Contacts of the strand formed by residues 36 - 41 (chain B) in PDB entry 1H8O
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 VAL 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LEU* 5.5 3.6 - - + -
26B CYS* 5.3 1.3 - - - -
32B VAL* 4.1 9.2 - - + -
34B THR 2.8 6.7 + - - +
35B ALA* 1.3 79.9 - - - +
37B ALA* 1.3 70.3 + - - +
38B TRP* 4.5 10.5 - - + +
51B ILE 3.7 0.7 - - - +
52B TYR* 3.5 0.7 - - - -
53B TRP 3.0 22.0 + - - -
54B ALA* 3.2 11.0 + - - +
74B PHE* 3.5 54.7 - - + -
91B CYS* 4.4 13.7 - - + -
92B GLN 3.2 13.2 - - - +
93B GLN* 4.5 5.8 - - + -
94B TYR* 3.4 4.4 - - - -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 1.3 72.0 - - - +
38B TRP* 1.3 63.9 + - - +
39B TYR* 3.9 2.7 - - + +
49B LEU* 3.9 16.8 - - + -
51B ILE 2.8 15.0 - - - +
52B TYR* 4.3 3.4 - - - -
91B CYS* 3.2 5.7 - - - +
92B GLN* 2.8 55.8 + - - +
94B TYR* 3.8 11.6 - - + -
230B TRP* 4.5 3.8 - - + -
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Residues in contact with TRP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 4.6 3.1 - - - -
24B ILE* 3.4 32.5 - - + -
25B THR 4.7 0.2 - - - -
26B CYS* 3.4 32.8 - - + -
36B VAL* 4.5 10.9 - - + +
37B ALA* 1.3 77.1 - - - +
39B TYR* 1.3 61.1 + - - +
49B LEU* 3.6 5.7 - - - +
50B LEU* 3.0 31.3 + - + -
51B ILE* 2.7 39.2 + - + +
54B ALA* 4.7 7.6 + - - +
67B GLY* 5.0 0.7 - - - -
68B SER 5.2 0.8 + - - -
74B PHE* 4.4 6.5 - - + +
75B THR* 4.1 10.5 + - - -
76B LEU* 3.3 61.4 - - + +
90B PHE* 3.5 25.4 - - - -
91B CYS* 3.9 15.7 - - + -
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 3.9 7.6 - - + -
38B TRP* 1.3 76.7 - - - +
40B GLN* 1.3 61.3 + - - +
47B PRO* 4.1 13.5 - - + -
48B LYS 3.1 22.0 - - - -
49B LEU* 3.5 29.5 - - + +
50B LEU* 4.6 2.5 - - - +
88B ASP 3.6 0.6 - - - +
89B TYR* 3.3 10.8 - - - -
90B PHE* 2.8 68.2 + + + -
92B GLN* 2.7 44.7 + - + -
101B PHE* 4.1 3.4 - + - -
230B TRP* 4.1 13.9 - - - -
231B GLY* 5.5 3.2 + - - -
233B TRP* 3.5 27.1 + + - -
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Residues in contact with GLN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TYR* 1.3 76.9 - - - +
41B GLN* 1.3 64.4 + - - +
42B LYS* 4.5 15.2 + - - +
46B SER 4.4 0.2 - - - +
47B PRO* 3.1 5.0 - - - +
48B LYS* 2.7 47.8 + - + +
50B LEU* 4.1 16.6 - - + +
65B PHE* 4.1 13.5 - - - -
84B GLU 4.4 11.3 + - - -
85B ASP* 4.6 1.4 + - - +
87B ALA* 3.6 16.1 - - + +
88B ASP 3.1 4.3 - - - -
89B TYR* 3.0 38.9 + - + -
90B PHE* 5.4 0.2 - - - -
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Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN* 1.3 77.6 - - - +
42B LYS* 1.3 65.5 + - - +
43B PRO* 4.8 0.2 - - - +
45B GLN* 3.3 28.0 - - - +
46B SER 4.0 2.5 - - - -
47B PRO* 3.9 23.4 - - + +
48B LYS* 6.1 0.2 - - - -
87B ALA* 3.4 0.9 - - - +
88B ASP* 2.7 55.5 + - + +
90B PHE* 3.9 19.1 - - + -
170B GLN* 3.0 41.2 + - - -
226B PHE* 4.0 6.1 - - - -
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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