Contacts of the strand formed by residues 48 - 52 (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 LYS 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TYR* 3.1 10.5 - - - -
40B GLN* 2.7 53.1 + - + +
41B GLN* 6.1 0.2 - - - -
45B GLN* 5.8 5.6 - - - +
46B SER 4.3 7.2 - - - +
47B PRO* 1.3 79.0 - - - +
49B LEU* 1.3 65.8 + - - +
50B LEU* 3.6 9.0 + - + +
58B HIS* 6.2 1.6 - - - -
231B GLY 5.8 3.8 + - - -
232B TYR* 6.2 2.6 - - - -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 3.9 17.5 - - + -
38B TRP 3.6 13.7 - - - +
39B TYR* 3.5 31.9 - - + +
48B LYS* 1.3 77.7 - - - +
50B LEU* 1.3 63.9 + - - +
51B ILE 4.0 9.6 - - - +
52B TYR* 4.4 6.3 - - + -
58B HIS* 3.8 38.3 + - + +
61B VAL* 4.1 4.0 - - - +
230B TRP* 4.0 28.0 - - + +
231B GLY* 3.8 34.5 + - - +
233B TRP* 5.8 1.4 - - - -
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 3.0 14.5 + - + +
39B TYR 4.8 1.1 - - - -
40B GLN* 4.1 19.7 - - + +
48B LYS* 4.2 15.5 - - + +
49B LEU* 1.3 80.3 - - - +
51B ILE* 1.3 78.5 + - + +
57B ARG* 3.7 0.9 - - - -
58B HIS* 3.0 25.7 + - - -
61B VAL* 4.0 28.3 - - + +
65B PHE* 3.5 37.7 - - + -
76B LEU* 5.0 7.2 - - + -
89B TYR* 3.8 21.1 - - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 2.8 14.7 - - - +
38B TRP* 2.7 44.5 + - + -
49B LEU* 3.9 3.3 - - - +
50B LEU* 1.3 97.6 - - + +
52B TYR* 1.3 57.2 - - - +
54B ALA* 3.0 36.6 - - - +
55B SER 3.9 4.9 - - - +
56B THR 3.3 13.9 - - - +
57B ARG* 4.3 7.0 - - + +
65B PHE* 4.4 10.1 - - + +
66B THR* 3.9 10.3 - - - +
67B GLY* 3.2 31.9 - - - +
76B LEU* 4.6 12.6 - - + -
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Residues in contact with TYR 52 (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 3.5 3.6 - - - -
37B ALA* 4.2 2.2 - - + +
49B LEU* 4.4 9.0 - - + -
51B ILE* 1.3 75.0 - - - +
53B TRP* 1.3 92.2 + + - +
54B ALA 3.3 1.6 - - - -
56B THR* 2.9 60.0 + - + +
57B ARG 4.5 2.9 + - - -
58B HIS* 3.8 36.9 - + + -
59B THR* 5.7 0.7 + - - -
94B TYR* 3.8 4.5 - - - +
230B TRP* 3.5 41.7 - + + -
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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