Contacts of the helix formed by residues 40 - 47 (chain A) in PDB entry 1S5E
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 ASN 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASN* 3.8 14.6 + - - +
39A ILE* 1.3 76.8 - - - +
41A LEU* 1.3 63.8 + - - +
42A TYR 3.3 4.0 + - - -
43A ASP* 2.9 48.0 + - - +
44A HIS* 2.9 23.2 + - - +
57A ASP 3.1 9.9 + - - +
59A TYR* 3.7 2.7 - - - -
164A LEU 5.3 0.4 - - - -
166A GLY* 3.1 36.2 + - - +
200A ASP* 4.4 12.1 + - - +
203A THR* 3.7 14.5 - - - +
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Residues in contact with LEU 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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40A ASN* 1.3 72.2 + - - +
42A TYR* 1.3 59.2 + - - +
44A HIS* 3.1 14.4 + - + +
45A ALA* 2.8 28.9 + - - +
59A TYR* 3.4 47.0 + - + +
95A PHE* 4.7 11.4 - - + -
97A VAL* 4.4 15.5 - - + -
100A VAL* 3.4 40.2 - - + -
101A LEU* 4.2 15.7 - - + -
114A SER* 4.3 8.5 - - - -
164A LEU* 3.8 9.4 + - + +
165A ALA* 3.7 8.7 + - - +
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Residues in contact with TYR 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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40A ASN* 3.3 6.9 + - - +
41A LEU* 1.3 75.6 - - - +
43A ASP* 1.3 68.8 + - - +
45A ALA* 3.5 1.0 + - - +
46A ARG* 3.2 69.4 + - + +
101A LEU* 4.3 15.9 - - + -
104A TYR* 4.1 16.3 - - + +
165A ALA 2.9 21.1 + - - +
166A GLY 3.6 7.4 - - - +
167A PHE* 3.6 28.3 - + - +
168A PRO* 3.7 33.2 - - + -
171A HIS* 3.6 21.7 + + - -
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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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38A ASN* 3.8 9.4 + - - -
40A ASN* 2.9 38.2 + - + +
42A TYR* 1.3 84.8 - - - +
44A HIS* 1.3 62.2 + - - +
46A ARG* 3.3 9.2 + - - +
47A GLY* 3.2 18.7 + - - -
57A ASP* 3.6 27.3 - - - +
166A GLY 4.9 0.7 - - - +
168A PRO* 5.8 1.4 - - - +
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Residues in contact with HIS 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 ASN 2.9 17.6 + - - +
41A LEU* 3.1 10.5 + - + +
43A ASP* 1.3 78.3 - - - +
45A ALA* 1.3 67.0 - - + +
47A GLY* 3.1 13.7 + - - -
54A ARG* 3.3 45.9 - - + +
55A HIS 4.3 0.2 + - - -
56A ASP* 2.8 33.4 + - - +
57A ASP* 3.8 4.2 - - + +
59A TYR* 3.3 46.7 + + + +
61A SER* 3.9 5.6 - - - -
97A VAL* 5.4 0.2 - - + -
112A GLU* 5.5 0.8 + - - -
114A SER* 3.0 29.4 + - - -
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Residues in contact with ALA 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 LEU 2.8 16.8 + - - +
42A TYR 4.0 1.8 - - - +
44A HIS* 1.3 83.6 - - + +
46A ARG* 1.3 57.8 + - - +
54A ARG* 3.3 23.2 + - - +
97A VAL* 3.9 18.2 - - + -
101A LEU* 3.7 24.5 - - + -
106A PRO* 3.4 19.0 - - + +
107A HIS* 3.6 6.8 - - - -
112A GLU* 5.0 3.9 - - - +
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Residues in contact with ARG 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 TYR* 3.2 65.7 + - + +
43A ASP* 3.8 7.8 + - - +
44A HIS 3.2 0.8 - - - -
45A ALA* 1.3 73.6 - - - +
47A GLY* 1.3 69.2 + - - +
48A THR* 3.5 3.3 + - - -
104A TYR 5.9 0.2 + - - -
106A PRO* 3.8 26.6 - - + +
107A HIS* 4.8 5.8 + - - -
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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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43A ASP 3.2 8.0 + - - -
44A HIS* 3.1 14.7 + - - -
46A ARG* 1.3 81.9 - - - +
48A THR* 1.3 61.4 + - - -
54A ARG* 2.9 33.3 + - - -
56A ASP* 5.8 7.6 - - - -
57A ASP* 5.8 0.7 - - - -
107A HIS* 4.7 1.0 + - - -
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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