Contacts of the strand formed by residues 151 - 156 (chain D) in PDB entry 3ALQ
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 TYR 151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D HIS* 3.4 32.8 - + + +
16D VAL 3.3 9.6 - - - +
17D VAL* 4.7 2.2 - - + -
28D TRP* 3.5 6.6 - - - -
59D TYR* 3.9 11.7 - + - -
60D SER* 2.9 19.4 + - - -
61D GLN* 2.7 61.1 + - + +
119D TYR* 3.4 6.5 - + - -
148D GLY* 3.4 29.2 - - - -
150D VAL* 1.3 76.6 - - - +
152D PHE* 1.3 64.2 + - - +
94E LEU* 3.3 24.4 - - + +
120E LEU* 3.9 1.0 - - - +
121E GLY 3.3 37.4 + - - -
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Residues in contact with PHE 152 (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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14D ALA 4.3 0.2 - - - -
15D HIS* 3.4 2.1 - - - -
16D VAL* 2.8 41.9 + - + +
28D TRP* 3.6 30.1 - + + -
46D ASN 5.4 0.4 - - - -
48D LEU* 3.5 38.2 - - + +
58D ILE* 4.1 10.3 - - + -
59D TYR* 3.5 13.0 - - - -
60D SER* 3.9 3.6 - - - +
80D ILE* 3.7 23.1 - - + -
132D LEU* 3.8 31.2 - - + -
133D SER* 4.3 1.3 - - - -
134D ALA* 3.7 31.6 - - + -
151D TYR* 1.3 78.8 - - - +
153D GLY* 1.3 69.9 - - - +
154D ILE* 4.8 0.2 - - + -
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Residues in contact with GLY 153 (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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14D ALA 3.0 14.6 - - - -
48D LEU* 4.7 2.7 - - - -
58D ILE* 4.0 0.7 - - - +
59D TYR* 2.9 55.5 + - - +
152D PHE* 1.3 78.2 - - - +
154D ILE* 1.3 68.9 + - - +
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Residues in contact with ILE 154 (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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13D VAL* 3.3 2.9 - - - +
14D ALA* 2.9 35.9 + - + +
41D VAL* 3.6 32.8 - - + -
48D LEU* 4.0 15.3 - - + -
50D VAL* 4.5 11.4 - - + -
56D TYR* 3.9 28.7 - - + -
57D LEU 3.1 8.1 - - - +
58D ILE* 4.0 13.5 - - + -
59D TYR* 5.0 1.3 - - - -
132D LEU* 3.5 34.3 - - + -
152D PHE* 4.8 0.7 - - + -
153D GLY* 1.3 80.6 - - - +
155D ILE* 1.3 63.6 + - - +
123E VAL* 5.5 0.4 - - - +
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Residues in contact with ILE 155 (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 MET* 5.2 4.9 - - + -
12D PRO 3.5 12.3 - - - +
13D VAL* 4.2 5.8 - - + -
56D TYR* 3.4 5.5 - - - -
57D LEU* 2.8 48.8 + - + +
59D TYR* 5.2 0.2 - - + -
154D ILE* 1.3 77.0 - - - +
156D ALA* 1.3 71.5 + - - +
157D LEU* 3.6 4.3 + - + -
55E LEU* 4.3 13.7 - - + -
123E VAL* 3.7 36.8 - - + -
157E LEU* 3.4 42.0 - - + -
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Residues in contact with ALA 156 (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 MET* 3.8 25.7 - - - +
12D PRO* 3.1 32.0 + - + -
52D SER* 5.4 1.6 - - - +
53D GLU 6.0 0.4 - - - +
54D GLY* 5.8 2.2 - - - -
55D LEU 3.7 5.6 - - - +
56D TYR* 3.5 33.0 - - + -
155D ILE* 1.3 77.0 - - - +
157D LEU* 1.3 64.6 + - - +
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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