.5 35.0 - - + -
338A LYS* 3.2 49.8 - - + +
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Residues in contact with ALA 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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9A ILE* 4.6 2.9 - - - -
41A THR 3.8 1.0 + - - -
42A HIS* 3.0 24.2 + - + +
45A TRP* 1.3 77.7 - - - +
47A GLY* 1.3 63.6 + - - +
48A ALA* 3.4 1.0 + - - -
269A GLY* 3.8 23.6 - - - +
270A GLU* 4.9 10.7 - - + +
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Residues in contact with GLY 47 (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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9A ILE* 3.5 26.5 - - - +
42A HIS 3.2 2.6 + - - -
43A THR 3.3 15.3 + - - -
44A VAL 4.0 1.2 + - - -
45A TRP 3.5 2.2 - - - -
46A ALA* 1.3 78.2 - - - +
48A ALA* 1.3 64.0 + - - +
49A ILE 3.2 4.3 + - - -
50A GLY* 3.2 12.8 + - - -
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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